Staphylococcus aureus

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Microbial Genomics Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis --Manuscript Draft-Manuscript Number:

MGEN-D-16-00028R1

Full Title:

Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis

Article Type:

Research Paper

Section/Category:

Systems Microbiology: Large-scale comparative genomics

Corresponding Author:

Lindsey N Shaw University of South Florida Tampa, FL UNITED STATES

First Author:

William H Broach

Order of Authors:

William H Broach Andy Weiss Lindsey N Shaw

Abstract:

Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus to other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, S. epidermidis and S. carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA content of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidis has the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behavior of these diverse staphylococcal strains.

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Manuscript Including References (Word document)

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Transcriptomic Analysis of Staphylococcal sRNAs:

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Insights into Species Specific Adaptation and the

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Evolution of Pathogenesis

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Running Title: Staphylococcal sRNAs

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Key Words: Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus carnosus, sRNA, RNAseq, genome annotation

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Subject: Identification and in silico analysis of small, regulatory RNAs in several

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Staphylococcus sp.

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Word Count: Abstract: 250, Impact Statement: 175, Main Body (including legends): 6733

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ABSTRACT

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Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains. These complete annotation files now serve as tools to compare the sRNA content of S. aureus to other bacterial strains to investigate the conservation of their sRNomes. Accordingly, in this study we performed RNAseq on two staphylococcal species, S. epidermidis and S. carnosus, identifying 118 and 89 sRNAs in these organisms, respectively. The sRNA content of all three species were then compared to elucidate their common and species-specific sRNA content, identifying a core set between 53 and 36 sRNAs encoded in each organism. In addition, we determined that S. aureus has the largest set of unique sRNAs (137) while S. epidermidis has the fewest (25). Finally, we identify a highly conserved sequence and structural motif differentially represented within, yet common to, both S. aureus and S. epidermidis. Collectively, in this study, we uncover the sRNome common to three staphylococcal species, shedding light on sRNAs that are likely to be involved in basic physiological processes common to the genus. More significantly, we have identified species-specific sRNAs that are likely to influence the individual lifestyle and behavior of these diverse staphylococcal strains.

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DATA SUMMARY

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1. The RNAseq results have been deposited to the NCBI Gene Expression Omnibus; GEO submission GSE77567 (url http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=olgjaisktxerfqz&acc=GSE77567)

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2. The updated genbank file, containing novel sRNA annotations (annotated as “misc. RNA”) has been deposited to Figshare; DOI: 10.6084/m9.figshare.2072890 (url – https://figshare.com/s/ac122d912782908e6359)

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I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ☐

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IMPACT STATEMENT

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Staphylococcus aureus is a leading cause of nosocomial infections and exhibits profound levels of antimicrobial resistance. The importance of this pathogen has been well established, forming the subject of extensive research, however, a comprehensive understanding of the regulatory processes governing its virulence has yet to be elucidated. Recently, our group has investigated the role of

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regulatory RNAs (sRNAs) by cataloging and annotating them in S. aureus genomes. The study presented here continues this line of research by performing transcriptomic analyses with two closely related species, S. epidermidis and S. carnosus, to annotate, for the first time, their genomes for sRNAs. The sRNAs of all three organisms were then compared to determine the common and species-specific sRNA content of each genome. In addition, we identified a subset of sRNAs shared between S. aureus and S. epidermidis that demonstrate high sequence and structural conservation. This study provides a platform to guide studies on sRNAs that are important for the general physiology of staphylococci (shared sRNAs) as well as the unique lifestyles of each organism (speciesspecific sRNAs).

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INTRODUCTION

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The wide availability of sequenced genomes and the decreasing cost of producing such data have revolutionized the way molecular biology research is performed (Dark, 2013). With the increasing knowledgebase of genomic information published each year there is an escalating demand for automated pipelines to identify and annotate genes within sequence data (Richardson & Watson, 2013). To highlight the vast amount of genetic information available, at the time of writing this manuscript, a total of 5,031 completed prokaryotic genomes were available in the NCBI Genome database (http://www.ncbi.nlm.nih.gov/genome), with a further 56,449 partially completed genomes. Furthermore, the rate of publication continues to increase exponentially each year for studies on such topics (Tatusova et al., 2015). Traditionally, the pipelines used for de novo genome assembly involve prediction of protein-coding genes, rRNAs and tRNAs, followed by comparison to a reference genome to assign ORF-function (Richardson & Watson, 2013). However, many drawbacks exist to such approaches, not the least of which is a lack of efficient detection for small, regulatory RNAs (sRNAs), some of which can also encode small peptides (71% of the sequences in the conserved region.

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The SERPsCon sequence and each S. epidermidis sRNA were subjected to secondary structure prediction using the mfold software (Fig. 5B and C, respectively) (Zuker, 2003). The predicted SERPsCon structure includes a stem with two single-stranded regions, and a terminal loop (bracketed) near the 5’ end of the molecule that includes 28 of the 38 residues conserved in all 21 sequences (Fig. 5A and B). The terminal single-stranded region of the SERPsCon structure within the bracket has a ten-nucleotide sequence that is variable only at the ninth residue, and defined by the sequence motif 5’ – GAAGACUAYA (Fig. 5B). Furthermore, mfold secondary structure predictions performed on the 21 S. epidermidis sRNAs suggest the sequence homology extends to structural conservation. The secondary structure predictions suggest that in all 21 of these elements, the region corresponding to SERPsCon (Fig. 5C, red regions) includes an extended stem-loop structure that is identical (for 17 of the 21) to the motif defined in SERPsCon (5’ – GAAGACUAYA). The remaining four sRNAs have the same sequence motif at the terminus of a stem, however, the optimal structure, as predicted by mfold, suggests less single-strandedness. The conserved region and terminal loop do not appear to be related to any known RNA families or motifs as determined by an Rfam analysis (http://rfam.xfam.org/) (Nawrocki et al., 2015), and thus may constitute a new regulatory RNA family.

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Initial sequence analysis of SAUSA300s205, SAUSA300s206, and SAUSA300s288 determined that these sRNAs share less sequence identity than their S. epidermidis counterparts (Fig. S3 and S4). SAUSA300s205 and SAUSA300s288 are more similar to each other than to SAUSA300s206 (Fig. 6A, S2 and S3), however, upon further examination it was noted that SAUSA300s205 and SAUSA300s288 share more identity with the reverse complement of SAUSA300s206 (RC-SAUSA300s206) (Fig. 6B, S2 and S3). Secondary structure predictions suggest at least partial structural conservation between SAUSA300s205 and SAUSA300s288 in relation to SERPsCon and the other S. epidermidis sRNAs (Fig. 6C). The predicted secondary structure of SAUSA300s288 has the highest level of structure and sequence conservation, with nine residues in the terminal loop structure; seven of which are perfectly conserved in relation to SERPsCon (Fig. 5B). SAUSA300s205 contains a 59 nt insert within the region corresponding to SERPsCon that necessarily shifts the structure, resulting in a slightly lower level of sequence conservation in the terminal loop (6 of 9 residues) (Fig. 6C). Folding predictions of SAUSA300s206 suggest very little, if any, structural conservation, mirroring the lack of sequence identity, with the other sRNAs (Fig. 6A and C). However, as perhaps is expected, mfold analysis of RC-SAUSA300s206 suggests structural conservation including the terminal loop (6 of 9 residues) (Fig. 6C).

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The antisense nature of SAUSA300s206 in comparison to SAUSA300s205 and SAUSA300s288 hints at the possibility of an interaction between SAUSA300s206 and the other two sRNAs. To evaluate this potential, we queried the SAUSA300s206 sequence against the target sequences SAUSA300s205 and SAUSA300s288 using RNA-RNA interaction prediction software, IntaRNA (http://rna.informatik.unifreiburg.de/) (Busch et al., 2008; Wright et al., 2014). Perhaps unsurprisingly, the predicted areas of interaction between SAUSA300s206 and both of the other sRNAs are extensive, and have a very low free energy (-181.7 kcal/mol and -95.3 kcal/mol, SAUSA300s205 and SAUSA300s288, respectively) thus making these interactions energetically favorable.

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Functional Prediction of S. aureus-specific sRNAs. A major goal of this study was to differentiate sRNA content between the staphylococci (Table S2); and to garner a better understanding of the potential physiological role for unique elements, particular in the context of S. aureus pathogenesis. As such, the complete set of S. aureus specific sRNAs (Table S7) was subjected to target prediction using TargetRNA2 (http://cs.wellesley.edu/~btjaden/TargetRNA2/) (Kery et al., 2014). The resulting list of putative targets (Table S8) was subjected to ontological classification, so as to identify those that are known virulence factors. Of note, 85 of the 137 (62%) sRNAs unique to S. aureus were found to have the capacity to interact with at least one virulence related transcript. Interestingly, the gene with the highest number of predicted sRNA regulators (10 different sRNAs) was splA, which encodes a well characterized serine protease (Stec-Niemczyk et al., 2009). This is particularly compelling as S. aureus proteases have a major role in pathogenesis via the global modulation of virulence determinant stability (Kolar et al., 2013). As such, this clearly suggests potential for sRNA based regulation of the infectious process in S. aureus. Ultimately, each of the predictions generated require further experimental verification to assess specific functional roles. However, we suggest that the data presented herein represents an important first step in exploring the influence of sRNAs in the staphylococci, and their impact on specific-specific adaptation.

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DISCUSSION

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The advent of next generation sequencing technologies has resulted in a vast amount of genomic and transcriptomic data available for all domains of life. This flood of data has resulted in the need for automated annotation software (Dark, 2013; Richardson & Watson, 2013). While automated annotation has become fairly robust for protein-coding regions, tRNAs, and rRNAs, the ability to accurately predict the presence of other non-coding RNAs lags behind, which necessitates the manual curation of such genes (Sridhar & Gunasekaran, 2013). Collectively, sRNAs are of growing interest, as the diverse roles they play in regulating carbon metabolism, virulence gene expression, iron acquisition, as well as many other cellular processes becomes increasingly apparent (Hoe et al., 2013; Beisel & Storz, 2010; Murphy, et al., 2014; Caron et al., 2010; Geissmann et al., 2006; Harris et al., 2013; Papenfort & Vanderpool, 2015; Oliva et al., 2015). The inability to efficiently identify and annotate these elements hinders research on sRNAs and creates a need for transcriptomic-based approaches to supplement automated annotation software pipelines. To this end, our group has begun manually cataloging and curating these molecules into their respective genomes within the staphylococci.

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In the present work, we have identified and annotated sRNAs in the genomes of both S. epidermidis RP62a and S. carnosus TM300 using RNAseq methodologies. The total sRNA content of S. epidermidis and S. carnosus were compared to our previous work in S. aureus, generating a fully comprehensive comparison of the shared and unique sRNA content of these common staphylococci. In so doing, we identified and annotated 118 and 89 novel sRNAs in S. epidermidis and S. carnosus,

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respectively. The sRNA content of these two genomes initially appears strikingly small compared to S. aureus (303 annotated sRNAs). The difference in the number of sRNAs between these organisms is likely not due to differences in genome size (2,872,769 bp, 2,616,530 bp, and 2,566,424 bp, respectively), but rather an artifact of the overall number of conditions tested for sRNA expression within each species. For S. epidermidis and S. carnosus, our study is the first assessment of their sRNA content, based on a single growth condition (mid-logarithmic phase, TSB at 37°C); whilst those sRNAs for S. aureus are derived from a wealth of different studies and experimental conditions (Pichon & Felden, 2005; Marchais et al., 2009; Geissmann et al., 2009; Abu-Qatouseh et al., 2010; Bohn et al., 2010; Beaume et al., 2010; Nielsen et al., 2011; Xue et al., 2014; Anderson et al., 2006; Olson, P. D. et al., 2011; Anderson et al., 2010; Howden et al., 2013; Carroll et al., 2016). The discrepancy in the number of studies that have examined the sRNA content of these three organisms also underlies the very different proportion of sRNAs common to the staphylococci in each genome. For example, considering only the transcriptionally active sRNA comparisons, S. aureus has a common sRNA set of 53 (~17.5%) while S. epidermidis and S. carnosus have 36 (~30.5%) and 39 (~43.8%) respectively. The sRNAs represented in all three genomes likely have similar roles within the cell, speculatively involved in evolutionary conserved processes such as basic metabolism and maintenance of cellular homeostasis. While the number of sRNAs shared by S. aureus increases to 87 sRNAs (~28.7%) if the homologous, but transcriptionally inactive, regions of S. epidermidis and S. carnosus are included, this is still a smaller proportion of the sRNAs compared to S. epidermidis , and considerably smaller than that of S. carnosus (~30.5% and ~43.8%, respectively). One could hypothesize that these sRNAs may be involved in conserved processes that are perhaps unnecessary under the conditions tested. Conversely, and of some interest, several regions within the S. aureus genome show high sequence homology to newly annotated sRNAs from S. epidermidis and S. carnosus , despite themselves being transcriptionally silent (data not shown). Either the presence of such regions suggests an evolutionary event that has silenced expression from these loci, or, perhaps a more likely scenario, we have yet to elucidate the permissive conditions for their expression in S. aureus. As such, a need exists for further research into lifestyle-specific and patho-physiologically relevant transcriptomic conditions and effects within the staphylococci.

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The presence of a set of highly conserved sRNAs from S. epidermidis and S. aureus is seemingly quite unusual. The high level of sequence homology within these sRNAs also results in a conserved structural motif that takes the form of a stem and multi-loop region, ending in a terminal hairpin with an unpaired, conserved 9 – 10 nt motif. Conservation of the multi-loop stem and terminal loop would suggest a common function for these sRNAs as a group and/or for the region of homology. Several possibilities for general function present themselves with such sequence and structure conservation. For example, it is possible that these structures act to bind and sequester proteins, as is the case for the CsrB/C sRNAs. CsrB/C sRNAs were originally identified in Escherichia coli as binding to and sequestering the CsrA protein through a conserved, repeated RNA motif, ultimately affecting carbon utilization and virulence gene expression (Liu, M. Y. et al., 1997; Jonas & Melefors, 2009). A second scenario, that has been demonstrated for several of the Rsa sRNAs in S. aureus (first characterized for their UCCC motif), is the terminal hairpin serves to bind conserved regions within a target RNA, and the surrounding, less conserved regions confer target specificity (Geissmann et al., 2009). More work is necessary to elucidate the function of each of these individual sRNAs as well as the conserved domain that characterizes them. Curiously, the homology searches also identified SAUSA300s206 within this group however, further in silico analysis demonstrated SAUSA300s206 has high sequence complementarity to SAUSA300s205 and SAUSA300s288 as well as SERPsCon. The presence of high levels of sequence complementarity begs the question: Is SAUSA300s206 a regulator of SAUSA300s205 and SAUSA300s288? Regulation of one sRNA by another (so-called anti-

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sRNAs) is not unprecedented in the literature. In E. coli the molecular mechanism for interaction of two such anti-sRNAs, AsxR and AgvB, with their targets has recently been elucidated (Tree et al., 2014). AsxR binds the sRNA FnrS, which normally represses the expression of a heme oxygenase, ChuS; thus AsxR acts to enhance expression of ChuS (Tree et al., 2014). In the context of AgvB, it binds the sRNA GcvB, repressing the GcvB-dependent repression of DppA expression (Tree et al., 2014). In a direct parallel to this, our group recently identified a set of highly transcribed, highly homologous sRNAs in Acinetobacter baumannii, termed Group 1 sRNAs, for which there appears to be an anti-sRNA, ABUWs043 (Weiss, A. et al., 2015). ABUWs043 is encoded in an antisense fashion to ABUWs042, and thus may regulate ABUWs042 through several means, including promoter interference and/or complementary binding (Weiss, A. et al., 2015). Importantly, ABUWs043 has a high level of sequence complementarity to the rest of the Group 1 sRNAs (21 such elements exist in the A. baumannii genome), albeit lower than that found for ABUWs042, suggesting ABUWs043 may regulate the rest of the Group 1 sRNAs in an anti-sRNA fashion (Weiss, A. et al., 2015). SAUSA300s206 shares many characteristics with these confirmed and putative anti-sRNAs, but ultimately more work must be done to characterize its function within S. aureus. Finally, and perhaps the most intriguing observation about these sRNAs, is the absence of an identified anti-sRNA encoded in S. epidermidis that shares homology with SAUSA300s206. The possibility that such a sRNA exists cannot be excluded, however, the potential that this is a S. aureus specific adaptation is a potentially fascinating point of evolution. Regardless, a better understanding of the function of these 24 sRNAs may underlie basic physiological and regulatory differences between S. aureus and S. epidermidis, and further our understanding of the staphylococci in general.

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ACKNOWLEDGEMENTS

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This study was supported in part by grant AI080626 (to L.N.S.) from the National Institute of Allergy and Infectious Diseases.

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623

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624

DATA BIBLIOGRAPHY

625

1.

Broach, W. H., Weiss, A. & Shaw, L. N. (2016) NCBI Gene Expression Omnibus,

626

2.

Broach, W. H., Weiss, A. & Shaw, L. N. (2016) Figshare 10.6084/m9.figshare.2072890.

GSE77567.

627 628 629

FIGURES AND TABLES

630 631 632 633 634 635 636 637 638 639

Figure 1: Staphylococcal phylogeny and sRNA content. A) Phylogenetic relationship was determined using the rpoB gene from a range of S. aureus isolates, alongside other species within the Staphylococcaceae. The three strains from this study (S. carnosus TM300, S. epidermidis RP62A, and S. aureus USA300) are highlighted (blue, red, and black respectively) within the tree. The tree was created using the CLC Main Workbench software and default settings. rpoB sequences were retrieved from NCBI. B) Circos file representing the S. aureus USA300 genome with recently annotated sRNAs (Carroll et al., 2016). Depicted from the outermost semi-circle inward: the genome of S. aureus, sRNA annotations, expression level of each sRNA under standard conditions, genomic landmarks (SCCmec [purple], pathogenicity islands, [red], prophages [orange], and other genomic islands [yellow]), sRNAs encoded on the forward strand and, innermost, the reverse strand.

640 641 642 643

Figure 2: Northern blot analysis of sRNAs in S. epidermidis and S. carnosus. Total RNA was isolated from S. epidermidis RP62a (A) and S. carnosus TM300 (B) cultures grown to the mid-logarithmic phase. Samples were analyzed using DNA probes specific to each transcript. Size markers, and the RNA probed for, are denoted on each gel.

644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661

Figure 3: Shared and unique sRNA content amongst the staphylococci. A) Depicted from the outermost semi-circle inward: the genome of S. aureus, sRNA annotations, expression level of each sRNA under standard conditions, genomic landmarks (SCCmec [purple], pathogenicity islands, [red], prophages [orange], and other genomic islands [yellow]), sRNAs encoded on the forward strand and, innermost, the reverse strand. The inner links connect sRNAs that have sequence conservation. Red and blue links show homologous sRNAs between S. aureus and either S. carnosus or S. epidermidis, respectively; and the black link indicates a single homologous sRNA shared between S. epidermidis and S. carnosus but with no relation to any in S. aureus. B) Pie charts represent the portion of sRNA content that is shared with each of the species in this study. The total sRNA content of each genome is indicated. C) Numbers used to generate images in (B). Shown is the number of small RNAs shared between a given species pairing (upper section of each cell) as well as the number of sRNAs unique to a given species pairing (lower section of cells). For example, S. aureus has 105 sRNAs in common with S. epidermidis, but only 52 of these 105 are unique to S. aureus and S. epidermidis (i.e. not found in S. carnosus). When viewing this data, an organism specific point-of-view must be employed to understand the differences in numbers from similar comparisons. Specifically, the numbers are different for S. aureus vs. S. epidermidis [105 and 52 sRNAs, shared and specific, respectively] compared with S. epidermidis vs. S. aureus [92 and 56 sRNAs, shared and specific, respectively] because S. aureus has 52 sRNAs that are homologous to 56 sRNAs in S. epidermidis.

662 663 664 665

Figure 4: The identification of transcriptionally silent S. aureus sRNAs in S. epidermidis and S. carnosus. A) Data is arranged in the same manner as Fig. 3A, with the following differences: Links connect annotated sRNAs of S. aureus to homologous regions within the chromosomes of S. epidermidis (blue) and S. carnosus (red) that do not show transcriptional activity in these latter

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666 667 668 669 670

species. Regions were considered homologous if BLAST search returned an E-value of < 10-10. B) Pie chart shows the total shared and unique sRNA content of S. aureus including the expressed sRNAs from figure 3 and the homologous unexpressed from (A). C) Numbers used to generate images in (B). Shown are the number of small RNAs shared between a given species pairing (upper section of cells) as well as the number of sRNAs unique to a given species pairing (lower section of cells).

671 672 673 674 675 676 677 678 679 680 681 682 683 684

Figure 5: Sequence and structural conservation of several highly related and newly identified S. epidermidis sRNAs. A) Shown is a sequence alignment of 21 newly identified sRNA genes from S. epidermidis, with a particular focus on the most conserved region within each. Within the zoomed in region, conservation at the nucleotide level is shown, with a consensus sequence generated from the alignment presented (SERPsCon). The level of conservation of each nucleotide is indicated by color, and the number of sequences containing the conserved residue from all 21 sRNAs. Purple = conservation in all 21 sequences, dark green = 20/21, yellow = 19/21, orange ≤ 18/21 and white = not conserved, and not included in the consensus sequence. Alignment, conservation analysis, and consensus sequence generation, were performed using the CLC Genomics Workbench software B) RNA secondary structure prediction for the consensus sequence generated in (A), with each residue color coded to its level of conservation, as detailed in (A). RNA secondary structure predictions were generated using the mfold software. C) RNA secondary structure predictions for each of the 21 sRNAs from the alignment. The most highly conserved region of each (from the zoomed in area in (A)) are highlighted red. RNA secondary predictions were again generated using the mfold software.

685 686 687 688 689 690 691 692 693 694 695

Figure 6: The S. epidermidis sequence and structural motif is conserved in homologous sRNAs in S. aureus. A) Sequence alignment of three sRNA genes (SAUSA300s205, SAUSA300s206, and SAUSA300s288) from S. aureus and the consensus sequence generated (SERPsCon) in Fig. 5A. Sequence annotations are shown on the left, and on the right total sequence length. Zoomed in areas show nucleotide conservation amongst the four sequences, with the conservation for each residue indicated by color. Purple is 100% conservation, green is 75%, and yellow is 50% or below. B) As in (A), but containing the reverse complement region of SAUSA300s206 (RC-SAUSA300s206) instead of its native orientation. C) Secondary structure predictions for each S. aureus sRNA as well as RC-SAUSA300s206. Regions sharing high level of homology to SERPsCon as determined in (A) (SAUSA300s206) or (B) (the rest) were highlighted in each structure prediction. RNA secondary predictions were generated using the mfold software.

696

Table 1: Newly annotated non-coding RNAs of Staphylococcus epidermidis RP62a

697

Table 2: Newly annotated non-coding RNAs of Staphylococcus carnosus TM300

698 699 700 701 702 703 704 705

Figure S1: Schematic representation of sRNA annotation. Reads generated from RNAseq experiments aligned to their respective genomes were examined for evidence of transcriptional activity in three general ways. In each example, red arrows represent newly annotated genes, gray arrows represent previously annotated genes, green and red horizontal lines are RNAseq reads in the forward and reverse directions, respectively. New sRNAs were annotated based on the presence of reads found antisense to a previously annotated gene (A), reads within an intergenic region (B), or reads demonstrating differential expression in the same direction as a previously annotated gene (C).

706 707 708 709

Figure S2: Alignment of highly related sequences from S. epidermidis and S. aureus alongside RCSAUSA300s206. Multi-sequence alignments were generated using CLC genomics workbench. Shown are the names for each corresponding sequence (left), nucleotide markers (top) and length of each sequence (right). Each color represents a particular nucleotide: Adenine (red), Thymine (green),

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710 711 712

Guanine (yellow), or Cytosine (blue). On the bottom is a graphical representation of nucleotide conservation across the multiple sequence alignments, with higher bars representing greater sequence conservation.

713 714 715 716 717 718 719

Figure S3: Pairwise comparison of twenty-five sequences from S. epidermidis and S. aureus including RC-SAUSA300s206. Pairwise comparisons were generated from the alignment in Fig. 6 using CLC genomics workbench. Comparisons are made between the two intersecting sequences for percent identity (below the diagonal black boxes) and the Jukes-Cantor corrected distance measurement (above the diagonal black boxes). The figure is color coded for relative percent identity/relatedness, with purple indicating higher identity & relatedness and red indicating lower identity & relatedness.

720 721 722 723 724 725

Figure S4: Alignment of highly related sequences from S. epidermidis. Multi-sequence alignments were generated using CLC genomics workbench. Shown are the names for each corresponding sequence (left), nucleotide markers (top) and length of each sequence (right). Each color represents a particular nucleotide: Adenine (red), Thymine (green), Guanine (yellow), or Cytosine (blue). On the bottom is a graphical representation of nucleotide conservation across the multiple sequence alignments, with higher bars representing greater sequence conservation.

726

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Click here to download Figure Fig. 1.pdf

Prophage

4 s10 3 0 5 s3 79 s12363 ss10575 s 262 s08 0 6 8 63 ss1761 s21805 s1 s2124 ss1980 s 51 s0 79 s1 88 s0 02 s10737 s3 110 1 s 5 s 0 s2 09 3 9 58 s1 11 s 29 8 s2256 s10780 s s29116 5 s s 30 s 05 2 69 s 8 s 16 2 s0058 s1055 s s10 84 4 s 3 0 8 2 s 10 s s1 254 28 s s 46 49 s0 53 2 s2 25 s 25

s0

s0

0kb

200

s01 s236 5 s063 s014 s174 s227 s289 s288 s013 s181 s143 s012 s011 s118 s112 s169 s093 s202 s094 s092 s060 s170 s134 s287 s059 54 s167 s1 s010 s205 s183 s091 s234 s285 s090 s284 s00991 s286 33 s1 77 s235 s2 s0 83 s2 s282 s232 s136 s008 s231 5 s1962 s133 s06 s0769 s07 8 s144 s03 9 s22 1 s23306 s035 s2252 s02581 s s0 s0

s1

s2 51 s s1 s 1 4 s0 12 41 8s s1 s s 13 61 2 s 29 64 s2 024 49 s 0 s0 12 7 3 s s 25 s 08 62 s 24 0 2 s1 296 3 958 s s03 s2 11 8 s s26 75 5 4 6 s20344 s 4 s 13 7 s10231 0 s s0 37 s0 s2161 s1 1 4 s 5 s 3 5 0 323 s s20223 s1099 s0994 5 2 ss03 8 09 1 7 s s0096 s0 45 s s2242 s1 70 s 93 s0 90 s 107 s0230 s20021 ss0279 6 241 s0 s0 20 s04 s0644 8 s0 8 s1219 s0 1 s1 18 s0 s s23290 s23187 s2114 s 1 s 40 s14379 s02237 s0 6 s29126 s043 s1 19 s2 91 s290 s259 s1 37 s106 s095 s187

kb

1500kb

0kb

100

0 s2826 0 s2 97 s1007 s1006 279 s0 75 s 173 8 s 166 s0 27 s 278 s12 s 225 s1054 s 5 s 0s s10467 s20 1 22 s 042 2 s 126 s 4 s2238 s 20 s2 50 s22223 s1 19 s0 49 s s2 98 s0 50 60 s1s1139 s1 40 s1 8 4 s0 47 ss107 s0 93 32 s1 18 s12176 68 2 s 42 s 21 s1 s1146 s 088 5 s 00 59 25 s s1 5 s s1 087 3 1 s2 20177 s s21 11 1 s 2 4 s2 04 6 s 21 4 s 17 s 00 5 s 76 6 s 16 03 s2 6 0 s s0 82 s0 21 1 s1 10512 s s07 s 2 s

b

0k

50

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Genomic Island

B

S. aureus USA300

s s2 19 75 4 s s1 s 1 s 2 58 s s1 17199 s2 17774 s1 89 ss20 09 s2 86 s 11 8 73 s0 05 7 s2 72 s 8 3 s0 05 6 s2 71 s1 646 s2 s1 57 69 s2 s2 92 s 4 s2 s20813 ss1870 s15 04 67 s 26 5 s1 6 s 5 s 2668 04 5 s2203 ss20820 s0 44 s2 65 02 s1 07 s0 72 01

0kb

00

A

25

Figure1

SCCmec PAI

ACME 1

A

Figure2

Click here to download Figure Fig. 2.pdf

300nt

300nt

1500nt

200nt

300nt

100nt

200nt

200nt

1000nt

100nt 800nt

s0 91 SE RP

5

100nt

100nt

s0 SC A

s0

s0

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74

100nt

69

300nt 200nt

38

300nt 200nt

SC A

SC A

s0

30

100nt

300nt 200nt

SC A

400nt 300nt 200nt

SE RP

B

s0 7

s0 5 SE RP

SE RP

s0 4

3

6

100nt

3

0kb

s0 s 34 s0033 s0 32 s0 31 s0 30 s0229 8

s088 s022 s020 s021 s019 s018 s017 s016 s015 s014 s071 s0135 s08 s012

s00

3

s00

9 s0701 2 s0 7 s00776 s 75 s0 74 s0 73 s0072 s 88 s0

s00

Total: 118

2000kb

Staphylococcus carnosus Staphylococcus aureus Staphylococcus epidermidis Staphylococcus carnosus

250

Common to all

0kb

Total: 89

s s 1 s1 00217 07 s00 s0 1 04

68 s0 65 3 s0 06 66 4 s 05 s0 06 s1 s 7 6 62 s0 s0 69

s116

s094 s103 s042 s092 s041 s040 s111 s039 s038 s087 s037 s036 s035 s110 s093 s034 s033 s115

6 s04

s045 s044 s043

s0

s s 09 s00575 56 s0 55 s s 09 s00547 5 3 84 s s0081 85 s08 0 s0 s 51 s00450 s04 9 8 s08 3

s s 0 s0 05960 58

kb

s027 s118

s0038 s101 s113 s02 s029 s030

s102 s104 s089 s032

s031

90 s0 14 6 09 s1 00 07 s0 s 0 8 s 00 0 7 s 1 04 1 s s0 01 52 s s00782 s 11 3 01 s 00 s s10124 s 1 9 s0 10 8 s 15 s0 16 s0179 s0 7 s0 1 s0 19 05 s0 99 21 s0 s0 20 s0022 s0082 ss091 s 023 s 8 s10096 s 4 s02 5 s02 6 s02 6 s08

s s0 06 98 1

s0

00

0k

b

C S. aureus

kb

b 0k

50

2

Stap hy

1000kb

1500

25

71 s0 06 s1 070 s

20

b

k 00

kb

s101 s02 s13 3 s2471 s246 s29 s034 s115 s2485 s2 49 s264 s038 s250 s0 24 s175 s296 s083 s130 s062 s061 s123 s1 s297 s1 22 s2 51 41 s164 s148 s046 s2 s2552 s0 s2 3 25 s1 54 s0 84 s14 9 s1084 s 2 s 162 s1 s 055 s2 03 s 116 s1055 s0 8 s 298 28 s3299 s s 01 s 300 s31010 s10178 ss058 s 2 s 1 06 9 s 07 s 10 s 08 9 s 25 9 s11950 s10737 ss256 2 8 s 8 58 s 26 0 s15 8 s 08 0 s1 1 s 05 5 s2 24 s 17 7 s1 61 s13039 ss2678 04 26 2 s1 3 s 35 16 3

s011 s010 s045 s009 s008 s080 s007

0kb

00

s292 s147 s239 s016 s139 s026 38 s120 s237 s2 s018 s240 s017 s114 21 s1 9 s048 s01 s068 s044 s020 s206 s241 s021 s027 s107 s029 s293 s030 s242 s190 s070 s045 s096 s097 s152 s031 s099 s032 s037 s033 s098 s294 s245 s022 s161 s153

s026 s07 s0255 s024 s023

06 5 s0 4 s00

Total: 303

0kb

150

06 7 s1895 s1 59 s119 s0 37 s2 91 s1 90 s2 s2 s043

s027

500kb

10

Sta ph ylo c 100

Staphylococcus epidermidis

1

44 s s 04 s 04 3 s 04 2 s 04 1 81 s 0390 07 s 0 3 s0 37 s0838 s 7 s0036 35 s08 3

Staphylococcus aureus

s reu au

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s0

B

us

s077 s072

49 6 s0 08 76 84 s s0 s0 48 s0

74 s0 082 s

30 s2 33 44 s1 s1 39 6 65 6 s0 3 s0 07 s 08 s1 35 2 7 6 0 2 s2 86 s0 19 31 s s28 3 s2 91 s 2 32 2334 s0 s 2 83 4 s s2 s 2 77 s 0 91 s2885 s 1 09 s2 05 s 0 90 2 7 s 0 83 s 6 s 1 0 s1 s 01 4 s 15 s 59 0 2 s0287 s 34 s06 4 s20 s1170 s0969 s 92 s1 s00932 2 s 11 1 0 s 118 s 181 s 011 s 88 s 43 s2 27 s1013 s2 s 289 s 4 s17 4 s01 3 015 s02636 s s

s s 0 s0 04 78 46 7

Click here to download Figure Fig. 3.pdf

Sta phy loc oc c

0kb

2500kb

50 s0089 s

kb

4

s05

00

5 s05

53 s0052 s 051 s

15

69 s068 s070 s0 s067 s065 s066 s063 s064 s062 s058 s059 s060 s057 s061 s056

0kb 200

A

sus o n r ca s cu c o

s001 s002 s172 s244 s207 s203 s265 s266 s267 s082 s268 s081 s040 s185 s243 s269 s155 s270 s156 s204 s192 s271 s272 s157 s064 s056 s086 s273 s053 s186 s117 s189 s208 s171 s209 s199 s177 s274 s275 s158 s194 s1 s0476 s0 s2 1 s1 03 65 s07 s2111 s0 3 04 s2 1 s0 s 87 s214 s06160 s2 s27 s 12 s 159 s2 6 105 s00805 s20717 s18 8 s215 2 s s22116 s13 7 s 2 s1146 s 4 500 s1074 s2182 s12 4 5 kb s1 0 ss0193 s 5 47 s s 04 0 s 16 8 s20509 s1089 20 s1 13 9 s2 8 s 19 s0042 s s1 67 16 0 s 45 ss12 s 27 22 6 s 1 8 1 s1 s 0 73 s s2 38 s 1 06 s 0 22 s2 22697 s0 12754 s 80 s0 75 s2223 s1 07 s 2 s 4 00 s 22 s 2 s2 166 5 s s2 05 81 79 2 28 1 s s1 00 s2 05 28 29 2 s0 35 s0 36

Figure3

loc o c c u s e p

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id id er m

S. epidermidis S. carnosus

S. aureus 303 92 47

S. epidermidis S. carnosus

187 56 8

105 118 40

52 25 1

64 37 89

11 1 41

3

0kb

s0 s 34 s0033 s0 32 s0 31 s0230 s02 9 8

kb 00

s292 s147 s239 s016 s139 s026 38 s120 s237 s2 s018 s240 s017 s114 s121 s048 s019 s068 s044 s020 s206 s241 s021 s027 s107 s029 s293 s030 s242 s190 s070 s045 s096 s097 s152 s031 s099 s032 s037 s033 s098 s294 s245 s022 s161 s153

s026 s075 s025 s024 s023

s088 s022 s020 s021 s019 s018 s017 s016 s015 s014 3 s071 s0185 s0 s012

s101 s02 s1313 s247 s246 s295 s034 s115 s248 s2 49 s264 s038 s250 s0 24 s175 s296 s083 s130 s062 s061 s123 s122 s2 s1 97 s141 s251 s04664 s148 s2 s2552 s0 s2 3 25 s1 54 s0884 s14 9 s1 4 s 02 s 162 s1 s 055 s2 03 s21916 s1055 s0 8 s 8 28 s3299 s s 01 s 300 s 110 s 078 s0 s 302 s 111 s0658 9 s 07 s 10 s10809 s02579 s2 9 7 s 5 s s 18 5 18 3 s2586 s 26 0 s15 8 s 08 0 s1 1 s 05 5 s2 24 s 17 7 s1 61 s13039 ss2678 04 26 2 s1 3 s 35 16 3

s011 s010 s045 s009 s008 s080 s007 06 5 s0 4 s00

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C

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SERPs103

Figure6

A

Click here to download Figure Fig. 6.pdf 262 300 238

SAUSA300s205 SAUSA300s206 SAUSA300s288 SERPsCon

103

100% Conservation

100% 75% ≤50%

0% SAUSA300s205 T GGC G AG AC T C C T G AGGG AGC AG T GC C AG T C G A AG AC C G - AGGC T G AG AC GGC AC C C T - AGG A AG SAUSA300s206 GGC T T C GC T T T C C T AGGG T GC C G T C T C AGC C T C GG T C T T C - G AC T GGC AC T GC T C C C T C AGG AG T SAUSA300s288 T GGC G AG AC T C C T G AGGG AGC AG T GC C AG T C G A AG AC C G - AGGC T G AG AC GGC AC C C T - AGG A A SERPsCon - GGC G AG AC T C T T G AGGG A AC AGG AC A AGC T G A AG AC T AC AGGC T G A AGC T G T C C C C T - A AG A A -

T AGC G A AGC C A T T C A A T AC G A AG T A T T G T A T A A A T AG AG A AC AGC A A A A T A AG AC AC T T T GC C C A AC T T AC AC T AC C A A T AG A A AC C T C T - AGC G A AGC C A T T C A A T AC G A AG T A T T G T A T A A A T AG AG A AC AGC - AGC G AGC C A A - - C A A T AC G A AG T A T T G T A A A T A A AG A AGC C AG -

B

262 300 238 103

SAUSA300s205 RC-SAUSA300s206 SAUSA300s288 SERPsCon 100% Conservation

100% 75% ≤50%

0% SAUSA300s205 T GGC G AG AC T C C T G AGGG AGC AG T GC C AG T C G A AG AC C G - AGGC T G AG AC GGC AC C C T AGG A AG RC-SAUSA300s206 T GGC G AG AC T C C T G AGGG AGC AG T GC C AG T C G A AG AC C G - AGGC T G AG AC GGC AC C C T AGG A A SAUSA300s288 T GGC G AG AC T C C T G AGGG AGC AG T GC C AG T C G A AG AC C G - AGGC T G AG AC GGC AC C C T AGG A A SERPsCon - GGC G AG AC T C T T G AGGG A AC AGG AC A AGC T G A AG AC T AC AGGC T G A AGC T G T C C C C T A AG A A -

C

A

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Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 SAUSA300s206 RC-SAUSA300s206 On: Sat, 30 Jul 2016 03:17:03 A

A

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G U A G C C A A G A A A U A A C A G U C G

A A

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U

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C G U A

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A

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A

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A C C G

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C G G C U U

A

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C G G C

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C

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G A

A

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U A G C

U G

A

A

C G C G

C C U A G C

U U A U A U

C G

C G U G G C A U

C G U A

C C

T AGC G A AGC C A T T C A A T AC G A AG T A T T G T A T A A A T AG AG A AC AGC - AGC G A AGC C A T T C A A T AC G A AG T A T T G T A T A A A T AG AG A AC AGC - AGC G A AGC C A T T C A A T AC G A AG T A T T G T A T A A A T AG AG A AC AGC - AGC G A - GC C A A - C A A T AC G A AG T A T T G T A A A T A A AG A AGC C AG -

C C A

G

Table 1

Click here to download Table Table 1 .docx

Table 1: Newly annotated non-coding RNAs of Staphylococcus epidermidis RP62a Locus ID SERPs001 SERPs002 SERPs003 SERPs004 SERPs005 SERPs006 SERPs007 SERPs008 SERPs009 SERPs010 SERPs011 SERPs012 SERPs013 SERPs014 SERPs015 SERPs016 SERPs017 SERPs018 SERPs019 SERPs020 SERPs021 SERPs022 SERPs023 SERPs024 SERPs025 SERPs026 SERPs027 SERPs028 SERPs029 SERPs030 SERPs031 SERPs032 SERPs033 SERPs034 SERPs035 SERPs036 SERPs037 SERPs038 SERPs039 SERPs040

Gene Name

Position

jaeL-1 jaeL-2 jaeL-3 jaeL-4 jaeL-5 jaeL-6 jaeL-7 jaeL-8 jaeL-9 jaeL-10 jaeL-11 jaeL-12 jaeL-13 jaeL-14 jaeL-15 jaeL-16 jaeL-17 jaeL-18 jaeL-19 jaeL-20 jaeL-21 jaeL-22 jaeL-23 jaeL-24 jaeL-25 jaeL-26 jaeL-27 jaeL-28 jaeL-29 jaeL-30 jaeL-31 jaeL-32 jaeL-33 jaeL-34 jaeL-35 jaeL-36 jaeL-37 jaeL-38 jaeL-39 jaeL-40

34999..35245 42907..43025 953853..954050 60337..60509 586811..586861 183818..183969 212119..212293 233449..233600 233917..234080 241408..241559 307532..307673 370776..370941 377942..378056 393987..394130 443311..443466 469574..469690 475770..475890 480754..480892 526358..526540 570220..570273 576526..576580 586669..586828 592434..592529 658364..658539 695170..695337 717301..717513 817973..818158 964074..964190 981290..981497 1007973..1008125 1099406..1099581 1150188..1150367 1227591..1227843 1231240..1231434 1279465..1279597 1281335..1281543 1308770..1308884 1318633..1318805 1337905..1338103 1379890..1380079

Upstream* Orientation Downstream* SERPs117 SERP0050 SERPs113 guaA SERPs022 rplA SERP0201 SERP0223 SERP0224 SERP0234 SERP0304 SERP0373 SERP0379 SERP0391 SERP0438 SERP0466 SERP0477 SERP0488 SERP0542 trpS SERPs082 SERP0592 SERP0599 SERP0662 SERP0697 SERP0720 sucD femB SERP0962 SERP0990 SERP1053 SERP1109 SERP1191 hisS infC SERP1245 dnaE SERP1273 SERP1292 leuS

< < > < < > < < > > < < < > > < < > < > > > < < < > < < > > < > < < < < < < >
< > < < < < < < < < < > < > < < < < > < > < < > < < < < < < > < < < > <
> < < > < < < > > > < > < > > > < > > > < < > < > > > < < < > > < > < >

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SERPs021 ilvD SERP1833 truA ileS dnaI SERP2414 aroK rpoB SERP0610 SERP1350 SERP1200 SERP1394 SERP2002 SERP0639 SERP1913 SERP2147 SERP0559 SERP0370 dmpI SERPs104 fumC SERP1100 SERP2164 SERP2324 xpt menA sufC SERP1229 SERP1294 scdA SERPs122 cysE SERP1183 glyS SERPs001 rpsO

RPKM# 218.24 7.73 2,448.19 873.11 321.15 297.65 122.31 699.48 60.59 269.26 20.57 16.46 4.82 134.68 18.05 18.6 22.86 39.41 22.28 6.66 36.06 284.41 262.79 22.81 12.38 197.29 85.11 34.58 389.21 157.46 68.74 19.16 138.17 381.25 550.56 139 510.43

Table 2

Click here to download Table Table 2.docx

Table 2: Newly annotated non-coding RNAs of Staphylococcus carnosus TM300 Locus ID

Gene Name

Position

SCAs001 SCAs002 SCAs003 SCAs004 SCAs005 SCAs006 SCAs007 SCAs008 SCAs009 SCAs010 SCAs011 SCAs012 SCAs013 SCAs014 SCAs015 SCAs016 SCAs017 SCAs018 SCAs019 SCAs020 SCAs021 SCAs022 SCAs023 SCAs024 SCAs025 SCAs026 SCAs027 SCAs028 SCAs029 SCAs030 SCAs031 SCAs032 SCAs033 SCAs034 SCAs035 SCAs036 SCAs037 SCAs038 SCAs039 SCAs040

jacL-1 jacL-2 jacL-3 jacL-4 jacL-5 jacL-6 jacL-7 jacL-8 jacL-9 jacL-10 jacL-11 jacL-12 jacL-13 jacL-14 jacL-15 jacL-16 jacL-17 jacL-18 jacL-19 jacL-20 jacL-21 jacL-22 jacL-23 jacL-24 jacL-25 jacL-26 jacL-27 jacL-28 jacL-29 jacL-30 jacL-31 jacL-32 jacL-33 jacL-34 jacL-35 jacL-36 jacL-37 jacL-38 jacL-39 jacL-40

9628..9890 16355..16590 68516..68644 114686..114974 144461..144729 144466..144711 195809..196025 239896..240240 248359..248731 286557..286798 302807..302992 349042..349212 370812..371006 386729..386902 409625..409751 435453..435577 439576..439686 449553..449930 465254..465398 475448..475663 478847..479060 519236..519323 704781..704974 736699..736810 754215..755140 809208..809442 954424..954574 1026107..1026242 1028624..1028907 1055393..1055592 1080768..1080936 1098995..1099432 1103951..1104094 1136220..1136427 1239320..1239485 1249565..1249804 1252944..1253215 1294117..1294234 1339350..1339494 1354036..1354126

Upstream* Orientation Downstream* SCA_0010 SCAs079 fcbC SCA_0114 SCA_0141 SCAs005 gltX proP SCA_0240 tagA SCA_0293 norA SCA_0365 SCA_0377 SCA_0399 SCA_0420 gapA smpB SCA_0454 int SCA_0469 glpQ SCA_0700 SCA_0733 SCA_0752 rluD mutS SCA_1009 SCA_1011 SCA_1036 SCA_1060 SCA_1079 pbp2 SCA_1116 alaS SCA_1240 hisS infC SCA_1325 fhs

< < > > > < > < > > < > > > > > > > > > < > < < > > > < > > > < < < < < < < >
3') CTTATGATTGATGCGCCTC GCTTCTACTTGGTTCGTTTCG CGGTCTCTGAAAGCGTCG GATGAATGGGGTACTCTGAGC CAGACGTATCGTGCTTAGG GAATTCGTCGTGTACTGTCATGC CCGAAAGCCTGAATGCAAGTC TTGCCCACTTTACCGGAAGA

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S. aureus SAUSA300s001 SAUSA300s002 SAUSA300s003 SAUSA300s004 SAUSA300s005 SAUSA300s006 SAUSA300s007 SAUSA300s008 SAUSA300s009 SAUSA300s010 SAUSA300s011 SAUSA300s012 SAUSA300s013 SAUSA300s014 SAUSA300s015 SAUSA300s016 SAUSA300s017 SAUSA300s018 SAUSA300s019 SAUSA300s020 SAUSA300s021 SAUSA300s022 SAUSA300s023 SAUSA300s024 SAUSA300s025 SAUSA300s026

SAUSA300s027

SAUSA300s028 SAUSA300s029 SAUSA300s030 SAUSA300s031 SAUSA300s032 SAUSA300s033 SAUSA300s034 SAUSA300s035

S. epiderdmidis SERPs077 SERPs076 SERPs001 SERPs107 SERP_SeSRP1 SERP_SetmRNA1 SERPs018 SERPs042 SERPs024 SERPs007 SERPs026 SERPs086 SERPs113 SERPs003 SERPs029 SERP_SernpB1 SERPs041 SERPs031 SERPs115 SERPs036 SERPs087 SERPs111 SERPs041 SERPs031 SERPs042 SERPs045 SERPs048 SERPs080 SERPs055 SERPs033 SERP2235 SERPs065 SERPs063 SERPs022 SERP2235 SERPs065 SERPs063 SERPs022 N/A N/A N/A N/A N/A N/A N/A

S. carnosus SCAs077 SCAs003 SCAs002 46330-46427 SCAs004 SCAs018 SCAs019 SCAs012 SCAs057 SCAs023 SCAs075 802831-803001 SCAs029 N/A SCAs030 SCAs032 SCAs034 SCAs043 SCAs035 SCAs073 SCAs081 N/A SCAs043 SCAs034 SCAs044 1561399-1561519 SCAs023 SCAs084 SCAs050 SCAs036

N/A

N/A N/A N/A N/A N/A N/A N/A N/A Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s036

N/A

SAUSA300s037

N/A

SAUSA300s038

N/A

SAUSA300s039 SAUSA300s040

SAUSA300s056 SAUSA300s057 SAUSA300s058 SAUSA300s059 SAUSA300s060 SAUSA300s061 SAUSA300s062 SAUSA300s063 SAUSA300s064 SAUSA300s065 SAUSA300s066 SAUSA300s067

N/A N/A SERPs001 SERPs117 SERPs012 SERPs116 SERPs040 SERPs112 SERPs054 SERPs010 N/A SERPs047 SERPs011 SERPs082 SERPs021 N/A SERPs015 SERPs067 SERPs064 SERPs066 SERPs022 N/A 2243354-2243427 N/A 807948-808018 865535-865623 SERPs081 N/A AS-hup N/A 662109-662236 N/A N/A

SAUSA300s068

N/A

SAUSA300s069

N/A

SAUSA300s070

N/A

SAUSA300s041 SAUSA300s042 SAUSA300s043 SAUSA300s044 SAUSA300s045 SAUSA300s046 SAUSA300s047 SAUSA300s048 SAUSA300s049 SAUSA300s050 SAUSA300s051 SAUSA300s052 SAUSA300s053 SAUSA300s054 SAUSA300s055

N/A SCAs005 SCAs006 SCAs070 SCAs070 SCAs005 SCAs006 N/A 1326396-1326450 SCAs079 SCAs085 SCAs083 N/A N/A SCAs089 N/A N/A N/A SCAs011 SCAs088 SCAs088 N/A SCAs016 N/A N/A N/A N/A 862611-862676 935214-935306 SCAs074 N/A AS-hup N/A N/A N/A N/A 616487-616544 1402848-1402905 1313671-1313728 N/A 1313680-1313725 616488-616535 1402849-1402896

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SAUSA300s071 SAUSA300s072 SAUSA300s073 SAUSA300s074 SAUSA300s075 SAUSA300s076 SAUSA300s077 SAUSA300s078 SAUSA300s079 SAUSA300s080 SAUSA300s081 SAUSA300s082 SAUSA300s083 SAUSA300s084 SAUSA300s085 SAUSA300s086 SAUSA300s087 SAUSA300s088 SAUSA300s089 SAUSA300s090 SAUSA300s091 SAUSA300s092 SAUSA300s093 SAUSA300s094 SAUSA300s095 SAUSA300s096 SAUSA300s097 SAUSA300s098 SAUSA300s099 SAUSA300s100 SAUSA300s101 SAUSA300s102 SAUSA300s103 SAUSA300s104 SAUSA300s105 SAUSA300s106 SAUSA300s107

SAUSA300s108

SAUSA300s109

N/A N/A SERPs091 629113-629285 N/A N/A N/A N/A SERPs016 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 2553249-2553369 N/A 2470888-2471003 2470888-2471003 N/A 2553249-2553369 1843789-1843850 1727843-1727908 N/A N/A N/A N/A N/A N/A N/A N/A rrfA 5s rRNA 280012-280159 SCAs045 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A SERPs044 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A SERPs067 SERPs064 N/A SERPs066 SERPs022 SERPs064 SERPs067 N/A SERPs066 SERPs022 SERPs067 DownloadedN/A from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s109

SAUSA300s110 SAUSA300s111 SAUSA300s112 SAUSA300s113 SAUSA300s114 SAUSA300s115 SAUSA300s116 SAUSA300s117 SAUSA300s118 SAUSA300s119 SAUSA300s120 SAUSA300s121 SAUSA300s122 SAUSA300s123 SAUSA300s124 SAUSA300s125 SAUSA300s126 SAUSA300s127 SAUSA300s128 SAUSA300s129 SAUSA300s130 SAUSA300s131 SAUSA300s132 SAUSA300s133 SAUSA300s134 SAUSA300s135 SAUSA300s136 SAUSA300s137 SAUSA300s138 SAUSA300s139 SAUSA300s140 SAUSA300s141 SAUSA300s142

SAUSA300s143

SERPs064 SERPs066 SERPs022 SERP2076 SERPs065 SERPs022 SERPs063 N/A SERP0908 293028-293185 N/A 1781437-1781588 SERPs108 N/A 1966418-1966486 2110662-2110729 2110721-2110788 1966364-1966427 SERPs089 SERPs110 AS-SERP1283 SERPs084 N/A N/A 189571-189663 N/A N/A SERPs109 N/A SERPs085 1764260-1764408 SERPs006 671622-671762 SERPs118 SERPs108 SERPs108 N/A N/A 1248727-1248787 N/A N/A SERPs090 695714-695909 526897-527093 1142175-1142370 2250781-2250940 1878793-1878966

N/A

N/A N/A N/A 279251-279397 N/A 1655578-1655698 N/A N/A N/A 1177689-1177807 SCAs087 SCAs039 1746560-1746659 N/A N/A 209017-209109 N/A N/A 468351-468405 N/A SCAs082 SCAs076 SCAs080 716707-716814 N/A N/A N/A N/A N/A 1269806-1269859 N/A N/A AS-SCA_0198

N/A

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SAUSA300s143

SAUSA300s144 SAUSA300s145 SAUSA300s146 SAUSA300s147 SAUSA300s148 SAUSA300s149 SAUSA300s150 SAUSA300s151 SAUSA300s152 SAUSA300s153 SAUSA300s154

SAUSA300s155

SAUSA300s156 SAUSA300s157 SAUSA300s158 SAUSA300s159 SAUSA300s160 SAUSA300s161

SAUSA300s162

SAUSA300s163 SAUSA300s164 SAUSA300s165 SAUSA300s166 SAUSA300s167 SAUSA300s168 SAUSA300s169 SAUSA300s170 SAUSA300s171 SAUSA300s172 SAUSA300s173 SAUSA300s174 SAUSA300s175 SAUSA300s176

N/A 904097-904207 N/A N/A N/A SCAs071 SERPs114 SCAs007 SERPs034 SCAs037 N/A N/A N/A N/A N/A N/A N/A N/A SERP1480 N/A SERPs083 SCAs078 N/A N/A 2482548-2483113 2500714-2501292 2504946-2505492 2499642-2500214 N/A 2502070-2502645 2481449-2481988 2518815-2519359 2506108-2506681 2437264-2437835 N/A N/A N/A N/A N/A AS-SCA_2391 72798-74051 N/A AS-SERP0318 AS-SCA_0311 N/A N/A 2021335-2021581 1914637-1914877 1450065-1450240 1449474-1449589 82197-82315 1048394-1048491 973856-973959 465894-465981 2224152-2224239 2306976-2307073 N/A AS-SERP2136 AS-sceB 1904408-1905205 N/A 19782-19880 38505-38610 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A AS-SERP0438 AS-SCA_0420 AS-ebh N/A AS-SERP1781 AS-SCA_1684 AS- SERP0033-0037 AS-metE-metC Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s177 N/A SAUSA300s178 AS- SERP2203 - 2204 SAUSA300s179 AS-manA-2 SAUSA300s180 N/A SAUSA300s181 AS-trpE-D SAUSA300s182 N/A

N/A N/A AS-pmi AS-SCA_0776 AS-trp operon N/A AS-SCA_2253 SAUSA300s183 AS-SERP2353 AS-SCA_2255 SAUSA300s184 AS-SERP1953-1954 AS-SCA_1863-1864 SAUSA300s185 SERPs088 N/A SAUSA300s186 N/A N/A SAUSA300s187 AS-SERP1064 N/A 2158616-2158997 SAUSA300s188 AS-ddh 2114825-2115217 SAUSA300s189 N/A AS-fadX-2408 SAUSA300s190 AS- SERP1384-1385 AS-SCA_1423-1424 SAUSA300s191 711139-712303 SCAs025 SAUSA300s192 2329384-2330440 N/A SAUSA300s193 N/A N/A SAUSA300s194 N/A AS-SCA_1829 SAUSA300s195 AS-SERP2141 2054108-2054839 SAUSA300s196 1821446-1821566 N/A SAUSA300s197 472054-472194 N/A SAUSA300s198 SERPs078 285761-286141 SAUSA300s199 N/A N/A SAUSA300s200 AS-SERP0475 N/A SAUSA300s201 N/A N/A SAUSA300s202 AS-SERP0886 - 0887 N/A SAUSA300s203 2580092-2580692 N/A SAUSA300s204 N/A N/A SERPs025 SERPs092 SERPs093 SERPs094 SERPs069 SERPs095 SERPs060 SERPs013 SERPs014 SERPs096 SERPs043 SAUSA300s205 N/A SERPs057 SERPs038 SERPs097 SERPs019 SERPs100 SERPs098 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s206

SAUSA300s207 SAUSA300s208 SAUSA300s209 SAUSA300s210 SAUSA300s211 SAUSA300s212 SAUSA300s213 SAUSA300s214 SAUSA300s215 SAUSA300s216 SAUSA300s217 SAUSA300s218 SAUSA300s219 SAUSA300s220 SAUSA300s221 SAUSA300s222

SERPs103 SERPs017 SERPs101 SERPs038 SERPs106 SERPs068 SERPs025 SERPs069 SERPs013 SERPs060 SERPs043 SERPs057 SERPs038 SERPs014 SERPs019 SERPs017 SERPs092 SERPs093 N/A SERPs094 SERPs095 SERPs096 SERPs097 SERPs098 SERPs099 SERPs100 SERPs101 SERPs102 SERPs103 SERPs104 SERPs105 SERPs106 2584169-2584460 2535721-2536010 N/A N/A SERPs108 N/A SERPs002 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A 175037-176256 194523-195764 194866-196622 214705-216455 N/A N/A 320228-320317 N/A N/A N/A N/A N/A Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s223 SAUSA300s224 SAUSA300s225 SAUSA300s226 SAUSA300s227 SAUSA300s228 SAUSA300s229 SAUSA300s230 SAUSA300s231 SAUSA300s232 SAUSA300s233 SAUSA300s234 SAUSA300s235 SAUSA300s236 SAUSA300s237 SAUSA300s238 SAUSA300s239 SAUSA300s240 SAUSA300s241 SAUSA300s242 SAUSA300s243 SAUSA300s244 SAUSA300s245 SAUSA300s246 SAUSA300s247 SAUSA300s248 SAUSA300s249 SAUSA300s250 SAUSA300s251 SAUSA300s252 SAUSA300s253 SAUSA300s254 SAUSA300s255 SAUSA300s256 SAUSA300s257 SAUSA300s258 SAUSA300s259 SAUSA300s260 SAUSA300s261 SAUSA300s262 SAUSA300s263 SAUSA300s264 SAUSA300s265 SAUSA300s266 SAUSA300s267 SAUSA300s268

N/A SERP0404 N/A N/A SERPs023 N/A 596758-596989 N/A N/A 655203-655423 N/A N/A SERPs108 1097889-1098037 N/A SERP1214 SERP1216 SERPs035 N/A N/A 1617553-1617676 1610234-1610359 N/A 1774668-1774784 N/A N/A N/A N/A 1875481-1876567 1928400-1929999 1934047-1935252 1965856-1966195 N/A N/A 2117957-2118147 N/A N/A N/A N/A 2274881-2276252 N/A N/A N/A N/A N/A 2278011-2278639

N/A N/A N/A N/A N/A 619778-620596 622607-622835 N/A N/A N/A N/A N/A N/A 1134999-1135131 N/A N/A SCA_1263 SCAs038 N/A N/A N/A N/A 1538303-1538303 1648741-1648856 N/A N/A N/A N/A N/A N/A 1823008-1824201 N/A N/A N/A N/A N/A N/A N/A N/A 2094509-2095853 2530579-2530811 616495-616552 N/A N/A N/A 2096511-2097137 2098167-2098727

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SAUSA300s269

SAUSA300s270 SAUSA300s271 SAUSA300s272 SAUSA300s273 SAUSA300s274 SAUSA300s275 SAUSA300s276 SAUSA300s277 SAUSA300s278 SAUSA300s279 SAUSA300s280 SAUSA300s281 SAUSA300s282 SAUSA300s283 SAUSA300s284 SAUSA300s285 SAUSA300s286 SAUSA300s287

SAUSA300s288

165200-165279 268360-268439 378566-378645 527350-527429 549771-549850 559668-559747 571117-571196 694910-694989 1008403-1008482 1405524-1405603 1767799-1767878 1932399-1932478 N/A SERPs108 SERPs108 N/A N/A N/A N/A 77203-77284 SERPs108 SERPs079 499991-500093 N/A SERP0665 N/A SERPs108 N/A N/A N/A SERPs025 SERPs069 SERPs013 SERPs060 SERPs043 SERPs057 SERPs038 SERPs014 SERPs019 SERPs017 SERPs092 SERPs093 SERPs094 SERPs095 SERPs096 SERPs097 SERPs098

N/A

N/A N/A N/A N/A N/A N/A N/A 83350-83426 N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A

N/A

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SAUSA300s289 SAUSA300s290 SAUSA300s291 SAUSA300s292 SAUSA300s293 SAUSA300s294 SAUSA300s295 SAUSA300s296 SAUSA300s297 SAUSA300s298 SAUSA300s299 SAUSA300s300 SAUSA300s301 SAUSA300s302 SAUSA300s303

SERPs099 SERPs100 SERPs101 SERPs102 SERPs103 SERPs104 SERPs105 SERPs106 SERPs030 N/A N/A N/A N/A N/A SERPs050 N/A N/A N/A N/A N/A N/A N/A N/A

SCAs031 N/A N/A N/A N/A N/A SCAs086 N/A N/A N/A N/A N/A N/A N/A N/A

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S. aureus USA 300 FPR_3757 50 SAUSA300s048 SAUSA300s001 SAUSA300s026 SAUSA300s052 SAUSA300s002 SAUSA300s037 SAUSA300s057 SAUSA300s003 SAUSA300s039 SAUSA300s067 SAUSA300s004 SAUSA300s090 SAUSA300s068 SAUSA300s005 SAUSA300s129 SAUSA300s069 SAUSA300s006 SAUSA300s135 SAUSA300s070 SAUSA300s007 SAUSA300s136 SAUSA300s071 SAUSA300s008 SAUSA300s140 SAUSA300s082 SAUSA300s009 SAUSA300s143 SAUSA300s088 SAUSA300s010 SAUSA300s145 SAUSA300s092 SAUSA300s011 SAUSA300s155 SAUSA300s095 SAUSA300s012 SAUSA300s158 SAUSA300s096 SAUSA300s013 SAUSA300s159 SAUSA300s097 SAUSA300s014 SAUSA300s164 SAUSA300s098 SAUSA300s015 SAUSA300s174 SAUSA300s099 SAUSA300s016 SAUSA300s175 SAUSA300s101 SAUSA300s017 SAUSA300s176 SAUSA300s102 SAUSA300s018 SAUSA300s177 SAUSA300s103 SAUSA300s019 SAUSA300s178 SAUSA300s105 SAUSA300s020 SAUSA300s179 SAUSA300s106 SAUSA300s021 SAUSA300s180 SAUSA300s107 SAUSA300s022 SAUSA300s181 SAUSA300s108 SAUSA300s023 SAUSA300s182 SAUSA300s111 SAUSA300s024 SAUSA300s183 SAUSA300s125 SAUSA300s025 SAUSA300s186 SAUSA300s127 SAUSA300s027 SAUSA300s187 SAUSA300s130 SAUSA300s028 SAUSA300s188 SAUSA300s138 SAUSA300s029 SAUSA300s189 SAUSA300s142 SAUSA300s030 SAUSA300s190 SAUSA300s170 SAUSA300s031 SAUSA300s191 SAUSA300s210 SAUSA300s032 SAUSA300s194 SAUSA300s276 SAUSA300s033 SAUSA300s195 SAUSA300s287 SAUSA300s034 SAUSA300s199 SAUSA300s290 SAUSA300s035 SAUSA300s200 SAUSA300s295 SAUSA300s036 SAUSA300s203 SAUSA300s212 SAUSA300s038 SAUSA300s272 SAUSA300s213 SAUSA300s040 SAUSA300s273 SAUSA300s215 SAUSA300s041 SAUSA300s281 SAUSA300s242 SAUSA300s042 SAUSA300s284 SAUSA300s262 SAUSA300s043 SAUSA300s285 SAUSA300s303 SAUSA300s044 SAUSA300s286 SAUSA300s045 SAUSA300s239 SAUSA300s046 SAUSA300s299 SAUSA300s047 SAUSA300s301 SAUSA300s049 SAUSA300s261

S. epidermidis RP62a 50 SERPs003 SERPs001 SERPs097 SERPs012 SERPs002 SERPs020 SERPs004 SERPs044 SERPs005 SERPs067 SERPs006 SERPs074 SERPs007 SERPs008 SERPs009 SERPs010 SERPs011 SERPs013 SERPs014 SERPs015 SERPs016 SERPs017 SERPs018 SERPs019 SERPs021 SERPs022 SERPs023 SERPs024 SERPs025 SERPs026 SERPs027 SERPs028 SERPs029 SERPs030 SERPs031 SERPs032 SERPs033 SERPs034 SERPs035 SERPs036 SERPs037 SERPs038 SERPs039 SERPs040 SERPs041 SERPs042 SERPs043 SERPs045 SERPs046 SERPs047 SERPs048 SERPs049

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S. carnosus TM300 50 SCAs007 SCAs025 SCAs026 SCAs052 SCAs063 SCAs072

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5+ AA ORFs 50+ AA ORFs

S. aureus S. epidermidis S. carnosus 3122 388 337 138 1 7

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Query SAUSA300s027 ORF

SAUSA300s028 ORF

SAUSA300s061 ORF SAUSA300s018 ORF

Lowest E-value Accession 7.40E-15 SERPs065_ORF SERPs063_ORF SERPs022_ORF 6.59E-12 SERPs063_ORF SERPs065_ORF SERPs022_ORF 4.71E-11 SERPs081_ORF 2.66E-10 SERPs087_ORF

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

Query SAUSA300s005 ORF SAUSA300s061 ORF

Lowest E-value Accession 2.31E-16 SCAs004_ORF 1.85E-10 SCAs074_ORF

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Unique S. aureus sRNAs SAUSA300s029 SAUSA300s030 SAUSA300s031 SAUSA300s032 SAUSA300s033 SAUSA300s034 SAUSA300s035 SAUSA300s036 SAUSA300s039 SAUSA300s048 SAUSA300s053 SAUSA300s056 SAUSA300s058 SAUSA300s062 SAUSA300s064 SAUSA300s066 SAUSA300s067 SAUSA300s069 SAUSA300s071 SAUSA300s073 SAUSA300s074 SAUSA300s076 SAUSA300s077 SAUSA300s078 SAUSA300s079 SAUSA300s080 SAUSA300s084 SAUSA300s085 SAUSA300s086 SAUSA300s087 SAUSA300s090 SAUSA300s091 SAUSA300s092 SAUSA300s093 SAUSA300s094 SAUSA300s095 SAUSA300s096 SAUSA300s098 SAUSA300s099 SAUSA300s100 SAUSA300s101 SAUSA300s102 SAUSA300s103 SAUSA300s104 SAUSA300s105 SAUSA300s106 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s111 SAUSA300s114 SAUSA300s117 SAUSA300s123 SAUSA300s124 SAUSA300s126 SAUSA300s127 SAUSA300s129 SAUSA300s137 SAUSA300s138 SAUSA300s140 SAUSA300s141 SAUSA300s144 SAUSA300s148 SAUSA300s149 SAUSA300s150 SAUSA300s151 SAUSA300s154 SAUSA300s156 SAUSA300s157 SAUSA300s161 SAUSA300s166 SAUSA300s167 SAUSA300s168 SAUSA300s169 SAUSA300s170 SAUSA300s171 SAUSA300s172 SAUSA300s177 SAUSA300s182 SAUSA300s186 SAUSA300s193 SAUSA300s199 SAUSA300s201 SAUSA300s204 SAUSA300s208 SAUSA300s211 SAUSA300s212 SAUSA300s213 SAUSA300s214 SAUSA300s215 SAUSA300s216 SAUSA300s219 SAUSA300s221 SAUSA300s222 SAUSA300s223 SAUSA300s225 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s226 SAUSA300s230 SAUSA300s231 SAUSA300s233 SAUSA300s234 SAUSA300s237 SAUSA300s241 SAUSA300s242 SAUSA300s247 SAUSA300s248 SAUSA300s249 SAUSA300s250 SAUSA300s255 SAUSA300s256 SAUSA300s258 SAUSA300s259 SAUSA300s260 SAUSA300s261 SAUSA300s265 SAUSA300s266 SAUSA300s267 SAUSA300s270 SAUSA300s273 SAUSA300s274 SAUSA300s275 SAUSA300s276 SAUSA300s281 SAUSA300s283 SAUSA300s285 SAUSA300s286 SAUSA300s287 SAUSA300s290 SAUSA300s291 SAUSA300s292 SAUSA300s293 SAUSA300s294 SAUSA300s296 SAUSA300s297 SAUSA300s298 SAUSA300s299 SAUSA300s300 SAUSA300s301 SAUSA300s302 SAUSA300s303

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Sequence GTAAAAATAAGACGACATGCGCGAACATGTCGTCTAAGCAAGCCAAACGCTGGCTTCTAAAATATTTTTTTAACCATTCCAAC AATATTTATATTATAATATAAATAAGTCAACGACCATGCGTGGACAGTAAAACGAAGTACATGCGAATGTAGTAGCCGTTTA GGGCGTTTTCAAGGAGCGCCTTTCATTTTTTATGTATTGCTCCCCTTCGGGCTAGTATATTAAATTTATTTTTGCGCTTTCCAAA GTGTTACACATGCATCAACTATTTACATCTATCCTTGTTCACCCAAGCATGTCACTGGGTGTTTTTTCTTATGATAGAGAGCAT ATATATAGAAAAAGGGCAACATGCGCAAACATGTTACCCTAATGAGCCCGTTAAAAAGACGGTGGCTATTTTAGATTAAAGA GTAGTAAGTAGAAGCAAAAGATGAAAATCATTAACTCTTGAAACACAAAAAGGGCAACACTCGGAAACATGTTACCCTAAT GTAAAAAGACGACATGCAGGAACATGTCGCCTAATGAGCCCGTTAAAAAGACGGTGACTAAATGAGATTTTCTTTAACCATC TAAATAGACGATATGCAGGAACATGTCGCCTATTGAGCCCGTTAAAAAGACGGTGACTAAATGAGATTTTCTTTAACCATCA GTTGAATTGATGGTGGCTATCTGAGTAAAGGGGGGTGGTGCCTATGGCATTACTTAACACTTTTGAAAGGAAAAGCCTATT ATTATTAGTGTTAATTGTAGCGCATCCCAATTAAATATTGCAACCTATTTTATTA CCCCGACGGCATGTGCGTGAAGAGATGAAAGATACTGCTTCTACCCTTGCAAATATATCATCTCTATGTCTCGGGGCAGATC TTGAAAACGCATACTTCACCATGCTAAAATAGGAGTCGCAAACAAATAAGATTCAATAAGATGTGATGGTAAGCTAGATAAA TGTAGATGTTCTTTAGACATTAAAAGCTTCTAACATGATACGGAATATGAGGTTCCTGTATCACATTAGAAGCTTTTTTGTTGC GTCGAAAATTTCAGTCGCTGTGCCTTCTTTATAGACAGTCCCTTTATTCATAACGATAACATGAT ATACATGTTTTACTTACGGGTGCTGGTGTCGCAAAGAAAATTACATCACAGTCATTATTGTCCACTGTAAGTGCTTCGAAATG ACAAATTCCCGGTAACCATTCCGGCTTCATTCTCTTGAAGAATGACATATTCTCAGCGTTTTAGCTGAAGGTCAGATGATACG GCGTATACAAGGATAAAGCTTATAACAGTAGTAATTGTTGCTATCAAACGAACAACATATATTCTATTTTCAGATAGCAA TTATCTTAATTAATTAGTTGGTTAGGCCAATAAAAATTATAAAGATATTTGCGCTTTTT GAGGAAAGAGACTTATAGGTCTCGCGAGTTATTTTAATTCGTATGCAAGAAAAAGAAGAGCTATGCATTTTATTTAAAATGC ACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTT ATAGAGAAAAGAAGTTATCGCAATCGCAATAACTGACACAAATAAGTCACCCAATCTATTTAAGTTTGTGTTCTCTATAATAA TGAATGGGTATATAGTTCGTAAGATATAGAGAAATGAGGTATGTAACGATGCGCCAATTCATTAAAAGAACTGTTAAAACAA TAAGCATATTAAAATGGCGTGAGATATCGACAATTGAGCTGCGCCGATTTTATATTTATAGTTTAATTACTGATTAAAGTGGC TTCTTATTGCCAATGATTACTACCCCTAGTCGGCGGCAATTGAAGTGTGATTGATGTAACTTGCCCTCGTTGGTGAGCAATTG GAATTAGATATCACTTGCGTGTTACTGGTAATGCAGGCATGAGCAAACAACCGCACTATGAGAATAGTCTTGTTTGTTCATG TCACCTAAGAATTGCAAATCCAGAAGTCATTTAAGTTTTACCTTTCATTCATACATCCTTTAATATTAATTACGACTTCTTTTAT CAAAAAACAATACATAGCCATTTTGAACTAACTTGCTAATCTTTTATTGATATTCAACTATGTTATAAAAAAAGCAAATTGACC AACACATAAAATGGGTAACTAACATCACGAAATCATTGTATTTGTTGTTACACTGATGAAGCGATGTCACAAAGAAATGTCG GTGCAACTTTATCACTGTATGGTCTGAAATAAATTGCGCGACTTCTGATGTGTTATGTTAGATGACTTTGTCATACTAACTATA TTATGTTATAAGTTTAAAACGAATAACACGTTAGGTCTCGTCTAGGCAAAGCATATTTATGAAGATGAATTGAACAGACAGA TTGAATGGTGAGCTTATTGGGATAAATAATATAAATAATTACTTAAAAGTGAATGCAATAGTTGTTTATGTTTTGAACAAGCG ATAAAAATCTTTATTAATTATTTTATTGGTATATTAGCCTTGGCGTTTGCTGCTTATATATTATTTAAATAAAGTTTAGAGTGAA TAATAATTTTATATAATATATAGAGCTTCAGTATACCTTTTGAGTA ATTTATTGCACGAAATTAGCATCGAATAAGGGAAAATAAGTGTTAAGTTTTAAATGATAAAAAAGATTGGAATGGATCGTCT AGGGAAAGTCCCTCCTGACTGATTAACGCTCGAATGTCCATTCAATCTTTATAAAGTAGAGATTTATTAAGATTAACAATTTG CATTCGCTCATTTATTTTTGTTTAACATGTGCGTTTTAATTCAATTATTGAATATCGTCCCACCAAT AAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTCGAT TGAATTAATTTTGTTAATCGTTTGTCACTGTTACTTGTTGACGCAAGTAGCAGTTTTTT AGACACAGCAATGTGTTCAAATTTTCATCTATTCATAAGCTAGCCTTCGGGCTAGTTTTT AGACACAGCAATGTGTTCAAATTTTCATCTATTCGTAAGTTAGCCTTCGGGCTGACTTTTTATTTCCATTATTCACATGTTAATC TTTTACATACTGAAAACTCGTTAATATTATTTC TAATATTAATCATTCCCTCTGTTGAAATTGATAACTA TATACTTAACTATTTCCTTACATTACTTCACATATTTAAGAGCTGCATATACACTCACTCCTTG TTTTTGTTACTAGTTTGTAATAATTAACTTACTTTTGTAAAAAAAGACATGAGATTATTTTTTTAAATCTATATAAAGTTGACAA GATCCATGAGAGTAGGAACCCCATCATACGGGAATTTCGAAATCATGGGTTTTTTG ATTTTATAAACTATATCTCAACTACCTATACAAAATCATACAATTAAAAATCCATCCATTATAAACGCATGTATTAATAAGTTAT Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

ATACATAATTAACTTTCTTTTGTTTTTATATTATTTCAATACCCTACTATATATCACAACACATAAATTAAGCATGACACTCATTC ACATTATCACCTTCAAACTTTCACTCATATTACTTTGGAAATTTATTATAAAATAGAAGTATGGATGTATTTCTGAAATGATAC GTTTGTAACTCTATCCAAAGACATACAGTCAATACAAAACATTACGTATCTTTACAACAGTAATCATGCATTCTATGATGCTTC TAATCTATCATTCAAGCAATAAATGCTTTTTGTTACATAAATTTGACTAGCATTGCTCTGAATACGTTATATTGATGAATTGCT GAGTATAGGTTTAAAATGCTATAAGCCAAATGTAGATTAAAACAATCGTTAGCTATTTGTTGTCAAATAATTATGATTGATTT GGCAGTAGTTGACTGAACGAAAATGCGCTTGTAACAAGCTTTTTTCAATTCTAGTCAACCTTGCCGGCGG ATTATGACGGTATAAATTAAATAAAGATTTTGAGTTCACGCTTAAATAAGTTCACGCTTAAATTTATAGCCTGCCACAGAGTT AAATATACGTGTTAATTCTTGGTAATAGTGTTACTGAGACGCATTACGAAGAAATTTATCTTGTTTTTCCTTTTTTAAAAAGAA ATATAGGTTAATCTAAGCGAATGGTTTACAATGAGCGCGGAAGGACAGGACGAATAAATTTTGTATGTAAAATGCATAATCT CCGCCGGCAAGGTTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCGTTCAGTCAACTACTGCC AAAGGAGGTAATATAGGTTATGATTATTTATCGACAGTATCACCATGAAGGCGCACCAGTTTATGAAATTATAACCAAAACG GCCAATCAGTACATCATAATTGCGTCTTGGGGACAGACAAATGATGAATAGAGATTGGC CGGGCTCATTAGGCGACATGTTCCTGCATGTCGTCTTTTTACATTTTTATAGTAACATATCTTTTATTTAATTGTCTATTTTTATT GTTGAAACACTTTAATCATTTATAATTGTAGCGGTTATAATTTGAAAAGGTTTTAACTTAGAATAAATATCCTCTATACATATA AAAAGAACCTTAGATTGTAGTTATGGATATTGTGATAATTCAGATCATATTAATGTTGACGTCTTTGGTAACAAGCCATGAAA TTTAATAAAACTTATTTAATGCAAAATTATGACTAACATATCTATAATAAATAAAGATTAGATATCAATATATTATCGGGCAAA TATAGATGATACTGCTAGCCTAAATATAACAACATCGGCATGCACATCTTAGAATTTAAGCTAGTGGCAGCTTATAACTTAAG AATTAAGTTAAAGGAGGGACGTTATGTTACATTATGTGATTCCAGTATTAGTCCTATTACTCGTATTCTTAATTGGTTGGATTT ATCCAGCTGTTACCAGTCCGATTGTGATAACTGTCGTACCTGAACTACTTTGTATTAAAATAGTTACAACGATACCTGCAATA GATATACATATCAAGCATCATAGATTGATGTGTTAAGTAATAATGATCATACGCTACTTTTTGATCATCAGTGATATCATCTCT GTCACCAGTATAAATAAAGCCATTCTCAATGTCAGGATTGGCTTTTTTACTTTGGAAAACTGCTGTTAAAACAGCACCAATAA ATTTGCCATATATAAGCTAATAGCTCTATTTGTAGTTTCAATTAATTGATGATCTGTGTAATTAGACATCACATATGCTCTAAT GATGACAATCATTTATTATTTGCGAATCATAGAGTTATAGTTATTACGAACTCTATGTGATAAGCAGTAATGCTGATTGTTTAT ATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGA TACTCAATAATCTGTAGTACCTTGTTTTGGAATAATGTAATTTTATATCATCAACGGCTACAAATGAGCAGTTTCATATATAAA TCATCTCATAAAGCTAGAATAATATCTAACTTTATGGGATACACTACAAATCGAGACTATAAGGTTTTTT GTGAAATAAATCACAAACTTAAAAGCGGATGACACATGACCTTTTAAGTTATGCGTTGAAAATAAAAGAGATGTTTATTTGC TCCCCTCCCCCTACCCTACTCCATCGATATAACTCATACTACATATCAACGAAATCAGTATTTTATCGCTTCCTTTCCTATATTG TTTATTAAAATATTCACTTGCCTTTTCGCCAGCAATTTCCTTAGCTTTTTGGAGGGATTCTTTATTTTTATCGATATCTTCACCCA TTACGTTCAACTTTCTTTTCACCTAATGGATAAAACCAGGTAATCGGGAATCCGTTAGTATCGTAGCCGACAATTTTATCACCA CTCACATAACTCGTTCAACTGTACCAAACCACATTACATTAGATTTTAGGCTAACTATTGTGATGTACATCAAAAACGAATTTG ATAATCATAACCTATATTACCTCCTTTGCTACTCTATGGTTATATTATAAATAACATTTTTATGTGTGACATCAACCTTAAGTAT ATCTCATTTTAAGTATACAAAATGCAAAACAACCGATTCACAAGCATATTTCACACAAGTAAACCGGCTATTTATCAACGTAT TTATAGATATATTCACTAAAGTCTTACGTATATAAATATATAATGAATTCCTATTACATTTCACAAGCTGAAAAGTTGGATTGA GATGACTATTTAGGGAGTTGGTAAGAAATGGAAAAGCTTGTTACAAGCGCAATTTCATTCAGTCAACTACTGCCAATATAAC AAATTGTTTGAATCATGTAACAATCATATAAATTGCTGTTTATATTGTTGTGAAAATGAGTTGACAAAAGTCGGTATAGATAT TCAAGAGGGCATTTGCAATTAAATGTAAACATGATGAAATTCGACCGTTGGCATAAGGGGATTTGTAAACAAATCGTTTTGA TAGGGAATGTGCTATTGAAGGGGTTAAAGATGTTTGAAATGTCTTG TTTGGACCCATCGAAAATTCGGGTTCTCAAATCATCGAACATAACAAAAGAAGCTAAGCAACATGTAGGC TGAAAAACAAATATATTTTAATGTTCAGGTTAAATGACTTTCATTATTTCATTTAGTTGTTTTACCGGATTATCGTTTACTACAA AGCTAACTTACGTTCCGCTAGAGTAGAACGTTGCTAGA CATACTTAGACAATCGAAAGTGTACATTATTAAATTATCATTTCCAGTTCTACTCTAGCGGAACGTAAGTTGGCTACCATCCTC CATTTTATAAATTTATACATTTTAATAAAGAACATACGATAGATGGTTTAAACCTTGTTAACTGAGAAATTTTGATATGTATTC AACACATTCATCCGATTTATAATAATAAGATAAACTAACATTTATTGAGAGCGGGACGGAAATGATAAAGAAC GAGAAAATGGTAATAAATGAAATTGATTTCTATAGAGTGGGACGAGAAAATATAGTTATAGCTG CTATGTTGGGGCCCCGCCAACTTGCACAATATTGTTAGCTGACTTTCCGCCTGCTTCTGTGTT AAGCTATTTTTATACTAGTAGGTGTCAGTCATGAATAACATTTTGTTAAATGCTATCAATATAGTTATTACTACCACTTTTGTTA Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

TGGTATGATTTTATAAATTTTTATTTTTTTATGCGTTATCTTGGCTTTGGTCGGCGAAAGATGACGCTTT GTTGTACCTCTTGCGTTGTTTATTTTCTATGATTTTTTAGTATTTAATAAATGTTATAATACGCTCTATTGACCCACCAATTATG TTGACTTACTTGAGCATTGCCTGTTTTGTTATTTGCTGTTTTTGGTTGGACAATAGCAGGGTCTTGATATACTTGAGTGCCAGA ATTTTTAAATCAAACAAATCATTAGTTTTAAAGAAATTAATCAATAAAATTAGCTATGTCTTTTCCTTGTTTCATAAAGAATTTA AATATCTTAGAATTAAATCAATTAATTAACTATTAAATAAAAATTAACTATATATTAACTAGTGTAAATTAATAAATAGAAATA AAATGTTTTTCATTATTATTTTCATTATGTTATTAAAAAATGGGAATTTTAGACGTTATACTAAATGTGCAACTGTATAAGAGC TTTTATGTTTGTATTAGTTCTAAATTATTTTGCACTTGATGACACGTATTTTTGAGTTTAAGTGGTGACTCAAGTTCAATAAAA TCTACGTGCGGATTATAAAGTAAAGCGTAGCATAACCAGGAGTTAGTCGATTTTTAATAAATTCGACTAAATTATTAATAAAG AAAACAAGTAATAATAGTAATTATTAACAAATTTGATGCCATTGCATTTCAACATTGTAAGCGTATCGCAATTAATGTTTTACA TTTTTTATTTACTTTAAATTTCTCAATCTACAGTGTAATCTTATTTCTTATTATTAACTTAGCGTTTGGTCATTCGTCTTATTCAAC ATTTTTATCATTAAGACAGATATAATAAATAAAATATAGAAAACTGATTAAAAGGTATACAGTTGCTCGTATGTGTGTCCAAC TATTTGAAGTATACTATAGAGTAAATTATATTGGGGAAATATGTAAACGAACCGGTTGATTTTATAGTGGATTAACACTTCAT TTTTTATAAATTTTTATAAAATTAAACTAATTTATTCATTCGCAACCCCTAAAAATAATTTTTAGCCTTTCTGCGAATTTTATGA CAACGATTACATATGGATATACGACTGAGGGAACGTGGGTCAATCTATTATTTAAATCTTTATCGCTCAGCATGATTATCGTT AGTGGAATAATTAATAATAATTGTATTTAAATGCAATGCTGTTGTTCTTTCATACTTACAAGCAAGTCATAAGAAATGAGAAA TTCTTGTTCGCCATTCATAACAATACGCTTTTTATATTTAAGTGGCATAAATTCATATCTCAAATAACGACCAATATGCTTTTTT TATTCCATTTGACTCTGAGGTGATACGAATGCGTTTAAAAGTATTGTTCCATTTCATTGCTGCTATTTTCATATCATTCATGTTG GATATTCAATATCTGCATCCAAGAAAAACATTACAATTACCTTTAATATTGAAAATTATTTTGAATCTTGCACTTATAGGTATT AAGCCAGGATAATGTAGTCTTAATCGTTCTGAAATACGAAAAATGTTGTGGAAATCGCGTGAAATAATCAGAGGAATCGTTT AGACACGTCTTCTGATTAAACTAATACAGTTGATGAATTAACAGAAAATCCAGTATGTACTGAGTACATAAGAGATCGAACA CCAATTTCTTATTATTATCTGTAAGAGAAAGATTCTCTGGAAATATAAGTACACCGTAGTTATAGTTATCTTCGACAGTGAAG TATCGTCACTTATTATGTAAATTTTCAGTGTGAAATGGCAGGTTTGCAATCACTTGTTTAACAAAATGATGCAATCAATCATGT TTTGAATACAAATAATCAAATCATTGATAAATTTTTTGTCTACGATTAATGGAGGGACTTGAATGGTGTTAATTACCTATCAA ATAATGAGTAGGAGTTTTAGGGCTATTATTTACAAATAATATAATACTGCAAAGACTCGAAATTATTTAGAATTCCAGTTATC CGGGCCTCATGTTATTTTCACTATTTTTTGGAGCCGGAAATTTAATATTCCCGCCCATGCTTGGCCATACAGCGGGTCAAAAT GGTGAAATGTAAATTGGTGCGCATAGCTTATACAAAAAGGATGCATCAATCGATATCGTCGT ATTCCTCAATGTCTGATTTTAATGTAAACTATGCGTAAGAGTTTTCTATAAGTGGGAGTGATCAAATGTTGAAAAAATGGCTT AAAGAACTACATTTTGTTAATGACACATAGTTGTTTAATTAGTTAGCAACAACATTCCATTGAAATTAACATAAATCATAAAA TTGAAAAAGATTTCTAGAAATACAATTAATGTTCATCTAGATATTGTACGAAGTTGTATGAATAAGTTAAACTTAAGTTGAAT TGGTAAATATGTATTTGCTGTAAACAGTTTTTGTAACACATGATACATATGGTTGTGAAAATAGCATATATAAAGGATGGCTA AAAAGGCAATGAAATAATAAATGGC GCTTATTATTTTCATAAACGATTTTCTAAAATCCTTTACGAAATTTTTAATAAAAATCACATCCCAGTTATTTTTTTAACACTTAT GTGTAGCTTTTAGCGTATGCAGGCGCAGAAATGCAAGCACGGAGTGCGTTAAGCATTTGGGCGGAGCCTGCGACAAATACG TAGGCGGACTTGATGAACAACTACATACACCTAGACGTAATCAGCCAAGGTTAAAAATTCATGCAGGTTCTGTAGG AGGGGGTTTTATCTTTGGAAAAAGTTCTTGATTTAGACGTGCAAGTTAAAGGAAATAACAACACTAATGATTCAGCGGGTGA ATATTAAAGGTTTATCCTTTAAAACACGTATATATTCGTTACCATTTTTGGTAATTAACCATGTAATCTTATAACTATAAGTGG TGGGTGATGCGGAAAATTTGGGTGATCGATTGTTTATATGCATCAACATTCTTTGTGGATTGTTTGACAGTAGACAGTCATTT GAAGTTATTTATTCAGCATTGGGACATAAAATTAACTTAAAATTTAAATATTGAAGATGCTTTAATTAAAGTTAAAGACTAGC AAGCGTGCTTTATTTAGATATACTGTCGTTCTAAAAACGAGCCATATAGAATGTTTCATGTCCTAGCATGAAGCACATGAATC AATACATATTACTTTTAAAAAGCGTATCACAATTCATATAACGGTCATAATAACTCGCTTCATTTTCATAGATAAATTACATTA ATTATTTTTAAAACGATTACCTACAAGATTTACATATAAAATTCTATCATGTCTGCTATATATAAACGAAATGATATTAGAATC TAATGAAAGGCTCTAAACAAATACTTTTGATTATGGGCATTATATCTCTTATTGTTTTATTTATTTTTACACTATTCATCATGGC CTTGTAACAAGCTTTTTGGGCCCCAACACAGAAGCTGACGAAAAGTCAGCTTACAATAATGTGCGAGTTGGGGTGGGACGA GGCACCAATCACTAGAAAAATCGATATAGGATTTTAATAATTAGTGATGAACC

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S. aureus specific sRNA SAUSA300s029

Rank Gene Synonym

Energy Pvalue sRNA_start sRNA_stop

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

oppD lpdA lpl3 glpD arcA thrC glmM

SAUSA300_0894 SAUSA300_0996 SAUSA300_1275 SAUSA300_0486 SAUSA300_1409 SAUSA300_0415 SAUSA300_1977 SAUSA300_1742 SAUSA300_2624 SAUSA300_1193 SAUSA300_0349 SAUSA300_0647 SAUSA300_1695 SAUSA300_1584 SAUSA300_1474 SAUSA300_2570 SAUSA300_2138 SAUSA300_1227 SAUSA300_2111

-12.71 -12.52 -12.13 -10.67 -10.24 -10.12 -9.72 -9.53 -9.51 -9.26 -8.93 -8.85 -8.79 -8.67 -8.63 -8.55 -8.5 -8.48 -8.33

0.005 0.005 0.007 0.017 0.021 0.022 0.027 0.029 0.03 0.033 0.038 0.04 0.041 0.043 0.044 0.045 0.046 0.046 0.049

52 76 44 76 82 47 75 50 75 73 100 52 71 97 48 43 73 82 56

71 90 58 86 95 61 88 59 90 88 110 64 90 110 62 55 86 90 73

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

hisS phoB alr2 thrC ung -

SAUSA300_1582 SAUSA300_1978 SAUSA300_0638 SAUSA300_1587 SAUSA300_2561 SAUSA300_2539 SAUSA300_0365 SAUSA300_1351 SAUSA300_0284 SAUSA300_2493 SAUSA300_2247 SAUSA300_1207 SAUSA300_1292 SAUSA300_1227 SAUSA300_2538 SAUSA300_2262 SAUSA300_2156 SAUSA300_0563 SAUSA300_0082

-13.55 -13.54 -11.63 -10.19 -10.08 -9.84 -9.78 -9.65 -9.64 -9.57 -9.36 -9.29 -9.11 -9.08 -8.86 -8.83 -8.66 -8.62 -8.54

0.002 0.002 0.009 0.021 0.022 0.025 0.026 0.028 0.028 0.029 0.032 0.033 0.035 0.036 0.04 0.04 0.043 0.044 0.045

90 24 91 29 62 42 105 104 30 61 26 32 31 95 107 83 56 30 32

109 36 102 38 74 50 117 119 43 75 43 40 43 110 122 97 65 42 42

SAUSA300_1121 SAUSA300_0484

-15.9 -15.57

0 0

17 27

37 45

SAUSA300s030

SAUSA300s031 12-

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3-

SAUSA300_1012 4 uvrC SAUSA300_1045 5 purC SAUSA300_0968 6 bccT SAUSA300_2549 7SAUSA300_1969 8 glyA SAUSA300_2067 9SAUSA300_2578 10 rnc SAUSA300_1126 11 tag SAUSA300_1612 12 hemH SAUSA300_1782 13 norA SAUSA300_0680 14 ahpF SAUSA300_0379 15 SAUSA300_0650 16 rocD SAUSA300_0860 17 SAUSA300_0775 18 menB SAUSA300_0948 19 ung SAUSA300_0563 20 birA SAUSA300_1347 21 gltA SAUSA300_1641 22 nhaC SAUSA300_2250 23 gnd SAUSA300_1459 24 SAUSA300_0628 25 SAUSA300_1436 26 SAUSA300_2531 27 SAUSA300_1172 28 SAUSA300_1491 29 SAUSA300_0874 30 SAUSA300_0210 31 rbsK SAUSA300_0262 32 asnC SAUSA300_1345 33 cls SAUSA300_2044 34 SAUSA300_1386 35 SAUSA300_1941 36 nrdD SAUSA300_2551 37 SAUSA300_1218 38 SAUSA300_1500 39 SAUSA300_0681 40 SAUSA300_1483 41 SAUSA300_2279 42 SAUSA300_2383 43 dnaN SAUSA300_0002 44 SAUSA300_1388 45 ureC SAUSA300_2240 46 gntR SAUSA300_2444

-15.18 -15.08 -13.35 -13.31 -13.2 -13.18 -12.82 -12.77 -12.53 -12.31 -12.23 -12.07 -12 -11.73 -11.57 -11.53 -11.33 -11.16 -11.13 -11.07 -11.06 -10.9 -10.75 -10.72 -10.67 -10.65 -10.57 -10.46 -10.44 -10.4 -10.36 -10.24 -10.18 -10.1 -10.09 -10.07 -10.06 -10.05 -10.02 -9.89 -9.88 -9.85 -9.58 -9.49

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0.001 0.001 0.003 0.003 0.003 0.003 0.004 0.004 0.005 0.006 0.006 0.007 0.007 0.009 0.01 0.01 0.011 0.013 0.013 0.013 0.013 0.014 0.016 0.016 0.016 0.017 0.017 0.018 0.019 0.019 0.019 0.021 0.021 0.022 0.022 0.023 0.023 0.023 0.023 0.025 0.025 0.025 0.029 0.03

32 39 35 37 134 39 62 22 111 89 136 14 33 39 32 36 1 128 40 35 134 84 25 137 14 95 1 95 1 3 105 122 44 35 40 36 35 131 32 1 110 40 2 73

49 49 52 48 150 49 77 42 122 101 150 24 53 48 45 48 15 142 54 50 150 99 44 152 33 109 16 111 12 14 122 136 58 55 54 49 53 140 44 11 128 50 20 82

47 rplD

SAUSA300_2203 48 SAUSA300_0300 49 SAUSA300_1462 50 rplR SAUSA300_2188 51 oppA SAUSA300_0891 52 SAUSA300_0130 53 SAUSA300_0113 54 SAUSA300_0003 55 hlgC SAUSA300_2366 56 SAUSA300_0070 57 SAUSA300_2339 58 SAUSA300_0912 59 SAUSA300_1069 60 lacF SAUSA300_2151 61 oppD SAUSA300_0889 62 SAUSA300_1384 63 SAUSA300_1451 64 SAUSA300_0667 65 fumC SAUSA300_1801 66 agrD SAUSA300_1990 67 SAUSA300_0582 68 SAUSA300_0609 69 SAUSA300_2382 70 SAUSA300_1448 71 SAUSA300_1503 72 SAUSA300_1759 73 sucD SAUSA300_1139

-9.31 -9.31 -9.3 -9.25 -9.21 -9.18 -9.18 -9.16 -9.15 -9.07 -9.02 -8.97 -8.93 -8.91 -8.86 -8.84 -8.8 -8.7 -8.67 -8.65 -8.59 -8.49 -8.45 -8.39 -8.38 -8.36 -8.35

0.032 0.032 0.032 0.033 0.034 0.034 0.034 0.035 0.035 0.036 0.037 0.038 0.038 0.039 0.039 0.04 0.041 0.042 0.043 0.043 0.044 0.046 0.047 0.048 0.048 0.049 0.049

16 33 12 131 35 73 29 138 1 79 18 4 94 34 133 32 17 87 39 112 121 39 136 33 105 34 37

32 51 28 149 49 88 41 152 8 93 32 15 114 54 152 44 32 105 53 126 141 53 149 49 118 44 49

-14.47 -14.45 -13.74 -13.65 -13.57 -13.05 -12.68 -12.61 -12.6 -12.11 -12.07 -11.97 -11.84 -11.52 -11.33 -11.24

0.001 0.001 0.002 0.002 0.002 0.004 0.005 0.005 0.005 0.007 0.007 0.008 0.008 0.01 0.011 0.012

145 97 21 97 94 54 46 26 27 46 123 91 90 31 51 1

157 110 38 105 104 71 58 41 42 54 135 108 108 41 62 17

SAUSA300s032 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

sufB moaD -

SAUSA300_0822 SAUSA300_2221 SAUSA300_0203 SAUSA300_2552 SAUSA300_2350 SAUSA300_0430 SAUSA300_1395 SAUSA300_0716 SAUSA300_1961 SAUSA300_1450 SAUSA300_2543 SAUSA300_0284 SAUSA300_1947 SAUSA300_1656 SAUSA300_2375 SAUSA300_0418

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17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

ackA nirB ftsZ splD lgt lctP deoC folE sdaAA oppA -

SAUSA300_0211 SAUSA300_1903 SAUSA300_1657 SAUSA300_2346 SAUSA300_0495 SAUSA300_1212 SAUSA300_1740 SAUSA300_0735 SAUSA300_1080 SAUSA300_0709 SAUSA300_0205 SAUSA300_0646 SAUSA300_1755 SAUSA300_0744 SAUSA300_0112 SAUSA300_1483 SAUSA300_2519 SAUSA300_0140 SAUSA300_0713 SAUSA300_0283 SAUSA300_1702 SAUSA300_0239 SAUSA300_1805 SAUSA300_0081 SAUSA300_0516 SAUSA300_0595 SAUSA300_1082 SAUSA300_0246 SAUSA300_1052 SAUSA300_1792 SAUSA300_2232 SAUSA300_0600 SAUSA300_0057 SAUSA300_2469 SAUSA300_0604 SAUSA300_0954 SAUSA300_0891 SAUSA300_2326

-11.22 -11.02 -10.82 -10.8 -10.66 -10.63 -10.6 -10.56 -10.48 -10.4 -10.26 -10.2 -10.13 -9.7 -9.62 -9.51 -9.48 -9.31 -9.28 -9.25 -9.24 -9.22 -9.2 -9.07 -9 -8.98 -8.85 -8.67 -8.64 -8.62 -8.48 -8.44 -8.44 -8.38 -8.35 -8.33 -8.33 -8.29

0.012 0.014 0.015 0.015 0.017 0.017 0.017 0.018 0.018 0.019 0.021 0.021 0.022 0.027 0.028 0.03 0.03 0.032 0.033 0.033 0.033 0.034 0.034 0.036 0.037 0.038 0.04 0.043 0.043 0.044 0.046 0.047 0.047 0.048 0.049 0.049 0.049 0.05

97 31 143 143 58 146 97 82 32 138 85 25 147 88 96 146 16 92 143 57 91 94 27 21 45 92 26 49 24 34 90 147 85 48 97 94 101 46

107 45 163 161 74 163 107 102 42 148 101 41 165 105 105 161 30 107 157 73 108 107 41 35 54 104 43 63 37 45 102 162 98 58 105 107 110 55

1 2 3 4 5 6 7

rpe phnE

SAUSA300_1022 SAUSA300_2337 SAUSA300_0544 SAUSA300_0277 SAUSA300_1115 SAUSA300_0551 SAUSA300_0142

-18.24 -11.2 -10.77 -10.03 -10 -9.03 -9.01

0 0.012 0.016 0.023 0.023 0.037 0.037

13 59 61 88 21 49 64

27 78 75 103 29 64 73

SAUSA300s033

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

8 9 10 11 12 13 14

icaA ddh asnC

SAUSA300_0226 SAUSA300_2600 SAUSA300_1207 SAUSA300_2463 SAUSA300_0834 SAUSA300_0903 SAUSA300_1345

-8.88 -8.82 -8.73 -8.68 -8.54 -8.49 -8.29

0.039 0.04 0.042 0.043 0.045 0.046 0.05

59 60 59 72 60 111 90

74 75 74 86 73 119 104

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

ald def aldA2 lacB tnp ribH gpsA -

SAUSA300_2324 SAUSA300_1331 SAUSA300_0292 SAUSA300_1108 SAUSA300_1912 SAUSA300_2112 SAUSA300_1901 SAUSA300_0677 SAUSA300_2359 SAUSA300_2429 SAUSA300_2154 SAUSA300_2115 SAUSA300_1810 SAUSA300_1842 SAUSA300_0551 SAUSA300_2424 SAUSA300_2619 SAUSA300_0474 SAUSA300_1712 SAUSA300_2543 SAUSA300_1363 SAUSA300_1552

-13.99 -12.15 -12.06 -10.72 -10.52 -10.18 -10.11 -9.82 -9.75 -9.75 -9.66 -9.49 -9.49 -9.04 -9.03 -8.91 -8.88 -8.81 -8.78 -8.59 -8.52 -8.43

0.002 0.007 0.007 0.016 0.018 0.021 0.022 0.025 0.026 0.026 0.028 0.03 0.03 0.037 0.037 0.039 0.039 0.04 0.041 0.044 0.046 0.047

53 53 27 99 125 123 140 120 129 100 125 15 15 54 87 100 126 32 125 125 125 27

63 63 41 113 133 142 156 134 148 115 134 26 26 64 102 115 145 42 136 133 141 40

1 2 3 4 5 6 7 8 9 10 11 12 13 14

leuC tuf pfkA fhs opuCd

SAUSA300_0052 SAUSA300_0793 SAUSA300_2386 SAUSA300_2472 SAUSA300_0385 SAUSA300_0349 SAUSA300_0632 SAUSA300_0375 SAUSA300_2012 SAUSA300_0533 SAUSA300_0218 SAUSA300_1645 SAUSA300_1678 SAUSA300_2390

-11.94 -11.39 -11.13 -11.1 -10.83 -10.62 -10.19 -10.09 -10.08 -9.93 -9.63 -9.53 -9.04 -8.87

0.008 0.011 0.013 0.013 0.015 0.017 0.021 0.022 0.022 0.024 0.028 0.029 0.037 0.039

93 77 28 53 24 13 70 54 24 62 62 7 54 7

112 88 39 68 33 23 80 67 35 81 73 18 67 21

SAUSA300s034

SAUSA300s035

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

15 16 17 18 19 20 21 22

mutM pstB lysS pheT -

SAUSA300_1635 SAUSA300_0646 SAUSA300_1280 SAUSA300_0496 SAUSA300_2350 SAUSA300_1421 SAUSA300_1038 SAUSA300_0210

-8.71 -8.63 -8.55 -8.55 -8.46 -8.44 -8.39 -8.38

0.042 0.043 0.045 0.045 0.047 0.047 0.048 0.048

18 33 55 67 10 72 15 24

26 41 70 79 19 92 33 33

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

ansA betB fabF mfd asnC fhs greA mutM metE pstB lysS coa

SAUSA300_1354 SAUSA300_0418 SAUSA300_1368 SAUSA300_2546 SAUSA300_0349 SAUSA300_0886 SAUSA300_2134 SAUSA300_2472 SAUSA300_0481 SAUSA300_1742 SAUSA300_0933 SAUSA300_0210 SAUSA300_0632 SAUSA300_0375 SAUSA300_0052 SAUSA300_0630 SAUSA300_0218 SAUSA300_0341 SAUSA300_0793 SAUSA300_1345 SAUSA300_1678 SAUSA300_0551 SAUSA300_1567 SAUSA300_1421 SAUSA300_1349 SAUSA300_1635 SAUSA300_0357 SAUSA300_1280 SAUSA300_0496 SAUSA300_0825 SAUSA300_2556 SAUSA300_0224

-13.4 -13.07 -12.03 -12.02 -12 -11.91 -11.34 -11.1 -10.91 -10.65 -10.38 -10.24 -10.19 -10.09 -10.05 -9.91 -9.63 -9.58 -9.21 -9.13 -9.04 -9.03 -8.94 -8.87 -8.85 -8.71 -8.56 -8.55 -8.55 -8.48 -8.38 -8.31

0.003 0.004 0.007 0.007 0.008 0.008 0.011 0.013 0.014 0.017 0.019 0.021 0.021 0.022 0.023 0.024 0.028 0.029 0.034 0.035 0.037 0.037 0.038 0.039 0.04 0.042 0.045 0.045 0.045 0.046 0.048 0.05

79 77 98 93 11 79 82 52 84 85 75 78 69 53 93 59 61 92 76 67 53 40 85 71 79 17 85 54 66 85 81 44

98 91 109 113 22 92 93 67 94 99 86 92 79 66 113 74 72 107 90 86 66 55 93 86 92 25 93 69 78 99 91 58

SAUSA300_0644 SAUSA300_0692 SAUSA300_0933

-16.24 -14.28 -13.44

0 0.001 0.003

149 155 188

164 168 202

SAUSA300s036

SAUSA300s039 123-

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

dnaN vraS fmtB truA rexA cobI greA rplW sucC rpmJ ddl arcA cdr menA recF manA

SAUSA300_0002 SAUSA300_1274 SAUSA300_1866 SAUSA300_1408 SAUSA300_2110 SAUSA300_2173 SAUSA300_0266 SAUSA300_1875 SAUSA300_1294 SAUSA300_0413 SAUSA300_0870 SAUSA300_2323 SAUSA300_1567 SAUSA300_2384 SAUSA300_0417 SAUSA300_2202 SAUSA300_1138 SAUSA300_1510 SAUSA300_2181 SAUSA300_2039 SAUSA300_2408 SAUSA300_0192 SAUSA300_0915 SAUSA300_2570 SAUSA300_2378 SAUSA300_0419 SAUSA300_0549 SAUSA300_0873 SAUSA300_0944 SAUSA300_0409 SAUSA300_0004 SAUSA300_1971 SAUSA300_2509 SAUSA300_2096

-12.66 -12.1 -11.95 -11.72 -11.51 -11.12 -10.77 -10.72 -10.63 -10.6 -10.36 -10.28 -10.2 -9.97 -9.96 -9.87 -9.82 -9.67 -9.63 -9.51 -9.44 -9.15 -9.15 -9.01 -8.95 -8.86 -8.83 -8.79 -8.72 -8.68 -8.58 -8.52 -8.48 -8.37

0.005 0.007 0.008 0.009 0.01 0.013 0.016 0.016 0.017 0.017 0.019 0.02 0.021 0.024 0.024 0.025 0.025 0.027 0.028 0.03 0.03 0.035 0.035 0.037 0.038 0.039 0.04 0.041 0.042 0.043 0.044 0.046 0.046 0.048

146 151 190 85 147 214 185 93 87 189 82 67 81 206 189 81 72 230 216 73 154 69 200 88 202 189 84 81 150 82 79 190 189 76

161 165 200 100 163 230 200 105 100 205 100 77 98 216 201 96 86 241 225 84 165 79 217 108 213 201 97 92 163 96 96 200 199 87

1 2 3 4 5 6 7 8 9 10 11

lctP coaBC mutS lgt ssaA -

SAUSA300_1677 SAUSA300_1742 SAUSA300_0112 SAUSA300_1486 SAUSA300_1104 SAUSA300_1188 SAUSA300_0744 SAUSA300_1057 SAUSA300_1106 SAUSA300_2249 SAUSA300_1532

-17.49 -11.62 -11.43 -11.15 -10.92 -10.29 -10.21 -10.11 -9.82 -9.38 -9.36

0 0.01 0.011 0.013 0.014 0.02 0.021 0.022 0.025 0.031 0.032

18 1 37 20 24 30 35 24 22 14 8

38 18 53 34 42 42 52 34 30 23 24

SAUSA300s048

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

12 13 14 15 16 17 18 19 20

atpG -

SAUSA300_1383 SAUSA300_2235 SAUSA300_0353 SAUSA300_0407 SAUSA300_2059 SAUSA300_1665 SAUSA300_0700 SAUSA300_1859 SAUSA300_2267

-9.22 -9.06 -9.05 -8.84 -8.69 -8.68 -8.43 -8.4 -8.37

0.034 0.036 0.036 0.04 0.042 0.043 0.047 0.048 0.048

10 4 14 21 8 7 6 24 1

24 14 27 33 19 19 24 33 19

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

mfd SAUSA300_0481 SAUSA300_2168 nusA SAUSA300_1159 SAUSA300_1842 moaD SAUSA300_2221 SAUSA300_1736 SAUSA300_1422 SAUSA300_0241 SAUSA300_0924 SAUSA300_1743 ltrA SAUSA300_0354 SAUSA300_2382 SAUSA300_1864 SAUSA300_1631 SAUSA300_2374 SAUSA300_2637 SAUSA300_0775 SAUSA300_1474 srtA SAUSA300_2467 SAUSA300_1964 arcC SAUSA300_0061 SAUSA300_2267 SAUSA300_1070 SAUSA300_0475 empbp SAUSA300_0774 SAUSA300_0052 sdrE SAUSA300_0548 eno SAUSA300_0760 SAUSA300_1204 dnaE SAUSA300_1649 SAUSA300_1328 SAUSA300_1683 SAUSA300_0030 pheT SAUSA300_1038 atpG SAUSA300_2059 SAUSA300_2522

-19.88 -15.6 -15.55 -15.09 -14.82 -14.75 -14.26 -13.6 -13.43 -13.33 -13.27 -13.26 -12.95 -12.82 -12.79 -12.36 -12.34 -12.24 -11.41 -11.39 -11.27 -11.22 -11.14 -11.03 -10.96 -10.95 -10.91 -10.73 -10.72 -10.66 -10.63 -10.61 -10.57 -10.49 -10.44 -10.29

0 0 0 0.001 0.001 0.001 0.001 0.002 0.003 0.003 0.003 0.003 0.004 0.004 0.004 0.006 0.006 0.006 0.011 0.011 0.012 0.012 0.013 0.013 0.014 0.014 0.014 0.016 0.016 0.017 0.017 0.017 0.017 0.018 0.019 0.02

162 78 59 163 80 8 103 86 55 106 72 37 6 43 8 30 100 32 119 13 34 132 39 52 86 21 87 7 57 11 57 101 38 34 163 56

180 93 72 178 93 23 119 99 72 117 82 51 17 52 20 41 115 44 133 27 43 148 49 66 99 38 97 21 71 23 72 116 52 49 174 71

SAUSA300s053

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65

glpT hpt fhuA ctsR miaB hisIE clfA rplO

SAUSA300_0495 SAUSA300_0049 SAUSA300_2326 SAUSA300_0056 SAUSA300_0337 SAUSA300_0488 SAUSA300_0633 SAUSA300_0507 SAUSA300_1185 SAUSA300_2246 SAUSA300_1334 SAUSA300_2605 SAUSA300_0339 SAUSA300_2020 SAUSA300_0990 SAUSA300_0706 SAUSA300_0027 SAUSA300_0609 SAUSA300_1413 SAUSA300_0469 SAUSA300_1951 SAUSA300_1194 SAUSA300_0943 SAUSA300_1329 SAUSA300_1275 SAUSA300_1710 SAUSA300_1965 SAUSA300_0772 SAUSA300_2185

-10.24 -9.98 -9.86 -9.71 -9.67 -9.61 -9.46 -9.37 -9.21 -9.14 -9.12 -9.06 -9.03 -9.02 -9.02 -8.97 -8.92 -8.86 -8.8 -8.77 -8.74 -8.71 -8.69 -8.6 -8.53 -8.45 -8.44 -8.43 -8.42

0.021 0.024 0.025 0.027 0.027 0.028 0.03 0.032 0.034 0.035 0.035 0.036 0.037 0.037 0.037 0.038 0.038 0.039 0.041 0.041 0.042 0.042 0.042 0.044 0.045 0.047 0.047 0.047 0.047

7 151 7 53 162 57 78 47 106 77 163 32 34 167 29 85 84 37 57 56 103 55 80 36 29 31 21 80 37

17 167 20 66 177 68 94 66 118 93 179 46 44 181 40 96 98 51 71 68 117 70 99 51 42 43 39 96 51

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

fruB cap5G hisD prmA accB int gatC

SAUSA300_0295 SAUSA300_0684 SAUSA300_0842 SAUSA300_1207 SAUSA300_0158 SAUSA300_0034 SAUSA300_2611 SAUSA300_2638 SAUSA300_0123 SAUSA300_0553 SAUSA300_1538 SAUSA300_2579 SAUSA300_1564 SAUSA300_1972 SAUSA300_0107 SAUSA300_1882

-13.59 -13.57 -12.53 -11.37 -11.11 -11.01 -10.59 -10.22 -10.09 -9.98 -9.94 -9.71 -9.63 -9.62 -9.53 -9.45

0.002 0.002 0.005 0.011 0.013 0.014 0.017 0.021 0.022 0.024 0.024 0.027 0.028 0.028 0.029 0.03

10 58 9 17 186 164 174 173 199 190 13 163 68 143 158 145

21 71 21 27 200 178 189 192 208 208 28 173 80 153 169 156

SAUSA300s056

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

trpA fabD ptsI tcaA rpoF fabG rho scrR atl cdsA folA

SAUSA300_0551 SAUSA300_1380 SAUSA300_1268 SAUSA300_1123 SAUSA300_1332 SAUSA300_2247 SAUSA300_0984 SAUSA300_2302 SAUSA300_1100 SAUSA300_0745 SAUSA300_2022 SAUSA300_0489 SAUSA300_1124 SAUSA300_1385 SAUSA300_0122 SAUSA300_2075 SAUSA300_1995 SAUSA300_0955 SAUSA300_1154 SAUSA300_1319

-9.3 -9.3 -9.15 -9.06 -8.93 -8.92 -8.89 -8.89 -8.88 -8.88 -8.81 -8.76 -8.76 -8.75 -8.69 -8.68 -8.6 -8.52 -8.48 -8.39

0.032 0.033 0.035 0.036 0.038 0.039 0.039 0.039 0.039 0.039 0.04 0.041 0.041 0.041 0.042 0.043 0.044 0.046 0.046 0.048

175 185 107 193 162 13 107 9 18 7 99 68 101 132 186 160 9 89 99 148

193 195 120 209 172 26 122 21 27 20 119 78 115 148 196 174 21 106 114 160

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

secG rsbW moaD prmA ftsK ctpA sufB murF -

SAUSA300_2480 SAUSA300_0762 SAUSA300_1395 SAUSA300_0906 SAUSA300_1224 SAUSA300_2023 SAUSA300_0304 SAUSA300_1483 SAUSA300_2221 SAUSA300_1858 SAUSA300_0072 SAUSA300_0399 SAUSA300_2314 SAUSA300_0023 SAUSA300_0302 SAUSA300_0805 SAUSA300_1538 SAUSA300_0309 SAUSA300_1169 SAUSA300_2559 SAUSA300_1695 SAUSA300_1313 SAUSA300_0822 SAUSA300_2038 SAUSA300_1277

-15.9 -15.13 -14.47 -14.36 -13.53 -13.21 -12.53 -12.5 -12.33 -12.22 -11.88 -11.84 -11.79 -11.77 -11.55 -11.5 -11.41 -11.38 -11.17 -10.91 -10.88 -10.66 -10.62 -10.61 -10.61

0 0.001 0.001 0.001 0.002 0.003 0.005 0.005 0.006 0.006 0.008 0.008 0.009 0.009 0.01 0.01 0.011 0.011 0.012 0.014 0.015 0.017 0.017 0.017 0.017

186 155 121 109 6 154 116 81 196 150 198 115 147 196 172 7 196 151 202 6 128 191 84 4 200

200 169 134 127 21 170 134 92 214 165 214 126 167 212 191 22 211 161 212 19 141 201 92 20 212

SAUSA300s058

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

SAUSA300_1240 SAUSA300_1716 SAUSA300_1161 SAUSA300_0239 ansA SAUSA300_1368 sdrC SAUSA300_0546 SAUSA300_0859 SAUSA300_1480 ychF SAUSA300_0364 SAUSA300_2589 SAUSA300_0328 SAUSA300_0495 SAUSA300_1254 SAUSA300_1004 argF SAUSA300_1062 pdp SAUSA300_2089 opp-3C SAUSA300_0075 SAUSA300_1911 SAUSA300_2162 hup SAUSA300_1362 SAUSA300_2523 manA SAUSA300_2096 gap SAUSA300_1633 SAUSA300_0797 cap5H SAUSA300_0159 SAUSA300_0407 rplV SAUSA300_2199 fnbA SAUSA300_2441 SAUSA300_0311 SAUSA300_1656 epiE SAUSA300_1761 mnhF SAUSA300_0850 SAUSA300_0464

-10.56 -10.51 -10.38 -10.15 -9.97 -9.97 -9.84 -9.75 -9.65 -9.57 -9.49 -9.42 -9.4 -9.39 -9.39 -9.02 -8.96 -8.94 -8.93 -8.87 -8.8 -8.78 -8.68 -8.64 -8.61 -8.52 -8.48 -8.43 -8.42 -8.4 -8.38 -8.38 -8.3

0.017 0.018 0.019 0.022 0.024 0.024 0.025 0.026 0.028 0.029 0.03 0.031 0.031 0.031 0.031 0.037 0.038 0.038 0.038 0.039 0.041 0.041 0.043 0.043 0.044 0.045 0.046 0.047 0.047 0.048 0.048 0.048 0.05

116 190 6 118 107 119 201 80 197 115 114 101 184 157 92 191 200 80 193 7 193 92 15 117 129 168 160 184 115 155 119 6 200

130 205 18 132 121 128 212 94 212 133 126 109 197 169 106 205 212 94 205 22 208 108 31 134 137 185 172 200 125 168 133 17 211

1 2 3 4 5 6 7 8 9 10 11 12

ahpF trpC mnhD

-14.64 -13.61 -13.41 -12.21 -11.99 -11.95 -11.77 -11.4 -10.9 -10.76 -10.67 -10.36

0.001 0.002 0.003 0.007 0.008 0.008 0.009 0.011 0.014 0.016 0.017 0.019

19 19 19 21 18 16 1 38 17 38 54 13

31 35 33 33 33 32 17 50 29 50 65 31

SAUSA300s062 SAUSA300_0379 SAUSA300_0089 SAUSA300_0600 SAUSA300_0050 SAUSA300_1946 SAUSA300_0257 SAUSA300_0435 SAUSA300_1971 SAUSA300_1265 SAUSA300_2087 SAUSA300_0334 SAUSA300_0852

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

mvaD rpsR oppF oppD sirA gltA folA -

SAUSA300_1858 SAUSA300_2382 SAUSA300_0573 SAUSA300_0368 SAUSA300_0893 SAUSA300_2256 SAUSA300_0889 SAUSA300_1941 SAUSA300_0943 SAUSA300_0414 SAUSA300_1194 SAUSA300_0117 SAUSA300_1641 SAUSA300_2403 SAUSA300_1412 SAUSA300_1319 SAUSA300_0385 SAUSA300_0321 SAUSA300_2624 SAUSA300_2045 SAUSA300_0200 SAUSA300_1433

-10.26 -10.23 -10.06 -9.94 -9.72 -9.68 -9.58 -9.42 -9.36 -9.35 -9.21 -9.1 -9.09 -8.74 -8.71 -8.63 -8.57 -8.51 -8.46 -8.42 -8.38 -8.32

0.02 0.021 0.023 0.024 0.027 0.027 0.029 0.031 0.032 0.032 0.034 0.036 0.036 0.042 0.042 0.044 0.045 0.046 0.047 0.047 0.048 0.049

16 17 14 16 43 23 8 17 35 22 8 36 38 10 18 17 37 1 37 19 16 34

31 33 22 31 56 43 22 31 46 37 22 52 49 20 33 31 47 19 54 32 30 52

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

pstB sdhB dnaN ruvA secG gpsA mfd tyrS

SAUSA300_1280 SAUSA300_1059 SAUSA300_1599 SAUSA300_2257 SAUSA300_1194 SAUSA300_1455 SAUSA300_1656 SAUSA300_2626 SAUSA300_1857 SAUSA300_0592 SAUSA300_1048 SAUSA300_0059 SAUSA300_0733 SAUSA300_0002 SAUSA300_1327 SAUSA300_1598 SAUSA300_0762 SAUSA300_1363 SAUSA300_0748 SAUSA300_2433 SAUSA300_0481 SAUSA300_2317 SAUSA300_1675

-14.24 -13.97 -12.62 -12.1 -12.05 -11.83 -11.71 -11.67 -11.62 -11.42 -11.25 -11.23 -11.07 -11.07 -10.95 -10.92 -10.73 -10.7 -10.69 -10.62 -10.54 -10.32 -10.32

0.001 0.002 0.005 0.007 0.007 0.008 0.009 0.009 0.01 0.011 0.012 0.012 0.013 0.013 0.014 0.014 0.016 0.016 0.016 0.017 0.018 0.02 0.02

202 135 49 48 48 188 62 49 51 49 48 143 43 17 131 129 50 49 51 138 197 17 50

213 149 69 66 60 205 78 64 64 64 60 155 57 26 145 141 69 63 65 157 209 33 64

SAUSA300s064

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57

rpe crr leuC isaA phoU rluB accB fabD -

SAUSA300_0359 SAUSA300_2401 SAUSA300_0098 SAUSA300_1115 SAUSA300_2604 SAUSA300_0056 SAUSA300_0048 SAUSA300_1315 SAUSA300_2012 SAUSA300_1970 SAUSA300_0244 SAUSA300_0740 SAUSA300_2332 SAUSA300_0709 SAUSA300_0082 SAUSA300_2102 SAUSA300_0601 SAUSA300_1955 SAUSA300_2169 SAUSA300_2506 SAUSA300_0036 SAUSA300_0646 SAUSA300_0123 SAUSA300_0441 SAUSA300_2456 SAUSA300_1279 SAUSA300_2262 SAUSA300_0401 SAUSA300_0746 SAUSA300_1443 SAUSA300_0880 SAUSA300_1564 SAUSA300_1123 SAUSA300_1945

-10.14 -10.07 -10.05 -9.99 -9.94 -9.83 -9.75 -9.74 -9.7 -9.64 -9.58 -9.57 -9.55 -9.53 -9.47 -9.38 -9.32 -9.3 -9.26 -9.23 -9.23 -9.23 -9.08 -8.89 -8.89 -8.81 -8.74 -8.55 -8.47 -8.43 -8.41 -8.39 -8.32 -8.31

0.022 0.023 0.023 0.023 0.024 0.025 0.026 0.026 0.027 0.028 0.029 0.029 0.029 0.029 0.03 0.031 0.032 0.033 0.033 0.034 0.034 0.034 0.036 0.039 0.039 0.04 0.042 0.045 0.047 0.047 0.048 0.048 0.049 0.05

129 57 196 200 19 131 64 205 196 65 21 197 140 13 124 57 60 19 10 135 131 129 46 50 203 50 54 190 197 49 59 142 5 40

146 69 210 213 32 146 77 216 210 78 37 210 151 22 138 73 69 31 20 150 146 140 55 63 215 65 69 208 214 64 70 161 17 56

1 2 3 4 5 6 7 8 9 10 11 12

ung srtB menA pyrR pdhB -

SAUSA300_0324 SAUSA300_0563 SAUSA300_1034 SAUSA300_0944 SAUSA300_1732 SAUSA300_2350 SAUSA300_0881 SAUSA300_0428 SAUSA300_1091 SAUSA300_0611 SAUSA300_0994 SAUSA300_2459

-16.72 -13.98 -13.73 -13.72 -12.81 -12.59 -11.9 -11.86 -11.82 -11.57 -11.29 -11.29

0 0.002 0.002 0.002 0.004 0.005 0.008 0.008 0.008 0.01 0.012 0.012

14 11 23 61 64 76 24 74 43 21 23 71

28 24 39 81 79 95 39 84 58 37 37 85

SAUSA300s066

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13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46

rexA cdsA gap feoB norA asnC atpC ychF ftsL phnE obgE pepF ilvA -

SAUSA300_0870 SAUSA300_1154 SAUSA300_1349 SAUSA300_0756 SAUSA300_2487 SAUSA300_0680 SAUSA300_1742 SAUSA300_0735 SAUSA300_1345 SAUSA300_1701 SAUSA300_2057 SAUSA300_0364 SAUSA300_1074 SAUSA300_2419 SAUSA300_1941 SAUSA300_0143 SAUSA300_0871 SAUSA300_1277 SAUSA300_0859 SAUSA300_0545 SAUSA300_1419 SAUSA300_1600 SAUSA300_2508 SAUSA300_0587 SAUSA300_1734 SAUSA300_0464 SAUSA300_0902 SAUSA300_0901 SAUSA300_1352 SAUSA300_2014 SAUSA300_0036 SAUSA300_0916 SAUSA300_1518 SAUSA300_0768

-11.28 -11.25 -11.12 -11.08 -10.99 -10.91 -10.84 -10.73 -10.61 -10.5 -10.4 -10.37 -10.23 -10.12 -10.01 -9.94 -9.81 -9.56 -9.54 -9.47 -9.45 -9.28 -9.21 -9.07 -9.04 -8.94 -8.93 -8.89 -8.81 -8.77 -8.53 -8.43 -8.41 -8.34

0.012 0.012 0.013 0.013 0.014 0.014 0.015 0.016 0.017 0.018 0.019 0.019 0.021 0.022 0.023 0.024 0.026 0.029 0.029 0.03 0.03 0.033 0.034 0.036 0.037 0.038 0.038 0.039 0.04 0.041 0.045 0.047 0.048 0.049

82 52 20 88 15 87 21 85 21 24 15 26 82 82 24 77 47 21 25 88 24 85 73 9 40 23 76 82 82 82 79 82 81 18

96 66 38 98 33 98 29 98 38 38 28 38 96 92 37 91 58 37 36 98 38 98 83 23 59 37 94 93 91 91 93 97 98 26

1 2 3 4 5 6 7 8 9 10 11

icaA ftsA isaA ctpA femA metE

SAUSA300_0215 SAUSA300_2334 SAUSA300_1354 SAUSA300_2600 SAUSA300_0733 SAUSA300_1079 SAUSA300_2506 SAUSA300_1313 SAUSA300_1269 SAUSA300_0095 SAUSA300_0357

-12.26 -11.22 -11.11 -10.91 -10.84 -10.7 -10.66 -10.45 -10.4 -10.23 -10.07

0.006 0.012 0.013 0.014 0.015 0.016 0.017 0.019 0.019 0.021 0.023

10 25 25 27 39 27 25 35 61 33 27

22 44 39 41 52 40 39 47 72 46 41

SAUSA300s067

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

dnaN tagG fabF -

SAUSA300_1483 SAUSA300_0136 SAUSA300_0377 SAUSA300_1867 SAUSA300_1198 SAUSA300_2461 SAUSA300_2004 SAUSA300_2360 SAUSA300_0002 SAUSA300_0617 SAUSA300_0625 SAUSA300_2493 SAUSA300_0086 SAUSA300_0886 SAUSA300_1742

-10.06 -10.02 -10.02 -9.87 -9.57 -9.51 -9.01 -9.01 -9.01 -9 -8.99 -8.84 -8.8 -8.34 -8.3

0.023 0.023 0.023 0.025 0.029 0.03 0.037 0.037 0.037 0.037 0.037 0.04 0.041 0.049 0.05

55 33 26 34 34 72 64 26 22 44 27 34 60 61 28

71 44 37 45 43 80 77 40 40 54 41 50 79 72 42

1 hslV 2 ahpC 3-

SAUSA300_1146 SAUSA300_0380 SAUSA300_1377

-11.98 -8.85 -8.32

0.008 0.04 0.049

11 48 25

27 57 34

1 2 3 4 5 6 7

sbcC dapA -

SAUSA300_0076 SAUSA300_2472 SAUSA300_1965 SAUSA300_1806 SAUSA300_1243 SAUSA300_1288 SAUSA300_0322

-10.85 -10.85 -9.75 -9.34 -8.92 -8.67 -8.43

0.015 0.015 0.026 0.032 0.039 0.043 0.047

48 1 1 32 31 27 2

66 11 10 47 43 43 11

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

sucC phnE hpt -

SAUSA300_0177 SAUSA300_1194 SAUSA300_1945 SAUSA300_1138 SAUSA300_1181 SAUSA300_0417 SAUSA300_1700 SAUSA300_2522 SAUSA300_1413 SAUSA300_0142 SAUSA300_0266 SAUSA300_0781 SAUSA300_0418 SAUSA300_0488 SAUSA300_0479 SAUSA300_0484

-16.59 -14.91 -12.02 -10.96 -10.53 -10.51 -10.01 -9.96 -9.45 -9 -8.94 -8.91 -8.88 -8.6 -8.44 -8.42

0 0.001 0.007 0.014 0.018 0.018 0.023 0.024 0.03 0.037 0.038 0.039 0.039 0.044 0.047 0.047

5 6 8 40 16 2 15 6 7 44 10 7 7 36 7 12

21 26 23 51 26 21 26 21 21 53 21 20 23 52 19 29

SAUSA300s069

SAUSA300s071

SAUSA300s073

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

17 -

SAUSA300_0292

-8.4

0.048

13

28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

SAUSA300_0887 SAUSA300_2213 SAUSA300_1172 SAUSA300_2442 SAUSA300_0367 SAUSA300_1859 SAUSA300_0395 SAUSA300_0545 SAUSA300_1215 SAUSA300_0892 SAUSA300_1532 SAUSA300_1506 SAUSA300_2552 SAUSA300_0592 SAUSA300_0755 SAUSA300_2408 SAUSA300_1352 SAUSA300_0401 SAUSA300_1591 SAUSA300_2480 SAUSA300_0437 SAUSA300_2300 SAUSA300_2578 SAUSA300_1152 SAUSA300_0664 SAUSA300_0552 SAUSA300_2451 SAUSA300_0293 SAUSA300_0400 SAUSA300_2281 SAUSA300_2031 SAUSA300_0979 SAUSA300_0968 SAUSA300_1012 SAUSA300_2483 SAUSA300_1378 SAUSA300_1853 SAUSA300_0997 SAUSA300_1863 SAUSA300_2080 SAUSA300_0295 SAUSA300_0611 SAUSA300_1146 SAUSA300_1470

-16.16 -15.45 -14.23 -14.2 -13.74 -13.45 -13.31 -13.14 -12.59 -12.39 -12.37 -12.35 -12.04 -11.91 -11.8 -11.71 -11.56 -11.52 -10.98 -10.83 -10.53 -10.51 -10.5 -10.25 -10.17 -10.13 -10.08 -9.92 -9.85 -9.55 -9.47 -9.37 -9.36 -9.28 -9.15 -9.08 -8.95 -8.84 -8.83 -8.74 -8.7 -8.65 -8.59 -8.54

0 0 0.001 0.001 0.002 0.003 0.003 0.003 0.005 0.006 0.006 0.006 0.007 0.008 0.009 0.009 0.01 0.01 0.014 0.015 0.018 0.018 0.018 0.021 0.021 0.022 0.022 0.024 0.025 0.029 0.03 0.032 0.032 0.033 0.035 0.036 0.038 0.04 0.04 0.042 0.042 0.043 0.044 0.045

202 204 203 204 203 45 49 203 198 186 104 204 200 204 198 155 110 46 195 143 48 67 110 46 99 66 72 13 46 204 207 134 202 204 148 45 135 146 205 45 17 203 84 139

215 216 215 216 213 60 66 215 215 202 118 215 218 215 209 166 120 63 208 158 62 83 121 54 118 81 85 22 63 214 219 150 212 213 164 54 149 161 216 63 28 216 98 150

SAUSA300s074 oppB gntP ssb oppA apt frr hutG purC hslV -

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

45 46 47 48

rpmI feoA

SAUSA300_1626 SAUSA300_0285 SAUSA300_1561 SAUSA300_2488

-8.48 -8.45 -8.45 -8.34

0.046 0.047 0.047 0.049

200 98 196 13

211 116 210 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

agrB thrC rho ansA pstB tag cap5J menE betB acpS rpsK cmk pyrF rpsM ruvA -

SAUSA300_1989 SAUSA300_1227 SAUSA300_2075 SAUSA300_1368 SAUSA300_0119 SAUSA300_1280 SAUSA300_2406 SAUSA300_1057 SAUSA300_1612 SAUSA300_0161 SAUSA300_0559 SAUSA300_1462 SAUSA300_1737 SAUSA300_0428 SAUSA300_0874 SAUSA300_0598 SAUSA300_2546 SAUSA300_0365 SAUSA300_0218 SAUSA300_2028 SAUSA300_2179 SAUSA300_1111 SAUSA300_0657 SAUSA300_1367 SAUSA300_0442 SAUSA300_1097 SAUSA300_1327 SAUSA300_1736 SAUSA300_2336 SAUSA300_2180 SAUSA300_1685 SAUSA300_0013 SAUSA300_0709 SAUSA300_1598 SAUSA300_0335 SAUSA300_1050 SAUSA300_1581 SAUSA300_0369 SAUSA300_1606 SAUSA300_2258 SAUSA300_2234

-13.49 -12.16 -12.08 -11.97 -11.93 -11.77 -11.04 -10.89 -10.8 -10.71 -10.59 -10.55 -10.53 -10.5 -10.22 -10.2 -10.07 -10.01 -9.96 -9.87 -9.59 -9.56 -9.53 -9.52 -9.51 -9.4 -9.31 -9.28 -9.23 -9.14 -9.08 -8.98 -8.96 -8.86 -8.77 -8.75 -8.63 -8.57 -8.52 -8.45 -8.34

0.003 0.007 0.007 0.008 0.008 0.009 0.013 0.015 0.015 0.016 0.017 0.018 0.018 0.018 0.021 0.021 0.023 0.023 0.024 0.025 0.028 0.029 0.029 0.029 0.03 0.031 0.032 0.033 0.034 0.035 0.036 0.038 0.038 0.039 0.041 0.041 0.044 0.045 0.045 0.047 0.049

172 80 120 27 42 49 51 53 50 52 123 172 90 18 85 168 29 96 35 50 189 37 79 79 165 26 85 47 36 83 53 168 186 46 82 174 173 100 10 42 106

184 92 131 44 56 57 65 69 64 62 134 186 99 31 97 182 43 113 45 61 204 49 96 92 175 46 99 55 45 95 73 188 199 62 91 184 192 114 21 56 124

SAUSA300s076

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

SAUSA300s077 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

clpC radA rplV argJ nadE sdhC engB pbp2 ilvE alsS mnhA aldA2 scpA mvk -

SAUSA300_2615 SAUSA300_1569 SAUSA300_0510 SAUSA300_2147 SAUSA300_2233 SAUSA300_0511 SAUSA300_2199 SAUSA300_2218 SAUSA300_0578 SAUSA300_0343 SAUSA300_0185 SAUSA300_1742 SAUSA300_0637 SAUSA300_1199 SAUSA300_1893 SAUSA300_1046 SAUSA300_0934 SAUSA300_1620 SAUSA300_1341 SAUSA300_1851 SAUSA300_2286 SAUSA300_2406 SAUSA300_1420 SAUSA300_0539 SAUSA300_2166 SAUSA300_0855 SAUSA300_1479 SAUSA300_0246 SAUSA300_0320 SAUSA300_1402 SAUSA300_1901 SAUSA300_1445 SAUSA300_0572 SAUSA300_0432

-15.68 -15.22 -14.83 -13.51 -13.32 -11.97 -11.64 -11.56 -10.95 -10.68 -10.6 -10.58 -10.47 -10.47 -10.4 -9.68 -9.53 -9.37 -9.13 -9.06 -9.01 -8.88 -8.74 -8.73 -8.69 -8.68 -8.61 -8.59 -8.57 -8.49 -8.38 -8.37 -8.34 -8.3

0 0.001 0.001 0.003 0.003 0.008 0.009 0.01 0.014 0.016 0.017 0.017 0.018 0.018 0.019 0.027 0.029 0.032 0.035 0.036 0.037 0.039 0.042 0.042 0.042 0.043 0.044 0.044 0.045 0.046 0.048 0.048 0.049 0.05

19 88 88 88 82 112 87 87 28 113 90 82 107 112 89 32 85 107 108 90 87 112 66 97 107 81 107 112 88 113 81 115 102 88

37 104 104 105 96 127 102 105 40 125 105 102 127 130 101 42 101 122 125 101 107 124 77 110 117 101 122 126 104 129 88 128 118 101

1 2 3 4 5 6 7 8 9

mraZ nrdD arcB phoB

SAUSA300_1497 SAUSA300_0545 SAUSA300_1072 SAUSA300_0810 SAUSA300_1070 SAUSA300_2551 SAUSA300_1562 SAUSA300_2569 SAUSA300_2561

-14.75 -13.38 -13.34 -12.89 -12.87 -12.41 -12.27 -12.25 -11.82

0.001 0.003 0.003 0.004 0.004 0.006 0.006 0.006 0.008

86 89 109 134 19 87 90 60 73

104 99 129 149 28 99 102 77 86

SAUSA300s078

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56

purC ribBA gltD sucB sdhA hisB pepT acsA argR gltA parE glmS atpE argR rimI estA rocD truA -

SAUSA300_0968 SAUSA300_1713 SAUSA300_0446 SAUSA300_1559 SAUSA300_1305 SAUSA300_0721 SAUSA300_2232 SAUSA300_1561 SAUSA300_1047 SAUSA300_0132 SAUSA300_0537 SAUSA300_2609 SAUSA300_0727 SAUSA300_0729 SAUSA300_1679 SAUSA300_1349 SAUSA300_1975 SAUSA300_1437 SAUSA300_1426 SAUSA300_1296 SAUSA300_0650 SAUSA300_0066 SAUSA300_1641 SAUSA300_1250 SAUSA300_2169 SAUSA300_1916 SAUSA300_2138 SAUSA300_2104 SAUSA300_2063 SAUSA300_1469 SAUSA300_2473 SAUSA300_2003 SAUSA300_1722 SAUSA300_0372 SAUSA300_1008 SAUSA300_2379 SAUSA300_1112 SAUSA300_2564 SAUSA300_0070 SAUSA300_0860 SAUSA300_2083 SAUSA300_0581 SAUSA300_2102 SAUSA300_1492 SAUSA300_0735 SAUSA300_2173 SAUSA300_2134

-11.72 -11.63 -11.63 -11.58 -11.52 -11.42 -11.26 -11.25 -11.22 -11.18 -11.1 -11.09 -11.07 -10.85 -10.82 -10.81 -10.8 -10.76 -10.74 -10.7 -10.63 -10.61 -10.6 -10.6 -10.57 -10.56 -10.39 -10.38 -10.3 -10.27 -10.17 -10.13 -9.97 -9.92 -9.67 -9.59 -9.59 -9.52 -9.48 -9.48 -9.43 -9.43 -9.41 -9.41 -9.07 -9.02 -8.88

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0.009 0.009 0.009 0.01 0.01 0.011 0.012 0.012 0.012 0.012 0.013 0.013 0.013 0.015 0.015 0.015 0.015 0.016 0.016 0.016 0.017 0.017 0.017 0.017 0.017 0.017 0.019 0.019 0.02 0.02 0.021 0.022 0.024 0.024 0.027 0.028 0.029 0.029 0.03 0.03 0.031 0.031 0.031 0.031 0.036 0.037 0.039

114 19 91 111 22 44 172 115 114 86 167 72 89 73 113 59 44 22 1 88 114 90 91 3 173 68 7 3 45 132 13 75 45 20 110 87 59 84 16 91 21 63 60 13 17 76 47

128 28 105 127 31 58 188 123 122 102 185 86 103 87 122 72 58 30 20 99 122 104 100 19 185 77 26 19 59 148 25 90 65 31 124 101 72 99 31 104 32 75 69 28 28 88 66

57 58 59 60 61 62 63 64

ltrA fadE -

SAUSA300_1902 SAUSA300_0354 SAUSA300_0616 SAUSA300_0180 SAUSA300_0228 SAUSA300_1981 SAUSA300_2265 SAUSA300_2579

-8.84 -8.8 -8.65 -8.64 -8.59 -8.56 -8.47 -8.36

0.04 0.041 0.043 0.043 0.044 0.045 0.046 0.049

16 84 41 85 91 114 2 37

28 92 55 99 100 126 12 57

1 2 3 4 5 6 7 8 9

hemB holA gatC -

SAUSA300_1395 SAUSA300_0872 SAUSA300_1979 SAUSA300_1615 SAUSA300_1576 SAUSA300_1546 SAUSA300_1882 SAUSA300_2394 SAUSA300_2500

-11.97 -11.03 -10.28 -9.92 -9.9 -9.86 -9.45 -9.28 -8.87

0.008 0.014 0.02 0.024 0.024 0.025 0.03 0.033 0.039

14 6 18 15 13 9 14 4 4

28 23 30 30 27 21 30 21 19

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

oppF arsB cdsA gid holA splA nrdD glmM sspA opuCd -

SAUSA300_1374 SAUSA300_1433 SAUSA300_0485 SAUSA300_0479 SAUSA300_2237 SAUSA300_0893 SAUSA300_1718 SAUSA300_1154 SAUSA300_1551 SAUSA300_1144 SAUSA300_0304 SAUSA300_1546 SAUSA300_0205 SAUSA300_1758 SAUSA300_2551 SAUSA300_0418 SAUSA300_0276 SAUSA300_1902 SAUSA300_2406 SAUSA300_2111 SAUSA300_0273 SAUSA300_0844 SAUSA300_2617 SAUSA300_0951 SAUSA300_2390 SAUSA300_1716

-13.49 -12.82 -11.87 -11.78 -11.62 -11.28 -11.03 -10.86 -10.42 -10.4 -10.38 -10.32 -10.18 -10.17 -10.17 -10.11 -9.98 -9.9 -9.78 -9.72 -9.7 -9.61 -9.53 -9.42 -9.23 -9.09

0.003 0.004 0.008 0.009 0.01 0.012 0.013 0.015 0.019 0.019 0.019 0.02 0.021 0.021 0.021 0.022 0.024 0.025 0.026 0.027 0.027 0.028 0.029 0.031 0.034 0.036

40 38 47 35 35 46 63 35 53 25 49 41 47 29 34 40 34 33 34 51 81 1 37 36 37 48

58 54 62 50 47 60 75 55 63 39 69 58 60 46 47 58 50 47 50 65 95 17 47 50 51 62

SAUSA300s079

SAUSA300s080

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

27 28 29 30 31 32 33 34

gmk sspC rplR

SAUSA300_1031 SAUSA300_1584 SAUSA300_0343 SAUSA300_1102 SAUSA300_0171 SAUSA300_0949 SAUSA300_0385 SAUSA300_2188

-8.95 -8.9 -8.86 -8.8 -8.54 -8.35 -8.33 -8.3

0.038 0.039 0.04 0.04 0.045 0.049 0.049 0.05

88 34 36 69 42 33 29 33

98 47 56 83 55 47 47 46

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

rplT pheS scdA spsA aldA2 nupC glnR rplX

SAUSA300_1625 SAUSA300_1037 SAUSA300_1395 SAUSA300_2300 SAUSA300_0253 SAUSA300_0867 SAUSA300_2635 SAUSA300_0031 SAUSA300_1867 SAUSA300_2480 SAUSA300_2233 SAUSA300_0733 SAUSA300_2279 SAUSA300_2633 SAUSA300_1254 SAUSA300_2087 SAUSA300_2086 SAUSA300_1901 SAUSA300_0506 SAUSA300_0247 SAUSA300_0418 SAUSA300_1200 SAUSA300_2193

-11.69 -11.42 -11.23 -10.81 -10.56 -10.53 -10.34 -10.21 -9.83 -9.74 -9.67 -9.64 -9.4 -9.29 -8.97 -8.94 -8.87 -8.71 -8.7 -8.57 -8.38 -8.37 -8.33

0.009 0.011 0.012 0.015 0.017 0.018 0.02 0.021 0.025 0.026 0.027 0.028 0.031 0.033 0.038 0.038 0.039 0.042 0.042 0.045 0.048 0.048 0.049

35 34 30 42 69 60 52 28 36 17 34 81 35 50 12 39 32 54 13 79 40 27 37

51 50 46 59 87 71 64 43 51 28 51 94 48 64 28 54 52 66 32 93 54 40 51

1 2 3 4 5 6 7 8 9 10

hisA rpe oppB gltS ubiE -

SAUSA300_1566 SAUSA300_1981 SAUSA300_2607 SAUSA300_1923 SAUSA300_1115 SAUSA300_2005 SAUSA300_0887 SAUSA300_2291 SAUSA300_1360 SAUSA300_0879

-15.3 -15.24 -14.48 -14.19 -14.03 -13.09 -12.7 -12.36 -12.27 -12.12

0.001 0.001 0.001 0.001 0.002 0.004 0.005 0.006 0.006 0.007

179 144 178 11 29 79 173 179 151 145

190 157 190 25 42 92 192 190 165 154

SAUSA300s084 SAUSA300s085

SAUSA300s086

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55

rpiA cinA oppA msrB oppF sufB uvrC nrdR splB dut glmU purQ sdaAA mreD rpmJ carA ahpF fumC acnA ctsR ilvD aspS

SAUSA300_1121 SAUSA300_2283 SAUSA300_2552 SAUSA300_2234 SAUSA300_1177 SAUSA300_2288 SAUSA300_0892 SAUSA300_1316 SAUSA300_0257 SAUSA300_0893 SAUSA300_2485 SAUSA300_0822 SAUSA300_0687 SAUSA300_1099 SAUSA300_0208 SAUSA300_2559 SAUSA300_1045 SAUSA300_1632 SAUSA300_1757 SAUSA300_1949 SAUSA300_0055 SAUSA300_1400 SAUSA300_0905 SAUSA300_1215 SAUSA300_2215 SAUSA300_1483 SAUSA300_0477 SAUSA300_0970 SAUSA300_2469 SAUSA300_0317 SAUSA300_1604 SAUSA300_1332 SAUSA300_2181 SAUSA300_1095 SAUSA300_0379 SAUSA300_1801 SAUSA300_2286 SAUSA300_1246 SAUSA300_0507 SAUSA300_1401 SAUSA300_1732 SAUSA300_0285 SAUSA300_2006 SAUSA300_1414 SAUSA300_1586

-11.98 -11.78 -11.71 -11.68 -11.68 -11.63 -11.44 -11.42 -11.34 -11.33 -11.18 -11.1 -11.01 -10.96 -10.82 -10.69 -10.51 -10.5 -10.44 -10.44 -10.39 -10.36 -10.32 -10.26 -10.25 -9.99 -9.88 -9.64 -9.61 -9.49 -9.47 -9.45 -9.4 -9.34 -9.29 -9.01 -9 -8.92 -8.83 -8.79 -8.37 -8.37 -8.35 -8.34 -8.31

SAUSA300s087 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0.008 0.009 0.009 0.009 0.009 0.009 0.011 0.011 0.011 0.011 0.012 0.013 0.014 0.014 0.015 0.016 0.018 0.018 0.019 0.019 0.019 0.019 0.02 0.02 0.021 0.023 0.025 0.028 0.028 0.03 0.03 0.03 0.031 0.032 0.033 0.037 0.037 0.039 0.04 0.041 0.048 0.049 0.049 0.049 0.05

142 122 181 180 182 150 143 157 86 144 173 119 3 82 148 6 174 157 157 151 148 144 76 173 182 122 147 6 11 144 116 158 13 182 116 6 102 182 144 161 116 101 179 150 164

156 136 190 190 190 162 162 176 100 157 190 136 19 97 165 19 190 171 176 165 162 153 90 190 190 131 156 21 26 153 130 174 26 190 130 19 116 190 153 175 128 115 191 161 176

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

pbuX pckA rexB lacC ilvD oppA menC -

SAUSA300_1241 SAUSA300_0387 SAUSA300_0805 SAUSA300_1543 SAUSA300_1879 SAUSA300_1921 SAUSA300_0581 SAUSA300_1731 SAUSA300_1206 SAUSA300_1100 SAUSA300_2425 SAUSA300_1170 SAUSA300_0869 SAUSA300_2153 SAUSA300_2145 SAUSA300_1789 SAUSA300_1036 SAUSA300_2006 SAUSA300_0892 SAUSA300_1963 SAUSA300_1735 SAUSA300_2414 SAUSA300_2206 SAUSA300_0696 SAUSA300_0373 SAUSA300_0724 SAUSA300_1734

-13.74 -13.29 -11.11 -11.05 -10.66 -10.63 -10.42 -10.12 -9.99 -9.93 -9.81 -9.73 -9.37 -9.35 -9.2 -9.15 -9.13 -9.08 -9.06 -9.02 -8.97 -8.71 -8.66 -8.53 -8.49 -8.47 -8.38

0.002 0.003 0.013 0.013 0.017 0.017 0.019 0.022 0.023 0.024 0.026 0.027 0.032 0.032 0.034 0.035 0.035 0.036 0.036 0.037 0.038 0.042 0.043 0.045 0.046 0.046 0.048

110 174 39 151 76 181 45 22 100 150 114 39 3 98 83 78 78 185 90 59 45 177 137 83 50 58 50

120 189 47 162 88 189 59 35 112 159 123 53 17 108 95 96 88 204 106 74 53 189 146 95 61 73 69

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

cls acpS sdrE dgkA sucB cysK coaD betA lytN -

SAUSA300_2044 SAUSA300_2028 SAUSA300_0126 SAUSA300_0548 SAUSA300_1529 SAUSA300_1305 SAUSA300_0491 SAUSA300_0283 SAUSA300_0790 SAUSA300_2424 SAUSA300_0020 SAUSA300_0307 SAUSA300_1024 SAUSA300_1021 SAUSA300_2545 SAUSA300_2459 SAUSA300_1140 SAUSA300_0495

-12.47 -11.85 -11.76 -11.49 -11.33 -11.2 -10.81 -10.54 -10.52 -10.42 -10.33 -9.96 -9.95 -9.89 -9.76 -9.39 -9.37 -9.24

0.005 0.008 0.009 0.01 0.011 0.012 0.015 0.018 0.018 0.019 0.02 0.024 0.024 0.025 0.026 0.031 0.032 0.033

138 159 100 152 153 68 137 243 157 68 60 89 88 154 143 157 87 243

149 178 115 167 164 82 147 254 172 80 76 104 98 171 151 171 98 256

SAUSA300s090

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

19 20 21 22 23 24 25 26 27 28 29

recO ilvC femB rpe isaA -

SAUSA300_0824 SAUSA300_0613 SAUSA300_1526 SAUSA300_2009 SAUSA300_1270 SAUSA300_1020 SAUSA300_1115 SAUSA300_1221 SAUSA300_1502 SAUSA300_2506 SAUSA300_1585

-9 -8.98 -8.95 -8.87 -8.85 -8.68 -8.59 -8.59 -8.58 -8.49 -8.34

0.037 0.038 0.038 0.039 0.04 0.043 0.044 0.044 0.044 0.046 0.049

203 236 111 138 64 154 138 82 192 60 240

219 254 127 152 77 167 152 96 209 75 252

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

atpH sspC glnR nrdG smpB leuB fba hisB aroC narK -

SAUSA300_2061 SAUSA300_1517 SAUSA300_1734 SAUSA300_1361 SAUSA300_2158 SAUSA300_0949 SAUSA300_0740 SAUSA300_2384 SAUSA300_1200 SAUSA300_0441 SAUSA300_2305 SAUSA300_2550 SAUSA300_0832 SAUSA300_2290 SAUSA300_1432 SAUSA300_1916 SAUSA300_0765 SAUSA300_2011 SAUSA300_0638 SAUSA300_2079 SAUSA300_1844 SAUSA300_2609 SAUSA300_0555 SAUSA300_1357 SAUSA300_2333 SAUSA300_2321 SAUSA300_1275 SAUSA300_1683 SAUSA300_0568 SAUSA300_1086

-13.36 -13.34 -12.32 -12.03 -11.97 -11.77 -10.84 -10.61 -10.44 -10.16 -10.15 -9.73 -9.71 -9.6 -9.56 -9.42 -9.37 -9.24 -9.24 -9.15 -9.15 -9.07 -8.98 -8.93 -8.82 -8.79 -8.71 -8.48 -8.38 -8.37

0.003 0.003 0.006 0.007 0.008 0.009 0.015 0.017 0.019 0.022 0.022 0.027 0.027 0.028 0.029 0.031 0.031 0.034 0.034 0.035 0.035 0.036 0.038 0.038 0.04 0.041 0.042 0.046 0.048 0.048

199 45 168 191 129 200 198 137 137 6 134 134 51 138 129 50 43 198 169 171 159 146 163 136 49 198 44 8 138 166

216 58 180 205 141 211 213 155 148 20 148 147 66 155 140 67 58 213 178 184 179 161 177 144 64 211 56 26 153 177

SAUSA300_0111 SAUSA300_2513

-9.79 -9.78

0.026 0.026

33 33

44 46

SAUSA300s091

SAUSA300s092 12-

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

3 4 5 6 7 8 9

ppnK narK rpsN -

SAUSA300_0908 SAUSA300_2333 SAUSA300_0638 SAUSA300_2191 SAUSA300_0939 SAUSA300_1967 SAUSA300_0979

-9.7 -9.37 -9.05 -9.02 -8.85 -8.44 -8.4

0.027 0.032 0.036 0.037 0.04 0.047 0.048

22 33 29 22 24 23 31

30 43 44 30 36 31 44

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

agrA gcvT gltD comK argC aldA2 aur modB rnc

SAUSA300_1992 SAUSA300_1498 SAUSA300_0446 SAUSA300_0630 SAUSA300_0341 SAUSA300_1492 SAUSA300_0928 SAUSA300_2472 SAUSA300_0186 SAUSA300_1901 SAUSA300_2501 SAUSA300_1858 SAUSA300_2529 SAUSA300_2572 SAUSA300_2229 SAUSA300_0109 SAUSA300_2528 SAUSA300_0942 SAUSA300_1126

-15.32 -14.94 -12.93 -12 -11.12 -10.33 -10.12 -9.98 -9.68 -9.64 -9.61 -9.46 -9.38 -9.29 -8.89 -8.87 -8.81 -8.77 -8.41

0.001 0.001 0.004 0.007 0.013 0.02 0.022 0.024 0.027 0.028 0.028 0.03 0.031 0.033 0.039 0.039 0.04 0.041 0.048

72 78 15 70 66 81 40 29 77 42 64 75 26 78 39 78 57 22 73

84 95 26 84 78 91 58 41 92 57 72 87 35 93 50 87 72 35 84

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

rpsE rnr rpsJ rpmI oppB malR atpE purL

SAUSA300_2187 SAUSA300_1453 SAUSA300_0027 SAUSA300_0764 SAUSA300_1118 SAUSA300_0284 SAUSA300_0463 SAUSA300_2552 SAUSA300_2205 SAUSA300_1626 SAUSA300_0995 SAUSA300_0771 SAUSA300_0887 SAUSA300_1172 SAUSA300_1457 SAUSA300_2063 SAUSA300_0971

-16.6 -15.67 -15.03 -14.95 -14.62 -13.74 -13.67 -13.27 -12.73 -12.62 -12.12 -11.95 -11.63 -11.58 -11.44 -11.31 -11.28

0 0 0.001 0.001 0.001 0.002 0.002 0.003 0.005 0.005 0.007 0.008 0.009 0.01 0.011 0.011 0.012

7 7 3 7 7 8 7 8 8 5 7 7 8 8 6 10 8

17 21 18 23 19 18 21 21 17 18 19 17 23 22 18 24 21

SAUSA300s093

SAUSA300s094

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50

pyrB rpmD glvC argC nanA eutD fruB arcD lipA nrdF ppnK pgi sufC lytH adk

SAUSA300_1093 SAUSA300_0025 SAUSA300_2361 SAUSA300_2186 SAUSA300_2270 SAUSA300_1387 SAUSA300_0186 SAUSA300_0592 SAUSA300_0315 SAUSA300_0570 SAUSA300_0194 SAUSA300_0684 SAUSA300_2568 SAUSA300_0236 SAUSA300_0829 SAUSA300_1483 SAUSA300_0717 SAUSA300_0423 SAUSA300_0908 SAUSA300_0865 SAUSA300_1501 SAUSA300_0278 SAUSA300_1361 SAUSA300_0818 SAUSA300_0052 SAUSA300_1588 SAUSA300_0340 SAUSA300_1792 SAUSA300_0181 SAUSA300_1334 SAUSA300_2386 SAUSA300_2402 SAUSA300_2183

-10.98 -10.92 -10.81 -10.72 -10.67 -10.51 -10.47 -10.41 -10.39 -10.39 -10.22 -10.07 -10.06 -9.83 -9.83 -9.78 -9.77 -9.72 -9.6 -9.58 -9.44 -9.4 -9.33 -9.26 -9.05 -9.03 -8.82 -8.78 -8.72 -8.6 -8.49 -8.36 -8.33

0.014 0.014 0.015 0.016 0.016 0.018 0.018 0.019 0.019 0.019 0.021 0.023 0.023 0.025 0.025 0.026 0.026 0.027 0.028 0.029 0.031 0.031 0.032 0.033 0.036 0.037 0.04 0.041 0.042 0.044 0.046 0.049 0.049

3 8 7 2 8 7 6 8 3 7 5 4 11 7 9 7 10 48 88 4 7 4 60 8 49 7 3 86 2 8 58 5 5

17 21 17 22 16 15 18 22 16 18 19 18 19 19 18 16 18 62 101 18 19 19 76 16 60 21 23 100 15 22 69 22 19

1 2 3 4 5 6 7 8 9 10 11 12

mtlA holA hslV ruvB

SAUSA300_1086 SAUSA300_0205 SAUSA300_2087 SAUSA300_2107 SAUSA300_1981 SAUSA300_1210 SAUSA300_1546 SAUSA300_0583 SAUSA300_1146 SAUSA300_1430 SAUSA300_1031 SAUSA300_1597

-14.31 -13.65 -12.33 -12.28 -12.09 -11.96 -11.47 -11.22 -11.12 -10.95 -10.93 -10.91

0.001 0.002 0.006 0.006 0.007 0.008 0.01 0.012 0.013 0.014 0.014 0.014

26 51 2 1 1 3 3 52 2 1 16 1

39 65 14 14 14 23 17 65 10 10 29 16

SAUSA300s095

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

cdsA mvk nhaC hemE dapB gltX lacC dprA -

SAUSA300_1932 SAUSA300_1971 SAUSA300_0097 SAUSA300_0430 SAUSA300_0101 SAUSA300_1154 SAUSA300_1728 SAUSA300_1035 SAUSA300_0602 SAUSA300_1496 SAUSA300_0572 SAUSA300_2494 SAUSA300_1579 SAUSA300_2250 SAUSA300_2259 SAUSA300_1864 SAUSA300_1783 SAUSA300_1129 SAUSA300_1955 SAUSA300_1289 SAUSA300_1121 SAUSA300_0513 SAUSA300_2153 SAUSA300_2043 SAUSA300_1142 SAUSA300_1175 SAUSA300_0292

-10.45 -10.35 -10.31 -10.29 -10.28 -9.78 -9.57 -9.46 -9.42 -9.36 -9.31 -9.28 -9.27 -9.13 -9.08 -9.05 -9 -8.97 -8.9 -8.63 -8.51 -8.46 -8.45 -8.45 -8.39 -8.37 -8.36

0.019 0.02 0.02 0.02 0.02 0.026 0.029 0.03 0.031 0.032 0.032 0.033 0.033 0.035 0.036 0.036 0.037 0.038 0.039 0.044 0.046 0.047 0.047 0.047 0.048 0.048 0.049

29 2 48 32 27 28 48 14 45 21 7 29 14 52 54 20 1 48 28 2 3 3 54 1 10 57 5

42 20 65 43 44 44 64 27 60 32 25 39 27 62 66 38 18 61 43 14 20 20 62 20 28 67 24

1 2 3 4 5 6 7

thrS -

SAUSA300_2402 SAUSA300_0241 SAUSA300_2632 SAUSA300_0545 SAUSA300_1036 SAUSA300_1629 SAUSA300_2590

-11.21 -11.03 -8.69 -8.56 -8.47 -8.45 -8.45

0.012 0.013 0.043 0.045 0.046 0.047 0.047

33 34 30 12 7 34 26

44 44 44 24 18 44 40

1 2 3 4 5 6 7 8 9

fruB hslO -

SAUSA300_1428 SAUSA300_1963 SAUSA300_1119 SAUSA300_0684 SAUSA300_0543 SAUSA300_0247 SAUSA300_0490 SAUSA300_2522 SAUSA300_0314

-17.57 -17.13 -14.62 -11.9 -11.47 -11.41 -10.75 -10.73 -10.71

0 0 0.001 0.008 0.01 0.011 0.016 0.016 0.016

19 6 3 23 16 17 14 17 13

36 26 20 32 28 34 28 33 27

SAUSA300s096

SAUSA300s098

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

trmE murE hfq -

SAUSA300_0288 SAUSA300_1861 SAUSA300_1318 SAUSA300_0458 SAUSA300_2646 SAUSA300_1395 SAUSA300_0919 SAUSA300_1387 SAUSA300_1581 SAUSA300_0103 SAUSA300_0770 SAUSA300_2318 SAUSA300_1414 SAUSA300_0675 SAUSA300_2174 SAUSA300_1040 SAUSA300_1196 SAUSA300_1902

-10.7 -10.66 -10.2 -10.15 -9.95 -9.86 -9.64 -9.57 -9.57 -9.5 -9.49 -9.47 -9.38 -9.23 -8.97 -8.93 -8.56 -8.44

0.016 0.017 0.021 0.022 0.024 0.025 0.028 0.029 0.029 0.03 0.03 0.03 0.031 0.034 0.038 0.038 0.045 0.047

16 17 15 19 12 17 24 5 11 9 13 17 16 17 4 19 11 17

34 34 33 33 27 36 34 22 27 24 26 36 30 28 16 27 26 34

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

mraW gidA topB accB moaD trmB lacF clpC norA trmD ilvA -

SAUSA300_0733 SAUSA300_1073 SAUSA300_2645 SAUSA300_2208 SAUSA300_1476 SAUSA300_2221 SAUSA300_1694 SAUSA300_2151 SAUSA300_1939 SAUSA300_0332 SAUSA300_1202 SAUSA300_0510 SAUSA300_0680 SAUSA300_2559 SAUSA300_2593 SAUSA300_1133 SAUSA300_2014 SAUSA300_1318 SAUSA300_1314 SAUSA300_0613 SAUSA300_1426 SAUSA300_1229

-14.1 -12.07 -11.49 -11.28 -11 -10.35 -10.24 -10.23 -9.65 -9.59 -9.51 -9.51 -9.47 -9.41 -9.35 -9.24 -9.05 -8.98 -8.97 -8.71 -8.6 -8.53

0.002 0.007 0.01 0.012 0.014 0.02 0.021 0.021 0.028 0.028 0.03 0.03 0.03 0.031 0.032 0.033 0.036 0.038 0.038 0.042 0.044 0.045

3 5 38 22 21 20 6 22 16 6 7 24 29 20 25 1 7 21 3 16 5 21

20 19 49 35 35 35 26 41 36 18 15 37 42 35 35 16 19 32 20 31 19 35

SAUSA300_0733 SAUSA300_1476 SAUSA300_0793

-14.1 -13.47 -12.32

0.002 0.003 0.006

3 21 59

20 36 74

SAUSA300s099

SAUSA300s100 12 accB 3-

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4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

mraW femA topB moaD trmB trmD clpC ilvA tmk ureF sgtB lacF -

SAUSA300_1073 SAUSA300_1954 SAUSA300_1269 SAUSA300_2482 SAUSA300_2208 SAUSA300_0030 SAUSA300_2542 SAUSA300_0857 SAUSA300_2324 SAUSA300_2221 SAUSA300_1694 SAUSA300_0618 SAUSA300_0610 SAUSA300_1186 SAUSA300_0332 SAUSA300_1202 SAUSA300_2559 SAUSA300_0325 SAUSA300_2593 SAUSA300_1133 SAUSA300_0510 SAUSA300_2014 SAUSA300_0459 SAUSA300_1318 SAUSA300_1277 SAUSA300_0613 SAUSA300_2242 SAUSA300_1426 SAUSA300_1855 SAUSA300_0081 SAUSA300_2394 SAUSA300_2151 SAUSA300_2580

-12.07 -11.75 -11.4 -11.39 -11.28 -11.26 -10.85 -10.72 -10.56 -10.35 -10.24 -10.17 -10.01 -9.88 -9.59 -9.51 -9.41 -9.38 -9.35 -9.24 -9.11 -9.05 -9 -8.98 -8.94 -8.71 -8.63 -8.6 -8.58 -8.53 -8.43 -8.38 -8.3

0.007 0.009 0.011 0.011 0.012 0.012 0.015 0.016 0.018 0.02 0.021 0.021 0.023 0.025 0.028 0.03 0.031 0.031 0.032 0.033 0.036 0.036 0.037 0.038 0.038 0.042 0.044 0.044 0.044 0.045 0.047 0.048 0.05

5 22 56 55 22 54 48 37 33 20 6 27 33 22 6 7 20 49 25 1 24 7 51 21 55 16 50 5 48 58 59 21 26

19 38 68 69 35 72 61 46 49 35 26 42 49 38 18 15 35 67 35 16 37 19 68 32 72 31 63 19 62 75 71 41 37

1 femA SAUSA300_1269 2SAUSA300_2304

-11.05 -9.06

0.013 0.036

16 4

26 20

1 2 3 4 5 6 7 8

-18.6 -12.38 -11.52 -11.37 -11.27 -11.26 -11.25 -11.05

0 0.006 0.01 0.011 0.012 0.012 0.012 0.013

8 9 3 12 19 11 13 14

21 25 19 27 33 21 27 25

SAUSA300s101

SAUSA300s102 moaD ychF codY clfA gltS -

SAUSA300_0324 SAUSA300_2221 SAUSA300_0364 SAUSA300_1904 SAUSA300_1148 SAUSA300_0772 SAUSA300_2291 SAUSA300_2475

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9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

rpmD fmhA rpsJ sufC cysK

SAUSA300_0206 SAUSA300_2186 SAUSA300_0025 SAUSA300_2356 SAUSA300_1327 SAUSA300_0239 SAUSA300_0408 SAUSA300_2205 SAUSA300_1387 SAUSA300_0127 SAUSA300_0825 SAUSA300_0410 SAUSA300_0133 SAUSA300_0802 SAUSA300_0475 SAUSA300_0653 SAUSA300_0205 SAUSA300_0818 SAUSA300_0491

-11.03 -10.59 -10.57 -10.23 -10.2 -10.19 -10.17 -10.12 -10.04 -9.89 -9.45 -9.31 -9.25 -9.23 -9.16 -8.99 -8.96 -8.34 -8.34

0.013 0.017 0.017 0.021 0.021 0.021 0.021 0.022 0.023 0.025 0.03 0.032 0.033 0.034 0.035 0.037 0.038 0.049 0.049

11 12 9 8 16 12 12 12 13 3 15 16 5 11 13 8 5 11 19

24 26 26 27 25 24 26 21 24 19 32 24 20 23 24 19 24 23 30

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

kdpD ureE pepS isaB mraY gnd ald -

SAUSA300_0781 SAUSA300_0269 SAUSA300_1945 SAUSA300_2259 SAUSA300_1387 SAUSA300_0381 SAUSA300_2286 SAUSA300_2035 SAUSA300_0987 SAUSA300_0147 SAUSA300_2241 SAUSA300_0745 SAUSA300_1021 SAUSA300_2232 SAUSA300_1860 SAUSA300_0769 SAUSA300_0111 SAUSA300_2573 SAUSA300_1076 SAUSA300_1459 SAUSA300_0657 SAUSA300_0409 SAUSA300_1331 SAUSA300_1981 SAUSA300_2483 SAUSA300_2423

-17.78 -14.49 -13.75 -13.64 -13.59 -13.44 -13.15 -12.71 -12.13 -12.11 -11.91 -11.68 -11.27 -11.07 -11.03 -10.96 -10.92 -10.88 -10.67 -10.54 -10.41 -10.39 -10.18 -10.1 -9.89 -9.88

0 0.001 0.002 0.002 0.002 0.003 0.003 0.005 0.007 0.007 0.008 0.009 0.012 0.013 0.014 0.014 0.014 0.015 0.017 0.018 0.019 0.019 0.021 0.022 0.025 0.025

46 53 45 8 53 52 22 42 53 45 41 20 47 50 53 14 12 13 4 17 51 54 45 52 22 51

64 64 64 28 63 64 34 54 64 64 53 32 62 64 63 29 31 25 20 32 64 64 61 61 35 62

SAUSA300s103

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56

spsA arcC mutS budA nusA scpB

SAUSA300_1082 SAUSA300_0867 SAUSA300_2436 SAUSA300_2235 SAUSA300_1805 SAUSA300_0574 SAUSA300_0295 SAUSA300_1804 SAUSA300_0681 SAUSA300_0882 SAUSA300_0304 SAUSA300_0425 SAUSA300_2275 SAUSA300_1063 SAUSA300_0199 SAUSA300_1188 SAUSA300_1946 SAUSA300_2165 SAUSA300_1159 SAUSA300_2087 SAUSA300_2542 SAUSA300_1383 SAUSA300_2473 SAUSA300_2581 SAUSA300_0054 SAUSA300_0273 SAUSA300_1083 SAUSA300_1479 SAUSA300_1481 SAUSA300_1444

-9.83 -9.83 -9.76 -9.75 -9.55 -9.45 -9.34 -9.24 -9.16 -9.08 -8.96 -8.95 -8.79 -8.78 -8.77 -8.72 -8.7 -8.64 -8.63 -8.59 -8.57 -8.44 -8.41 -8.39 -8.36 -8.34 -8.33 -8.32 -8.31 -8.3

0.025 0.025 0.026 0.026 0.029 0.03 0.032 0.033 0.035 0.036 0.038 0.038 0.041 0.041 0.041 0.042 0.042 0.043 0.044 0.044 0.045 0.047 0.048 0.048 0.049 0.049 0.049 0.049 0.05 0.05

53 54 45 38 54 9 23 53 10 53 53 36 39 10 26 41 16 53 20 43 38 20 54 16 25 51 53 54 54 54

64 64 64 54 64 22 32 64 22 64 64 56 47 26 38 49 30 64 34 58 47 30 64 30 34 62 64 64 64 64

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

ftsL srtA pyrF pbpA oppB aroA hisB

SAUSA300_1074 SAUSA300_1380 SAUSA300_2350 SAUSA300_2467 SAUSA300_0618 SAUSA300_1097 SAUSA300_1556 SAUSA300_2511 SAUSA300_0692 SAUSA300_1413 SAUSA300_1075 SAUSA300_0887 SAUSA300_0681 SAUSA300_1355 SAUSA300_2609

-13.82 -13.13 -12.97 -12.34 -12.22 -12.06 -11.74 -11.66 -11.38 -11.32 -11.29 -11.28 -11.28 -11.22 -10.94

0.002 0.003 0.004 0.006 0.006 0.007 0.009 0.009 0.011 0.011 0.012 0.012 0.012 0.012 0.014

277 356 276 174 356 358 351 49 331 277 260 278 278 175 362

290 371 294 186 368 372 365 66 349 288 268 294 293 186 375

SAUSA300s104

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

ilvA acnA gid pstC sufC rexA oppA pyrB rarD dnaA glpT saeR

SAUSA300_2135 SAUSA300_0312 SAUSA300_0462 SAUSA300_0399 SAUSA300_0646 SAUSA300_0398 SAUSA300_2014 SAUSA300_1230 SAUSA300_0174 SAUSA300_2264 SAUSA300_0244 SAUSA300_0209 SAUSA300_2311 SAUSA300_0592 SAUSA300_1246 SAUSA300_2234 SAUSA300_1144 SAUSA300_0293 SAUSA300_1282 SAUSA300_0818 SAUSA300_1352 SAUSA300_1957 SAUSA300_0779 SAUSA300_1462 SAUSA300_0870 SAUSA300_0891 SAUSA300_1407 SAUSA300_0211 SAUSA300_1093 SAUSA300_2628 SAUSA300_2134 SAUSA300_2218 SAUSA300_0001 SAUSA300_1297 SAUSA300_0540 SAUSA300_0337 SAUSA300_0691

-10.63 -10.62 -10.52 -10.43 -10.38 -10.27 -10.24 -10.22 -10.19 -10.15 -10.11 -10.07 -10.07 -9.95 -9.73 -9.37 -9.34 -9.26 -9.15 -9.11 -9.07 -9.02 -8.99 -8.92 -8.91 -8.77 -8.73 -8.69 -8.66 -8.58 -8.57 -8.53 -8.45 -8.42 -8.4 -8.4 -8.35

0.017 0.017 0.018 0.019 0.019 0.02 0.021 0.021 0.021 0.022 0.022 0.023 0.023 0.024 0.027 0.032 0.032 0.033 0.035 0.035 0.036 0.037 0.037 0.039 0.039 0.041 0.042 0.042 0.043 0.044 0.045 0.045 0.047 0.048 0.048 0.048 0.049

27 29 172 175 27 175 277 261 367 356 161 44 341 257 338 289 298 350 343 2 276 360 161 349 276 257 251 278 348 21 277 350 299 5 260 271 275

39 42 187 185 39 185 290 273 378 368 175 54 357 267 353 305 307 362 353 22 288 376 178 357 289 267 268 288 357 41 287 361 312 19 276 285 289

1 2 3 4 5 6 7 8

oppB -

SAUSA300_2326 SAUSA300_0887 SAUSA300_0417 SAUSA300_0076 SAUSA300_0695 SAUSA300_0171 SAUSA300_1232 SAUSA300_0479

-14.33 -13.24 -11.82 -11.02 -10.81 -10.38 -9.74 -9.69

0.001 0.003 0.008 0.014 0.015 0.019 0.027 0.027

34 18 17 19 26 19 16 19

51 26 28 27 38 31 27 31

SAUSA300s105

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

9 10 11 12 13 14 15 16 17 18 19 20 21 22

argJ tnp -

SAUSA300_1069 SAUSA300_1460 SAUSA300_0302 SAUSA300_1461 SAUSA300_0052 SAUSA300_0413 SAUSA300_1248 SAUSA300_0295 SAUSA300_1665 SAUSA300_0185 SAUSA300_2115 SAUSA300_1810 SAUSA300_2575 SAUSA300_1383

-9.64 -9.61 -9.59 -9.23 -9.12 -9.11 -9.11 -9 -8.89 -8.86 -8.82 -8.82 -8.72 -8.57

0.028 0.028 0.028 0.034 0.035 0.035 0.036 0.037 0.039 0.039 0.04 0.04 0.042 0.045

18 14 34 21 22 19 30 18 30 33 45 45 4 47

26 23 48 35 33 28 39 28 43 48 53 53 14 56

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

dltB lpdA mnhD crtN rplL pnpA purR mreD mnhE rpsA arlS tig apt accA

SAUSA300_0052 SAUSA300_0836 SAUSA300_0239 SAUSA300_0996 SAUSA300_0871 SAUSA300_0906 SAUSA300_1342 SAUSA300_0852 SAUSA300_1449 SAUSA300_2498 SAUSA300_1716 SAUSA300_0525 SAUSA300_0875 SAUSA300_1167 SAUSA300_1872 SAUSA300_1701 SAUSA300_0473 SAUSA300_1451 SAUSA300_0031 SAUSA300_1847 SAUSA300_1685 SAUSA300_1604 SAUSA300_0247 SAUSA300_0851 SAUSA300_1365 SAUSA300_1307 SAUSA300_1622 SAUSA300_1591 SAUSA300_0678 SAUSA300_1875 SAUSA300_1646

-15.04 -13.1 -12.44 -12.18 -11.82 -11.08 -10.51 -10.4 -10.32 -10.01 -9.84 -9.81 -9.72 -9.7 -9.58 -9.46 -9.45 -9.36 -9.29 -9.21 -9.15 -9.14 -9.05 -9.04 -9.03 -8.97 -8.94 -8.93 -8.92 -8.82 -8.8

0.001 0.003 0.006 0.007 0.008 0.013 0.018 0.019 0.02 0.023 0.025 0.026 0.027 0.027 0.029 0.03 0.03 0.032 0.033 0.034 0.035 0.035 0.036 0.037 0.037 0.038 0.038 0.038 0.038 0.04 0.041

110 50 50 14 15 59 101 97 53 17 49 50 50 80 81 10 11 35 78 33 48 106 53 122 89 80 24 85 58 60 122

128 61 61 27 28 73 116 113 69 31 58 63 60 92 97 20 24 54 95 46 67 119 67 131 103 97 35 94 71 76 131

SAUSA300s106

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

32 33 34 35 36 37

rarD murD folA rocD

SAUSA300_2628 SAUSA300_1077 SAUSA300_2503 SAUSA300_1013 SAUSA300_1319 SAUSA300_0860

-8.67 -8.58 -8.56 -8.41 -8.38 -8.37

0.043 0.044 0.045 0.048 0.048 0.048

98 96 35 43 72 11

111 107 54 56 87 24

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

lgt hslO lysS bccT ctsR isaB rplL hisH ackA hemB rsbV nirB map holA sarU rimM -

SAUSA300_0338 SAUSA300_0781 SAUSA300_0744 SAUSA300_0740 SAUSA300_0490 SAUSA300_0308 SAUSA300_0305 SAUSA300_0098 SAUSA300_0496 SAUSA300_1247 SAUSA300_0170 SAUSA300_1451 SAUSA300_2087 SAUSA300_2549 SAUSA300_0507 SAUSA300_1613 SAUSA300_2573 SAUSA300_0320 SAUSA300_1720 SAUSA300_0525 SAUSA300_0610 SAUSA300_1981 SAUSA300_2608 SAUSA300_1436 SAUSA300_1657 SAUSA300_1615 SAUSA300_2024 SAUSA300_2346 SAUSA300_1869 SAUSA300_1546 SAUSA300_2438 SAUSA300_1132 SAUSA300_2402 SAUSA300_0234 SAUSA300_1792 SAUSA300_0343 SAUSA300_0872 SAUSA300_2382

-16.68 -13.74 -12.57 -11.41 -11.29 -11.19 -11.17 -11.15 -10.97 -10.88 -10.77 -10.59 -10.48 -10.43 -10.22 -10.11 -10.1 -9.97 -9.96 -9.95 -9.91 -9.7 -9.63 -9.61 -9.54 -9.46 -9.46 -9.3 -9.23 -9.2 -9.17 -9.1 -9.01 -8.61 -8.57 -8.39 -8.38 -8.34

0 0.002 0.005 0.011 0.012 0.012 0.012 0.013 0.014 0.015 0.016 0.017 0.018 0.019 0.021 0.022 0.022 0.024 0.024 0.024 0.024 0.027 0.028 0.028 0.029 0.03 0.03 0.033 0.034 0.034 0.034 0.036 0.037 0.044 0.045 0.048 0.048 0.049

41 72 78 77 28 41 15 82 9 44 12 3 39 9 18 46 3 70 12 12 13 78 75 12 25 41 21 20 15 74 42 75 12 68 84 79 37 33

57 87 95 97 45 51 30 97 24 57 26 20 48 22 33 57 19 80 26 28 31 88 91 30 39 49 39 38 31 88 56 87 28 83 100 88 49 49

SAUSA300s111

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SAUSA300s114 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

rarD secY comK trmB acuC moaD moaC murA mvk pyrH rexB malR mraZ pyrP nadE phoB -

SAUSA300_2628 SAUSA300_1198 SAUSA300_2588 SAUSA300_0050 SAUSA300_0928 SAUSA300_1694 SAUSA300_1681 SAUSA300_2221 SAUSA300_0403 SAUSA300_2445 SAUSA300_0745 SAUSA300_0847 SAUSA300_0844 SAUSA300_1101 SAUSA300_2225 SAUSA300_2078 SAUSA300_0572 SAUSA300_2147 SAUSA300_1510 SAUSA300_2041 SAUSA300_1151 SAUSA300_0068 SAUSA300_0869 SAUSA300_1457 SAUSA300_1210 SAUSA300_1072 SAUSA300_2095 SAUSA300_1092 SAUSA300_0730 SAUSA300_1893 SAUSA300_2425 SAUSA300_2561 SAUSA300_1981 SAUSA300_2237 SAUSA300_0636

-17.4 -12.63 -12.22 -12.1 -11.87 -11.54 -11.3 -10.85 -10.78 -10.66 -10.64 -10.63 -10.17 -9.63 -9.51 -9.42 -9.35 -9.26 -9.14 -9.14 -9.08 -9.02 -8.91 -8.86 -8.86 -8.83 -8.82 -8.79 -8.76 -8.7 -8.69 -8.64 -8.64 -8.61 -8.55

0 0.005 0.006 0.007 0.008 0.01 0.012 0.015 0.016 0.017 0.017 0.017 0.021 0.028 0.03 0.031 0.032 0.033 0.035 0.035 0.036 0.037 0.039 0.039 0.04 0.04 0.04 0.041 0.041 0.042 0.042 0.043 0.043 0.044 0.045

6 110 104 6 108 112 143 8 135 114 10 149 110 6 101 111 1 1 1 2 109 122 135 1 125 3 5 139 142 1 3 109 3 10 149

22 125 118 15 122 130 158 22 150 127 26 164 122 15 117 122 14 15 15 14 122 138 151 15 135 20 18 149 157 15 23 120 16 24 164

1 2 3 4 5 6 7 8 9

nadE phoH arcC -

SAUSA300_1893 SAUSA300_1531 SAUSA300_1969 SAUSA300_0899 SAUSA300_0061 SAUSA300_0549 SAUSA300_0320 SAUSA300_2451 SAUSA300_0123

-13.09 -12.68 -11.55 -11.53 -11.46 -10.84 -10.54 -10.19 -10.09

0.004 0.005 0.01 0.01 0.01 0.015 0.018 0.021 0.022

129 68 166 88 72 44 152 227 22

149 84 181 107 86 55 163 240 35

SAUSA300s117

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

ptsG oppF galM clfB holA hisC

SAUSA300_0369 SAUSA300_0567 SAUSA300_2476 SAUSA300_0575 SAUSA300_2086 SAUSA300_1726 SAUSA300_0932 SAUSA300_0893 SAUSA300_1492 SAUSA300_0930 SAUSA300_1858 SAUSA300_1388 SAUSA300_2285 SAUSA300_2245 SAUSA300_0390 SAUSA300_2565 SAUSA300_1546 SAUSA300_2287 SAUSA300_2610

-9.88 -9.7 -9.55 -9.52 -9.51 -9.22 -9.03 -9.02 -8.97 -8.93 -8.91 -8.86 -8.58 -8.54 -8.5 -8.47 -8.42 -8.37 -8.29

0.025 0.027 0.029 0.029 0.03 0.034 0.037 0.037 0.038 0.038 0.039 0.04 0.044 0.045 0.046 0.047 0.047 0.048 0.05

129 76 144 1 1 14 130 151 129 134 138 119 78 2 8 227 130 153 73

144 91 156 16 17 27 147 165 148 148 153 136 90 19 23 247 147 163 91

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

splC moaD dnaI atpE nadE trpB srtB lytM ychF rpmD clfA sufC rocD -

SAUSA300_0324 SAUSA300_0328 SAUSA300_0203 SAUSA300_1756 SAUSA300_2221 SAUSA300_1630 SAUSA300_0876 SAUSA300_0585 SAUSA300_2063 SAUSA300_1893 SAUSA300_1267 SAUSA300_1034 SAUSA300_0954 SAUSA300_0270 SAUSA300_0580 SAUSA300_1971 SAUSA300_0364 SAUSA300_2186 SAUSA300_1118 SAUSA300_0772 SAUSA300_0818 SAUSA300_1981 SAUSA300_0860 SAUSA300_1508 SAUSA300_1387 SAUSA300_0206

-18.6 -14.03 -13.68 -12.93 -12.87 -12.81 -12.73 -12.65 -12.5 -12.22 -12.13 -12.09 -11.99 -11.96 -11.61 -11.59 -11.52 -11.49 -11.37 -11.26 -11.04 -10.96 -10.87 -10.8 -10.79 -10.48

0 0.002 0.002 0.004 0.004 0.004 0.005 0.005 0.005 0.006 0.007 0.007 0.008 0.008 0.01 0.01 0.01 0.01 0.011 0.012 0.013 0.014 0.015 0.015 0.015 0.018

8 219 183 203 9 96 234 193 219 189 108 97 221 219 191 109 3 12 182 11 11 100 181 107 13 11

21 229 199 222 21 111 245 206 228 204 120 114 236 228 203 125 19 26 196 21 25 119 196 120 23 28

SAUSA300s123

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64

SAUSA300_1463 SAUSA300_1879 mraZ SAUSA300_1072 serA SAUSA300_1670 SAUSA300_0425 rpsJ SAUSA300_2205 rsbV SAUSA300_2024 oxaA SAUSA300_2046 SAUSA300_0127 SAUSA300_1688 SAUSA300_2382 sbnC SAUSA300_0120 glvC SAUSA300_2270 SAUSA300_0027 SAUSA300_0409 gltX SAUSA300_0513 SAUSA300_1275 SAUSA300_0930 SAUSA300_0695 SAUSA300_0205 SAUSA300_1488 cap5M SAUSA300_0164 SAUSA300_0653 SAUSA300_1479 SAUSA300_2209 SAUSA300_2296 SAUSA300_2095 SAUSA300_1325 SAUSA300_1032 hslV SAUSA300_1146 SAUSA300_0290 SAUSA300_0410 SAUSA300_0288 SAUSA300_2262 SAUSA300_1008 SAUSA300_1842 mreD SAUSA300_1604 SAUSA300_0749

-10.36 -10.33 -10.25 -10.23 -10.2 -10.12 -10.08 -9.98 -9.89 -9.86 -9.86 -9.85 -9.85 -9.79 -9.78 -9.69 -9.51 -9.5 -9.31 -9.27 -9.16 -8.99 -8.99 -8.98 -8.98 -8.98 -8.9 -8.73 -8.72 -8.68 -8.66 -8.62 -8.61 -8.39 -8.38 -8.36 -8.34 -8.34

0.019 0.02 0.021 0.021 0.021 0.022 0.022 0.024 0.025 0.025 0.025 0.025 0.025 0.026 0.026 0.027 0.03 0.03 0.032 0.033 0.035 0.037 0.037 0.038 0.038 0.038 0.039 0.042 0.042 0.043 0.043 0.044 0.044 0.048 0.048 0.049 0.049 0.049

185 181 197 96 195 12 197 103 3 94 98 219 9 11 183 99 211 199 74 5 220 98 8 100 44 187 97 62 214 103 183 77 182 104 183 188 49 100

196 196 212 110 204 21 216 118 19 108 111 229 24 21 196 119 226 216 90 23 229 115 19 112 58 200 113 77 229 119 196 92 196 118 202 207 69 118

aldA2 rnr -

-13.15 -11.7 -10.79 -10.73 -10.27 -10.2 -10

0.003 0.009 0.015 0.016 0.02 0.021 0.023

1 73 83 73 86 84 125

10 86 97 84 100 97 136

SAUSA300s124 1 2 3 4 5 6 7

SAUSA300_2510 SAUSA300_1901 SAUSA300_0764 SAUSA300_2295 SAUSA300_1101 SAUSA300_1349 SAUSA300_0841

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8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

pcrB trmB murA cysS gyrA cap5P rplO phnE thiD -

SAUSA300_1887 SAUSA300_1694 SAUSA300_1344 SAUSA300_2078 SAUSA300_0515 SAUSA300_1745 SAUSA300_0006 SAUSA300_0167 SAUSA300_0613 SAUSA300_1946 SAUSA300_2185 SAUSA300_0143 SAUSA300_1486 SAUSA300_2049 SAUSA300_2539 SAUSA300_1426 SAUSA300_1852 SAUSA300_1859

-9.9 -9.81 -9.58 -9.56 -9.4 -9.38 -9.37 -9.2 -9.04 -9.02 -8.82 -8.79 -8.58 -8.46 -8.41 -8.37 -8.32 -8.32

0.025 0.026 0.029 0.029 0.031 0.031 0.032 0.034 0.037 0.037 0.04 0.041 0.044 0.047 0.048 0.048 0.049 0.049

104 21 81 85 8 1 88 107 87 85 85 87 82 5 89 89 87 87

118 34 95 100 21 16 104 123 98 98 100 102 102 15 105 99 102 99

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

lgt thrC engB sbcC pbp4 opuD dut moaD hlgB folC

SAUSA300_1892 SAUSA300_0744 SAUSA300_1227 SAUSA300_1978 SAUSA300_0609 SAUSA300_1620 SAUSA300_1243 SAUSA300_0373 SAUSA300_0933 SAUSA300_2167 SAUSA300_0629 SAUSA300_1245 SAUSA300_2637 SAUSA300_1949 SAUSA300_2221 SAUSA300_2367 SAUSA300_1610

-11.77 -11.72 -11.17 -10.85 -10.68 -10.24 -10.18 -9.92 -9.72 -9.68 -9.56 -9.5 -9.35 -8.69 -8.65 -8.57 -8.38

0.009 0.009 0.012 0.015 0.016 0.021 0.021 0.024 0.027 0.027 0.029 0.03 0.032 0.042 0.043 0.045 0.048

54 49 58 51 51 39 38 47 38 55 39 38 41 38 58 44 43

66 66 69 64 66 58 57 57 52 65 53 54 53 58 67 57 57

1 2 3 4 5 6 7 8

bioA -

SAUSA300_1058 SAUSA300_0857 SAUSA300_0825 SAUSA300_2372 SAUSA300_0192 SAUSA300_0393 SAUSA300_0721 SAUSA300_0945

-10.97 -10.61 -10.14 -10.13 -9.72 -9.6 -9.51 -9.33

0.014 0.017 0.022 0.022 0.027 0.028 0.03 0.032

79 85 80 80 79 87 82 85

89 97 92 92 93 100 92 97

SAUSA300s126

SAUSA300s127

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9 10 11 12 13 14

rexB dltA

SAUSA300_0831 SAUSA300_0466 SAUSA300_0268 SAUSA300_0607 SAUSA300_0869 SAUSA300_0835

-9.05 -8.61 -8.33 -8.29 -8.29 -8.29

0.036 0.044 0.049 0.05 0.05 0.05

1 33 9 25 45 8

15 48 28 38 55 24

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

ftsA splE hup rplT ruvA ilvA scdA sucB arlR -

SAUSA300_2004 SAUSA300_0608 SAUSA300_2041 SAUSA300_1079 SAUSA300_0495 SAUSA300_2539 SAUSA300_1754 SAUSA300_0349 SAUSA300_0232 SAUSA300_1362 SAUSA300_1625 SAUSA300_2433 SAUSA300_1584 SAUSA300_2271 SAUSA300_1939 SAUSA300_2560 SAUSA300_2053 SAUSA300_0730 SAUSA300_1598 SAUSA300_1426 SAUSA300_0274 SAUSA300_2616 SAUSA300_2014 SAUSA300_0253 SAUSA300_0040 SAUSA300_0606 SAUSA300_1305 SAUSA300_2436 SAUSA300_0940 SAUSA300_1308 SAUSA300_2451 SAUSA300_2622

-13.22 -10.3 -10.05 -10.03 -9.97 -9.95 -9.87 -9.83 -9.76 -9.49 -9.22 -9.14 -9.12 -8.91 -8.9 -8.83 -8.73 -8.69 -8.68 -8.66 -8.66 -8.65 -8.63 -8.57 -8.56 -8.52 -8.45 -8.44 -8.41 -8.35 -8.33 -8.3

0.003 0.02 0.023 0.023 0.024 0.024 0.025 0.025 0.026 0.03 0.034 0.035 0.035 0.039 0.039 0.04 0.042 0.042 0.043 0.043 0.043 0.043 0.044 0.045 0.045 0.046 0.047 0.047 0.048 0.049 0.049 0.05

28 106 45 21 24 114 109 18 48 99 58 63 16 55 7 120 106 21 71 103 18 104 106 69 1 83 70 90 86 54 120 1

42 120 53 38 37 128 122 28 65 114 69 78 28 69 19 134 119 36 86 117 29 115 120 82 16 96 84 98 98 67 135 15

SAUSA300_0418

-8.82

0.04

1

9

SAUSA300s129 SAUSA300s137

SAUSA300s138 1SAUSA300s140 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

nadE glpQ hlgB argR saeR rplL sucD argR mraZ tcaA pbpA tyrS gcvT

SAUSA300_2436 SAUSA300_1893 SAUSA300_0103 SAUSA300_0516 SAUSA300_1451 SAUSA300_0681 SAUSA300_0664 SAUSA300_0862 SAUSA300_0105 SAUSA300_2367 SAUSA300_2101 SAUSA300_0239 SAUSA300_2522 SAUSA300_1450 SAUSA300_2339 SAUSA300_1928 SAUSA300_2425 SAUSA300_0712 SAUSA300_1853 SAUSA300_0066 SAUSA300_0238 SAUSA300_0691 SAUSA300_0525 SAUSA300_1974 SAUSA300_1139 SAUSA300_1328 SAUSA300_0391 SAUSA300_1349 SAUSA300_0600 SAUSA300_0407 SAUSA300_1069 SAUSA300_0304 SAUSA300_1321 SAUSA300_2428 SAUSA300_2571 SAUSA300_1904 SAUSA300_2433 SAUSA300_0394 SAUSA300_1393 SAUSA300_1072 SAUSA300_2302 SAUSA300_0678 SAUSA300_1792 SAUSA300_1075 SAUSA300_1494 SAUSA300_1675 SAUSA300_1498

-16.31 -15.01 -14.95 -14.54 -14.17 -14.08 -14.01 -13.86 -13.44 -13.2 -13.19 -13.13 -12.89 -12.8 -12.65 -12.57 -12.4 -12.14 -12.13 -11.97 -11.69 -11.63 -11.54 -11.53 -11.49 -11.43 -11.09 -11.07 -10.96 -10.93 -10.84 -10.84 -10.81 -10.75 -10.74 -10.6 -10.57 -10.48 -10.45 -10.45 -10.34 -10.33 -10.18 -10.18 -10.14 -10.01 -9.99

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0 0.001 0.001 0.001 0.001 0.002 0.002 0.002 0.003 0.003 0.003 0.003 0.004 0.004 0.005 0.005 0.006 0.007 0.007 0.008 0.009 0.009 0.01 0.01 0.01 0.011 0.013 0.013 0.014 0.014 0.015 0.015 0.015 0.016 0.016 0.017 0.017 0.018 0.019 0.019 0.02 0.02 0.021 0.021 0.022 0.023 0.024

341 344 16 81 338 258 367 340 341 339 344 338 291 295 341 344 346 339 297 140 261 293 367 339 339 293 350 338 140 298 343 140 345 267 83 293 365 343 336 343 294 347 80 361 75 235 120

355 357 33 97 353 272 380 355 357 354 357 350 308 309 355 357 357 356 308 155 273 307 381 351 350 309 364 350 153 312 358 155 356 278 102 306 375 361 350 362 309 363 90 375 95 252 137

48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79

oppF SAUSA300_0893 moaD SAUSA300_2221 SAUSA300_1961 SAUSA300_1426 SAUSA300_1424 SAUSA300_1506 SAUSA300_1433 uhpT SAUSA300_0216 SAUSA300_1400 lukF-PVSAUSA300_1381 grpE SAUSA300_1541 SAUSA300_0642 lpdA SAUSA300_1467 glpD SAUSA300_1193 SAUSA300_2113 SAUSA300_0106 aroC SAUSA300_1357 SAUSA300_0094 SAUSA300_2361 SAUSA300_0024 SAUSA300_1440 atpH SAUSA300_2061 gpmI SAUSA300_0759 SAUSA300_0089 SAUSA300_0632 SAUSA300_1780 SAUSA300_1952 SAUSA300_0746 SAUSA300_1871 arsC SAUSA300_1719 SAUSA300_0882 SAUSA300_1271

1 2 3 4 5 6 7 8 9 10 11 12 13

argC dps scdA mnhG rpe -

-9.73 -9.7 -9.69 -9.6 -9.45 -9.44 -9.42 -9.38 -9.37 -9.33 -9.27 -9.1 -9.05 -9.05 -9.04 -9.03 -8.98 -8.97 -8.95 -8.94 -8.85 -8.81 -8.8 -8.78 -8.76 -8.74 -8.6 -8.58 -8.49 -8.48 -8.4 -8.36

0.027 0.027 0.027 0.028 0.03 0.031 0.031 0.031 0.032 0.032 0.033 0.036 0.036 0.036 0.037 0.037 0.038 0.038 0.038 0.038 0.04 0.04 0.041 0.041 0.041 0.042 0.044 0.044 0.046 0.046 0.048 0.049

254 289 362 334 338 142 338 293 342 340 333 342 346 74 343 79 338 227 288 338 259 18 15 140 260 339 299 347 342 349 134 157

268 306 380 353 349 154 352 309 357 352 349 357 364 87 357 93 356 242 308 354 271 36 30 153 268 354 310 362 353 364 151 170

-13.97 -12.95 -11.51 -11.27 -10.83 -10.05 -9.82 -9.28 -9.27 -9.18 -9.05 -8.99 -8.51

0.002 0.004 0.01 0.012 0.015 0.023 0.025 0.033 0.033 0.034 0.036 0.037 0.046

20 29 11 19 20 16 19 13 13 15 6 12 13

31 38 26 29 32 35 30 27 28 25 21 30 26

SAUSA300s141 SAUSA300_0565 SAUSA300_1879 SAUSA300_1464 SAUSA300_1742 SAUSA300_1948 SAUSA300_0186 SAUSA300_2092 SAUSA300_0253 SAUSA300_2069 SAUSA300_0784 SAUSA300_0849 SAUSA300_1115 SAUSA300_0222

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SAUSA300s144 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

norA truA cdsA holA hslU argR hlgA ruvB rbfA purK mnhA lacC -

SAUSA300_1354 SAUSA300_0706 SAUSA300_1470 SAUSA300_1430 SAUSA300_1981 SAUSA300_0680 SAUSA300_0486 SAUSA300_2173 SAUSA300_0933 SAUSA300_1154 SAUSA300_1742 SAUSA300_1979 SAUSA300_1546 SAUSA300_1400 SAUSA300_2522 SAUSA300_1147 SAUSA300_1418 SAUSA300_0681 SAUSA300_1374 SAUSA300_1978 SAUSA300_1510 SAUSA300_1469 SAUSA300_0282 SAUSA300_1952 SAUSA300_0417 SAUSA300_2365 SAUSA300_1597 SAUSA300_0252 SAUSA300_2428 SAUSA300_2410 SAUSA300_1163 SAUSA300_2209 SAUSA300_2102 SAUSA300_1485 SAUSA300_2368 SAUSA300_1323 SAUSA300_0967 SAUSA300_1898 SAUSA300_0176 SAUSA300_0055 SAUSA300_0855 SAUSA300_2153 SAUSA300_0081 SAUSA300_0413 SAUSA300_0526

-14.96 -13.38 -12.29 -11.98 -11.94 -11.43 -11.23 -11.12 -10.98 -10.67 -10.64 -10.52 -10.45 -10.41 -10.41 -10.2 -10.16 -10.11 -9.92 -9.8 -9.79 -9.77 -9.77 -9.61 -9.49 -9.39 -9.33 -9.33 -9.31 -9.24 -9.22 -9.02 -9 -9 -8.95 -8.93 -8.77 -8.73 -8.69 -8.66 -8.6 -8.57 -8.56 -8.51 -8.33

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0.001 0.003 0.006 0.008 0.008 0.011 0.012 0.013 0.014 0.016 0.017 0.018 0.019 0.019 0.019 0.021 0.022 0.022 0.024 0.026 0.026 0.026 0.026 0.028 0.03 0.031 0.032 0.032 0.032 0.034 0.034 0.037 0.037 0.037 0.038 0.038 0.041 0.042 0.042 0.043 0.044 0.045 0.045 0.046 0.049

306 353 30 224 345 354 307 326 300 156 73 81 299 341 353 354 302 301 287 350 342 123 43 304 301 231 3 308 2 150 156 128 114 356 218 211 229 71 322 73 87 147 73 301 2

321 368 50 238 359 368 321 342 312 170 93 96 314 359 365 367 314 319 306 364 357 138 57 321 314 244 19 326 14 169 166 142 133 368 233 226 240 84 334 87 101 167 88 315 18

SAUSA300s148 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

mfd glmM hslO atpG arlS arcC ybaK menC glnR recG gap rbsD murC oppF folA ggt cap1A

SAUSA300_0135 SAUSA300_0481 SAUSA300_1842 SAUSA300_1867 SAUSA300_1111 SAUSA300_1923 SAUSA300_1732 SAUSA300_2111 SAUSA300_1607 SAUSA300_1623 SAUSA300_1318 SAUSA300_0490 SAUSA300_0353 SAUSA300_0223 SAUSA300_0937 SAUSA300_1684 SAUSA300_2059 SAUSA300_1429 SAUSA300_0133 SAUSA300_2267 SAUSA300_0644 SAUSA300_0777 SAUSA300_0712 SAUSA300_0566 SAUSA300_1677 SAUSA300_1857 SAUSA300_1307 SAUSA300_0061 SAUSA300_0682 SAUSA300_1735 SAUSA300_2368 SAUSA300_1200 SAUSA300_1375 SAUSA300_1120 SAUSA300_1633 SAUSA300_2379 SAUSA300_0263 SAUSA300_1248 SAUSA300_1686 SAUSA300_0890 SAUSA300_1319 SAUSA300_0204 SAUSA300_0761 SAUSA300_0947 SAUSA300_2598

-15.9 -13.28 -13.13 -12.66 -12.32 -12.28 -12.05 -11.96 -11.76 -11.41 -11.21 -11.11 -10.81 -10.54 -10.49 -10.43 -10.34 -10.25 -10.18 -10.11 -10.03 -9.73 -9.6 -9.6 -9.59 -9.48 -9.4 -9.28 -9.25 -9.18 -9.15 -9.13 -9.12 -9.09 -9.04 -8.99 -8.98 -8.97 -8.93 -8.91 -8.89 -8.88 -8.84 -8.81 -8.65

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0 0.003 0.003 0.005 0.006 0.006 0.007 0.008 0.009 0.011 0.012 0.013 0.015 0.018 0.018 0.019 0.02 0.021 0.021 0.022 0.023 0.027 0.028 0.028 0.029 0.03 0.031 0.033 0.033 0.034 0.035 0.035 0.035 0.036 0.037 0.037 0.038 0.038 0.038 0.039 0.039 0.039 0.04 0.04 0.043

241 245 244 246 134 255 242 264 7 255 128 246 93 134 163 66 245 65 9 71 19 90 241 266 22 259 48 66 292 67 138 69 121 260 162 179 138 275 245 8 62 66 260 245 286

253 263 258 258 152 273 258 279 22 270 148 255 104 148 176 76 256 76 22 85 33 106 258 279 34 276 60 76 300 81 153 78 140 274 178 196 154 290 255 28 76 80 279 259 298

46 47 48 49 50

SAUSA300_0258 miaA SAUSA300_1195 opp-3B SAUSA300_0074 uvrC SAUSA300_1045 trpB SAUSA300_1267

-8.64 -8.64 -8.59 -8.45 -8.39

0.043 0.043 0.044 0.047 0.048

19 134 163 64 260

35 146 175 76 276

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

lytN fmtB aroK rocF sdaAA folC arsR spxA -

SAUSA300_0428 SAUSA300_2332 SAUSA300_1742 SAUSA300_0356 SAUSA300_1205 SAUSA300_1140 SAUSA300_2433 SAUSA300_2109 SAUSA300_1499 SAUSA300_2554 SAUSA300_0146 SAUSA300_2114 SAUSA300_0824 SAUSA300_0246 SAUSA300_2326 SAUSA300_1585 SAUSA300_2469 SAUSA300_0568 SAUSA300_0638 SAUSA300_0194 SAUSA300_1610 SAUSA300_0139 SAUSA300_0335 SAUSA300_2289 SAUSA300_2098 SAUSA300_0898 SAUSA300_1198 SAUSA300_2045

-16.3 -13.39 -12.96 -12.43 -11.77 -11.47 -11.04 -10.76 -10.71 -10.69 -10.66 -10.43 -10.39 -10.23 -10.01 -9.88 -9.68 -9.59 -9.33 -9.23 -9.18 -8.98 -8.97 -8.66 -8.47 -8.46 -8.41 -8.38

0 0.003 0.004 0.006 0.009 0.01 0.013 0.016 0.016 0.016 0.017 0.019 0.019 0.021 0.023 0.025 0.027 0.028 0.032 0.034 0.034 0.038 0.038 0.043 0.047 0.047 0.048 0.048

134 136 53 24 129 131 142 170 14 143 129 54 13 44 18 175 49 53 177 55 166 53 53 71 23 11 73 56

152 148 67 35 146 143 158 186 27 154 145 68 25 59 30 186 64 72 186 70 180 63 70 79 38 29 81 68

1 2 3 4 5 6 7 8 9 10

udk trmB dltD -

SAUSA300_1568 SAUSA300_1694 SAUSA300_2309 SAUSA300_0678 SAUSA300_0258 SAUSA300_0900 SAUSA300_1879 SAUSA300_1496 SAUSA300_0838 SAUSA300_0575

-12.81 -11.9 -11.73 -11.03 -11.02 -10.66 -10.61 -10.03 -10.01 -9.68

0.004 0.008 0.009 0.013 0.014 0.017 0.017 0.023 0.023 0.027

73 84 111 79 84 31 102 76 108 36

82 95 127 94 95 44 115 96 122 47

SAUSA300s149

SAUSA300s150

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

11 12 13 14 15 16 17 18 19 20

pbpA fruB fosB -

SAUSA300_1075 SAUSA300_0097 SAUSA300_1211 SAUSA300_0684 SAUSA300_2280 SAUSA300_0703 SAUSA300_1851 SAUSA300_2273 SAUSA300_1941 SAUSA300_2147

-9.48 -9.42 -9.38 -9.26 -9.23 -9.1 -8.78 -8.7 -8.62 -8.54

0.03 0.031 0.031 0.033 0.034 0.036 0.041 0.042 0.044 0.045

68 11 97 10 84 54 69 108 75 98

82 23 105 23 93 71 83 120 84 106

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

kdpD trmD aroE ureF rpmA yfiA ddh ilvC hisIE -

SAUSA300_2508 SAUSA300_2035 SAUSA300_0579 SAUSA300_1133 SAUSA300_1555 SAUSA300_2496 SAUSA300_0428 SAUSA300_2428 SAUSA300_2242 SAUSA300_1068 SAUSA300_0990 SAUSA300_1601 SAUSA300_1492 SAUSA300_0736 SAUSA300_0119 SAUSA300_0268 SAUSA300_2463 SAUSA300_2009 SAUSA300_2370 SAUSA300_1557 SAUSA300_2605 SAUSA300_0479 SAUSA300_0022 SAUSA300_1004 SAUSA300_0215

-18.06 -18.02 -13.99 -12.94 -10.65 -10.41 -10.31 -9.93 -9.85 -9.85 -9.82 -9.69 -9.66 -9.41 -9.26 -9.07 -9.04 -8.96 -8.82 -8.8 -8.76 -8.66 -8.53 -8.41 -8.39

0 0 0.002 0.004 0.017 0.019 0.02 0.024 0.025 0.025 0.025 0.027 0.028 0.031 0.033 0.036 0.037 0.038 0.04 0.04 0.041 0.043 0.045 0.048 0.048

25 37 32 28 28 60 4 67 17 11 7 30 36 82 28 1 39 61 16 4 9 32 83 44 1

45 53 44 41 42 74 13 86 26 21 18 44 47 95 37 11 48 71 26 20 22 42 95 58 17

1 2 3 4 5 6 7 8

ddl hslV lacG -

SAUSA300_0342 SAUSA300_2330 SAUSA300_2039 SAUSA300_1146 SAUSA300_2149 SAUSA300_1395 SAUSA300_2370 SAUSA300_2643

-13.26 -12.73 -12.64 -12.63 -11.75 -11.62 -11.56 -11.14

0.003 0.005 0.005 0.005 0.009 0.01 0.01 0.013

7 29 47 65 59 44 63 2

21 43 59 80 75 56 79 17

SAUSA300s151

SAUSA300s154

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

tgt nrdG zwf mraZ hsdM ccrB rnr gidB -

SAUSA300_1648 SAUSA300_1396 SAUSA300_1802 SAUSA300_0925 SAUSA300_2304 SAUSA300_1595 SAUSA300_2550 SAUSA300_2332 SAUSA300_2041 SAUSA300_1454 SAUSA300_1072 SAUSA300_0405 SAUSA300_0037 SAUSA300_0764 SAUSA300_0544 SAUSA300_0281 SAUSA300_1241 SAUSA300_1894 SAUSA300_2266 SAUSA300_0052 SAUSA300_2644 SAUSA300_2425 SAUSA300_1942 SAUSA300_0540 SAUSA300_1383 SAUSA300_2465 SAUSA300_1960

-11.11 -10.84 -10.79 -10.68 -10.65 -10.24 -10.19 -10.03 -10.03 -10.01 -9.9 -9.78 -9.74 -9.69 -9.55 -9.42 -9.3 -9.29 -9.09 -9.04 -8.93 -8.73 -8.57 -8.54 -8.37 -8.37 -8.3

0.013 0.015 0.015 0.016 0.017 0.021 0.021 0.023 0.023 0.023 0.025 0.026 0.027 0.027 0.029 0.031 0.033 0.033 0.036 0.037 0.038 0.042 0.045 0.045 0.048 0.049 0.05

162 163 40 19 155 19 16 1 15 59 60 32 17 29 19 163 119 158 32 153 164 59 163 165 65 26 59

174 172 55 34 167 31 24 19 30 77 71 44 34 43 31 172 138 171 43 167 176 79 171 173 78 39 79

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

argC nrdG arcD rpiA

SAUSA300_0186 SAUSA300_0526 SAUSA300_0241 SAUSA300_0295 SAUSA300_2130 SAUSA300_1040 SAUSA300_0023 SAUSA300_2559 SAUSA300_0132 SAUSA300_0417 SAUSA300_0681 SAUSA300_1556 SAUSA300_2550 SAUSA300_2568 SAUSA300_1018 SAUSA300_0419 SAUSA300_2560 SAUSA300_2283

-16.41 -16.26 -15.02 -14.79 -12.93 -12.93 -12.93 -12.89 -12.88 -12.84 -12.53 -12.46 -12.25 -12.01 -12 -11.82 -11.53 -11.52

0 0 0.001 0.001 0.004 0.004 0.004 0.004 0.004 0.004 0.005 0.006 0.006 0.007 0.007 0.008 0.01 0.01

68 238 11 241 132 93 157 131 3 236 227 158 91 132 195 236 243 157

80 252 29 253 146 106 167 145 20 253 245 168 104 142 210 253 257 168

SAUSA300s156

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

murQ scrB accB mutY rplQ frp crtM mtnN tpx folK holA sbcD obgE accC

SAUSA300_0193 SAUSA300_1938 SAUSA300_0014 SAUSA300_0413 SAUSA300_1523 SAUSA300_0252 SAUSA300_1994 SAUSA300_1935 SAUSA300_1476 SAUSA300_1849 SAUSA300_2029 SAUSA300_2634 SAUSA300_0199 SAUSA300_0844 SAUSA300_0998 SAUSA300_2083 SAUSA300_2168 SAUSA300_2177 SAUSA300_2416 SAUSA300_2462 SAUSA300_2499 SAUSA300_1698 SAUSA300_0793 SAUSA300_0044 SAUSA300_1558 SAUSA300_1434 SAUSA300_1489 SAUSA300_1659 SAUSA300_2041 SAUSA300_0721 SAUSA300_1412 SAUSA300_1843 SAUSA300_0978 SAUSA300_0494 SAUSA300_1546 SAUSA300_1915 SAUSA300_1242 SAUSA300_1926 SAUSA300_1506 SAUSA300_1600 SAUSA300_2288 SAUSA300_1475

-11.33 -11.23 -11.09 -10.87 -10.83 -10.69 -10.42 -10.37 -10.29 -10.02 -10.01 -9.98 -9.94 -9.79 -9.76 -9.68 -9.67 -9.65 -9.64 -9.62 -9.55 -9.47 -9.44 -9.38 -9.38 -9.25 -9.16 -9.08 -9.03 -9.03 -9.02 -9.01 -8.89 -8.86 -8.83 -8.83 -8.7 -8.67 -8.63 -8.53 -8.44 -8.41

0.011 0.012 0.013 0.015 0.015 0.016 0.019 0.019 0.02 0.023 0.023 0.024 0.024 0.026 0.026 0.027 0.027 0.028 0.028 0.028 0.029 0.03 0.031 0.031 0.031 0.033 0.035 0.036 0.037 0.037 0.037 0.037 0.039 0.04 0.04 0.04 0.042 0.043 0.043 0.045 0.047 0.048

234 136 238 236 234 153 12 258 153 138 238 84 81 250 197 63 235 220 69 157 229 156 233 143 244 222 87 129 239 139 220 81 126 69 227 240 239 213 130 241 230 238

248 151 252 253 248 167 20 273 162 149 253 98 99 269 211 77 253 231 79 167 243 165 247 153 253 239 98 143 253 153 233 101 138 80 242 255 252 225 142 253 243 252

SAUSA300_0860 SAUSA300_0484 SAUSA300_0769

-16.11 -15.44 -15.36

0 0 0

75 80 83

89 89 96

SAUSA300s157 1 rocD 23-

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4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50

mraZ oppB icaA cap5N ddl fumC ppnK ctsR moaD lysS nupC mnhG oppA glyA gnd dnaJ cbiO fhs murD yfiA -

SAUSA300_0177 SAUSA300_1194 SAUSA300_1072 SAUSA300_0887 SAUSA300_2600 SAUSA300_0165 SAUSA300_1561 SAUSA300_0613 SAUSA300_2039 SAUSA300_0930 SAUSA300_1346 SAUSA300_1801 SAUSA300_0908 SAUSA300_0507 SAUSA300_0308 SAUSA300_0119 SAUSA300_0664 SAUSA300_0373 SAUSA300_2221 SAUSA300_1069 SAUSA300_0496 SAUSA300_1979 SAUSA300_1945 SAUSA300_0506 SAUSA300_0849 SAUSA300_0892 SAUSA300_2067 SAUSA300_0591 SAUSA300_1459 SAUSA300_0268 SAUSA300_1539 SAUSA300_2176 SAUSA300_2542 SAUSA300_0271 SAUSA300_0300 SAUSA300_0417 SAUSA300_1899 SAUSA300_2423 SAUSA300_1678 SAUSA300_0127 SAUSA300_1530 SAUSA300_0252 SAUSA300_0688 SAUSA300_1077 SAUSA300_0736 SAUSA300_1321 SAUSA300_1068

-15.21 -15.03 -14.72 -14.34 -13.2 -12.87 -12.82 -12.35 -12.34 -12.25 -12.13 -11.66 -11.56 -11.51 -11.34 -11.24 -11.02 -11 -10.94 -10.84 -10.81 -10.76 -10.62 -10.57 -10.46 -10.41 -10.39 -10.39 -10.32 -10.21 -10.16 -10.13 -10.04 -9.97 -9.9 -9.87 -9.83 -9.79 -9.68 -9.63 -9.62 -9.51 -9.47 -9.42 -9.4 -9.39 -9.35

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0.001 0.001 0.001 0.001 0.003 0.004 0.004 0.006 0.006 0.006 0.007 0.009 0.01 0.01 0.011 0.012 0.014 0.014 0.014 0.015 0.015 0.016 0.017 0.017 0.018 0.019 0.019 0.019 0.02 0.021 0.022 0.022 0.023 0.024 0.025 0.025 0.025 0.026 0.027 0.028 0.028 0.029 0.03 0.031 0.031 0.031 0.032

74 69 75 83 14 5 81 74 93 74 78 76 93 51 79 73 79 98 71 83 79 23 83 13 9 83 81 81 83 22 78 76 45 58 81 84 77 57 51 79 79 74 74 52 78 70 78

87 89 91 92 32 25 91 89 108 88 87 94 107 70 88 86 87 108 86 97 87 34 101 27 24 97 92 89 97 36 92 87 56 73 89 93 87 73 64 91 93 89 92 67 87 85 92

51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73

glvC murQ mutL murA gltS queA cap5F -

SAUSA300_1436 SAUSA300_2270 SAUSA300_2265 SAUSA300_0193 SAUSA300_1189 SAUSA300_0128 SAUSA300_0790 SAUSA300_0987 SAUSA300_0569 SAUSA300_2147 SAUSA300_1562 SAUSA300_0082 SAUSA300_1437 SAUSA300_0844 SAUSA300_2078 SAUSA300_0512 SAUSA300_2031 SAUSA300_0683 SAUSA300_2275 SAUSA300_2291 SAUSA300_1596 SAUSA300_0157 SAUSA300_1338

-9.33 -9.24 -9.23 -9.13 -9.08 -8.99 -8.98 -8.97 -8.94 -8.89 -8.83 -8.78 -8.67 -8.64 -8.6 -8.57 -8.57 -8.5 -8.47 -8.4 -8.39 -8.38 -8.3

0.032 0.033 0.034 0.035 0.036 0.037 0.038 0.038 0.038 0.039 0.04 0.041 0.043 0.043 0.044 0.045 0.045 0.046 0.046 0.048 0.048 0.048 0.05

78 68 79 86 83 79 43 46 62 14 83 59 49 92 88 33 75 68 92 74 74 76 59

87 87 98 96 97 91 56 56 73 27 94 74 64 102 105 51 90 88 105 88 92 92 79

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

asnC lytM sarX adh ychF sbcC pdp mtnN cap5O ureC atl -

SAUSA300_1345 SAUSA300_0270 SAUSA300_2459 SAUSA300_2401 SAUSA300_0654 SAUSA300_0871 SAUSA300_0486 SAUSA300_0594 SAUSA300_0364 SAUSA300_1243 SAUSA300_2089 SAUSA300_1785 SAUSA300_1558 SAUSA300_0349 SAUSA300_0166 SAUSA300_0859 SAUSA300_0796 SAUSA300_2240 SAUSA300_0955 SAUSA300_1802 SAUSA300_1379 SAUSA300_1186

-12.47 -12.18 -12.18 -11.69 -10.69 -10.53 -10.31 -10.29 -10.05 -9.94 -9.89 -9.82 -9.81 -9.73 -9.34 -9.24 -9.06 -8.96 -8.9 -8.71 -8.51 -8.51

0.005 0.007 0.007 0.009 0.016 0.018 0.02 0.02 0.023 0.024 0.025 0.026 0.026 0.027 0.032 0.033 0.036 0.038 0.039 0.042 0.046 0.046

17 59 27 42 17 20 22 57 59 19 20 23 73 55 57 20 18 71 18 4 21 49

28 70 41 55 28 34 34 68 74 34 29 33 82 70 74 28 34 79 27 12 32 68

SAUSA300s161

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

23 -

SAUSA300_2419

-8.43

0.047

35

43

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

SAUSA300_0782 SAUSA300_1045 SAUSA300_1344 SAUSA300_2139 SAUSA300_1500 SAUSA300_1743 SAUSA300_1498 SAUSA300_0921 SAUSA300_0891 SAUSA300_0526 SAUSA300_2432 SAUSA300_0066 SAUSA300_0889 SAUSA300_0765 SAUSA300_0446 SAUSA300_1630 SAUSA300_1319 SAUSA300_1048 SAUSA300_0023 SAUSA300_0367 SAUSA300_1563 SAUSA300_1349 SAUSA300_2551 SAUSA300_2285 SAUSA300_2051 SAUSA300_2480 SAUSA300_0276 SAUSA300_2516 SAUSA300_1106 SAUSA300_1954 SAUSA300_2305 SAUSA300_1566 SAUSA300_2291 SAUSA300_2043 SAUSA300_1203 SAUSA300_0750 SAUSA300_0326 SAUSA300_2241 SAUSA300_1157 SAUSA300_2319 SAUSA300_1941 SAUSA300_1971 SAUSA300_1561 SAUSA300_1462

-19.65 -15.14 -14.86 -14.06 -13.67 -13.23 -13.21 -12.81 -12.79 -12.75 -12.73 -12.73 -12.59 -12.37 -12.36 -12.25 -12.23 -12.17 -11.66 -11.62 -11.46 -11.39 -11.26 -11.23 -11.13 -11.06 -10.92 -10.76 -10.71 -10.63 -10.52 -10.5 -10.47 -10.32 -10.31 -10.3 -10.17 -10.14 -10.11 -10.09 -9.98 -9.88 -9.81 -9.8

0 0.001 0.001 0.002 0.002 0.003 0.003 0.004 0.004 0.004 0.005 0.005 0.005 0.006 0.006 0.006 0.006 0.007 0.009 0.01 0.01 0.011 0.012 0.012 0.013 0.013 0.014 0.016 0.016 0.017 0.018 0.018 0.018 0.02 0.02 0.02 0.021 0.022 0.022 0.022 0.024 0.025 0.026 0.026

221 209 205 196 206 206 203 92 209 115 197 206 203 89 209 75 91 206 210 202 204 199 206 93 89 123 87 22 86 91 264 209 209 207 31 19 109 76 130 123 90 156 208 91

241 218 217 210 218 214 217 104 223 130 212 221 217 104 223 86 109 217 229 217 223 217 218 112 108 139 102 33 103 109 276 217 217 224 44 31 121 91 145 141 107 171 216 103

SAUSA300s166 uvrC gcvT prfC oppA argR oppD smpB gltD dnaI folA sdhB ssb accC nrdD galM gltS ureE polC -

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

cinA lacF hisIE mraW fhuB aroC hsdR fadE cidC sufS

SAUSA300_2435 SAUSA300_1177 SAUSA300_1328 SAUSA300_1259 SAUSA300_2151 SAUSA300_1853 SAUSA300_0172 SAUSA300_2029 SAUSA300_0031 SAUSA300_1184 SAUSA300_2605 SAUSA300_1073 SAUSA300_0634 SAUSA300_0174 SAUSA300_1318 SAUSA300_1357 SAUSA300_0808 SAUSA300_0196 SAUSA300_1396 SAUSA300_0228 SAUSA300_2477 SAUSA300_0901 SAUSA300_0820

-9.78 -9.73 -9.7 -9.62 -9.6 -9.44 -9.3 -9.26 -9.16 -9.16 -9.16 -8.95 -8.92 -8.91 -8.91 -8.86 -8.69 -8.69 -8.53 -8.42 -8.41 -8.33 -8.32

0.026 0.027 0.027 0.028 0.028 0.031 0.033 0.033 0.035 0.035 0.035 0.038 0.039 0.039 0.039 0.04 0.043 0.043 0.045 0.047 0.048 0.049 0.049

49 209 23 77 23 94 203 115 91 90 203 115 23 203 209 247 209 210 165 207 15 22 132

59 217 34 97 37 110 216 130 104 100 218 133 34 217 222 260 229 218 179 217 28 35 144

1 2 3 4 5 6 7 8 9 10 11 12 13 14

cysK trmB aroK trpA icd splC

SAUSA300_0491 SAUSA300_1398 SAUSA300_0672 SAUSA300_1694 SAUSA300_1499 SAUSA300_1268 SAUSA300_2508 SAUSA300_0082 SAUSA300_1640 SAUSA300_0600 SAUSA300_0673 SAUSA300_1274 SAUSA300_0103 SAUSA300_1756

-12.29 -11.71 -10.83 -10.82 -10.17 -10.17 -9.95 -8.95 -8.89 -8.61 -8.43 -8.42 -8.41 -8.31

0.006 0.009 0.015 0.015 0.021 0.021 0.024 0.038 0.039 0.044 0.047 0.047 0.048 0.049

76 73 73 46 32 30 31 32 32 34 33 32 76 73

89 89 88 59 44 50 41 43 46 46 46 42 87 86

1 2 3 4 5 6

crr trpF

SAUSA300_0911 SAUSA300_1315 SAUSA300_1259 SAUSA300_0011 SAUSA300_0338 SAUSA300_1266

-10.42 -10.15 -10.09 -8.79 -8.64 -8.45

0.019 0.022 0.022 0.041 0.043 0.047

68 11 24 10 31 18

81 23 38 23 41 32

SAUSA300s167

SAUSA300s168

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

7-

SAUSA300_0986

-8.43

0.047

23

34

ipk tpiA agrA mraZ rpsM accB aroK rpmE2

SAUSA300_0472 SAUSA300_0758 SAUSA300_0679 SAUSA300_0797 SAUSA300_1963 SAUSA300_1992 SAUSA300_1427 SAUSA300_1072 SAUSA300_0458 SAUSA300_0876 SAUSA300_2180 SAUSA300_1476 SAUSA300_1249 SAUSA300_2419 SAUSA300_2587 SAUSA300_0716 SAUSA300_2431 SAUSA300_2004 SAUSA300_0417 SAUSA300_0372 SAUSA300_1499 SAUSA300_1241 SAUSA300_1432 SAUSA300_2300 SAUSA300_2168 SAUSA300_0871 SAUSA300_1397 SAUSA300_2145 SAUSA300_2074

-11.46 -11.35 -11.33 -10.94 -10.71 -10.65 -10.64 -10.25 -10.16 -10.04 -9.98 -9.65 -9.6 -9.58 -9.55 -9.5 -9.47 -9.42 -9.37 -9.2 -9.15 -9.08 -9.05 -9 -9 -8.41 -8.41 -8.32 -8.31

0.01 0.011 0.011 0.014 0.016 0.017 0.017 0.021 0.022 0.023 0.024 0.028 0.028 0.029 0.029 0.03 0.03 0.031 0.032 0.034 0.035 0.036 0.036 0.037 0.037 0.048 0.048 0.049 0.05

67 19 67 119 19 19 15 88 18 19 14 90 53 40 26 17 91 62 88 14 66 55 55 67 101 96 18 35 19

82 30 80 133 30 32 31 101 34 30 29 100 66 53 40 29 101 77 100 29 82 68 72 80 114 108 29 49 29

1 2 3 4 5 6

rpsA spsA fnbA

SAUSA300_2245 SAUSA300_2127 SAUSA300_1365 SAUSA300_0697 SAUSA300_0867 SAUSA300_2441

-11.03 -9.73 -9.47 -9.28 -8.77 -8.33

0.013 0.027 0.03 0.033 0.041 0.049

47 39 38 32 24 13

59 49 49 46 34 33

1 2 3 4 5

panB -

SAUSA300_0602 SAUSA300_2534 SAUSA300_2304 SAUSA300_1328 SAUSA300_0768

-12.43 -11.97 -11.73 -11.32 -11.01

0.006 0.008 0.009 0.011 0.014

83 77 97 70 98

95 93 106 89 112

SAUSA300s169 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 SAUSA300s170

SAUSA300s171

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

SAUSA300_1106 gltX SAUSA300_0513 SAUSA300_1374 SAUSA300_2633 SAUSA300_0957 SAUSA300_0052 SAUSA300_1738 cinA SAUSA300_1177 thiD SAUSA300_2049 opp-1ASAUSA300_2411 SAUSA300_1241 coa SAUSA300_0224 SAUSA300_1352 hisZ SAUSA300_2613 kdpB SAUSA300_2033 SAUSA300_0028 nirB SAUSA300_2346 SAUSA300_0646 SAUSA300_1937 SAUSA300_0575 rexB SAUSA300_0869 SAUSA300_0435 SAUSA300_1377 SAUSA300_2513 estA SAUSA300_2564

-10.58 -10.35 -10.31 -10.09 -10.02 -9.95 -9.94 -9.82 -9.82 -9.76 -9.4 -9.4 -9.39 -9.38 -9.23 -9.01 -8.96 -8.75 -8.74 -8.63 -8.62 -8.59 -8.57 -8.43 -8.36

0.017 0.02 0.02 0.022 0.023 0.024 0.024 0.025 0.026 0.026 0.031 0.031 0.031 0.031 0.034 0.037 0.038 0.041 0.042 0.044 0.044 0.044 0.045 0.047 0.049

39 71 68 86 116 97 101 79 124 73 116 74 67 71 67 66 73 77 35 83 29 85 91 36 34

58 87 83 96 127 106 112 94 138 89 131 87 84 87 83 76 91 93 51 95 39 99 101 53 46

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

oppA SAUSA300_0891 SAUSA300_2454 oppB SAUSA300_0887 gltD SAUSA300_0446 SAUSA300_0561 acsA SAUSA300_1679 mqo SAUSA300_2312 SAUSA300_2400 SAUSA300_1172 lysP SAUSA300_1628 SAUSA300_1453 SAUSA300_2087 cap5M SAUSA300_0164 SAUSA300_2353 SAUSA300_2448 sucD SAUSA300_1139 SAUSA300_0592 SAUSA300_2626 bccT SAUSA300_2549 SAUSA300_0241

-17.26 -15.78 -14.87 -14.52 -14.46 -14.39 -13.61 -13.52 -13.46 -13.46 -13.1 -12.88 -12.87 -12.85 -12.75 -12.58 -12.56 -12.45 -12.32 -12.04

0 0 0.001 0.001 0.001 0.001 0.002 0.003 0.003 0.003 0.003 0.004 0.004 0.004 0.004 0.005 0.005 0.006 0.006 0.007

5 106 1 4 3 4 83 8 1 67 1 6 122 55 69 65 1 3 4 2

18 126 14 18 19 13 95 18 9 79 9 25 140 75 80 80 9 12 14 10

SAUSA300s172

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

ackA gltS dnaA aroC sucB arcC cdsA cinA sgtB mraZ moaD folA map lgt gntP purC -

SAUSA300_1220 SAUSA300_1902 SAUSA300_2423 SAUSA300_0796 SAUSA300_1657 SAUSA300_2232 SAUSA300_2291 SAUSA300_0809 SAUSA300_1566 SAUSA300_0001 SAUSA300_0609 SAUSA300_0295 SAUSA300_0574 SAUSA300_1357 SAUSA300_2213 SAUSA300_1305 SAUSA300_1393 SAUSA300_1063 SAUSA300_2234 SAUSA300_1154 SAUSA300_2516 SAUSA300_1177 SAUSA300_1855 SAUSA300_1072 SAUSA300_2221 SAUSA300_2552 SAUSA300_0203 SAUSA300_0957 SAUSA300_1877 SAUSA300_2005 SAUSA300_1440 SAUSA300_1012 SAUSA300_2624 SAUSA300_1319 SAUSA300_1559 SAUSA300_1869 SAUSA300_0744 SAUSA300_0483 SAUSA300_0646 SAUSA300_2442 SAUSA300_1956 SAUSA300_1069 SAUSA300_1981 SAUSA300_1032 SAUSA300_0968 SAUSA300_0954 SAUSA300_1562

-12 -11.99 -11.83 -11.82 -11.8 -11.63 -11.53 -11.48 -11.37 -11.36 -11.3 -11.29 -11.21 -11.14 -11.03 -11.03 -10.95 -10.91 -10.91 -10.84 -10.81 -10.75 -10.61 -10.59 -10.59 -10.51 -10.47 -10.46 -10.38 -10.38 -10.35 -10.25 -10.18 -10.15 -10.12 -10.07 -10.02 -9.97 -9.89 -9.85 -9.84 -9.81 -9.79 -9.79 -9.78 -9.74 -9.73

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0.007 0.008 0.008 0.008 0.008 0.009 0.01 0.01 0.011 0.011 0.012 0.012 0.012 0.013 0.013 0.014 0.014 0.014 0.014 0.015 0.015 0.016 0.017 0.017 0.017 0.018 0.018 0.018 0.019 0.019 0.02 0.021 0.021 0.022 0.022 0.023 0.023 0.024 0.025 0.025 0.025 0.026 0.026 0.026 0.026 0.026 0.027

111 1 122 135 18 12 5 67 5 16 3 12 58 65 5 5 67 65 5 10 83 5 61 60 122 5 4 85 2 73 5 4 1 126 4 127 14 66 70 1 135 71 54 86 1 32 18

126 9 140 151 27 23 13 78 13 26 11 32 73 82 20 14 78 76 13 27 95 13 78 73 140 20 16 95 10 88 14 13 9 140 12 142 27 78 86 8 153 86 73 106 8 47 32

68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96

hisA hutG recQ aspS moaE arcC fhuA hprK -

SAUSA300_1963 SAUSA300_2215 SAUSA300_0340 SAUSA300_1808 SAUSA300_1448 SAUSA300_0914 SAUSA300_1427 SAUSA300_2607 SAUSA300_2281 SAUSA300_0705 SAUSA300_2404 SAUSA300_1586 SAUSA300_2222 SAUSA300_0061 SAUSA300_0299 SAUSA300_0095 SAUSA300_1035 SAUSA300_1215 SAUSA300_1181 SAUSA300_1318 SAUSA300_0384 SAUSA300_0293 SAUSA300_0633 SAUSA300_2296 SAUSA300_0026 SAUSA300_1899 SAUSA300_0743 SAUSA300_0771 SAUSA300_0569

-9.69 -9.53 -9.52 -9.48 -9.44 -9.39 -9.3 -9.27 -9.23 -9.22 -9.18 -9.18 -9.12 -9.01 -9.01 -9 -8.99 -8.98 -8.97 -8.88 -8.85 -8.81 -8.78 -8.77 -8.74 -8.74 -8.66 -8.57 -8.41

0.027 0.029 0.029 0.03 0.031 0.031 0.033 0.033 0.034 0.034 0.034 0.034 0.035 0.037 0.037 0.037 0.037 0.038 0.038 0.039 0.04 0.04 0.041 0.041 0.042 0.042 0.043 0.045 0.048

98 5 1 2 1 5 109 5 5 134 3 111 106 137 4 140 126 1 115 5 3 56 126 7 77 72 13 1 61

117 20 9 10 15 14 126 13 13 149 14 126 126 153 14 153 140 8 129 13 11 73 140 15 96 89 26 9 76

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

ahpF oppB moaD ung splA oppA nusB panB -

SAUSA300_0285 SAUSA300_0379 SAUSA300_0887 SAUSA300_2221 SAUSA300_2552 SAUSA300_0563 SAUSA300_1758 SAUSA300_1453 SAUSA300_0891 SAUSA300_1473 SAUSA300_0872 SAUSA300_1939 SAUSA300_1435 SAUSA300_2534 SAUSA300_1742 SAUSA300_2143

-18.31 -16.71 -16.57 -16.5 -16.28 -15.71 -15.48 -14.35 -14.31 -14.17 -13.95 -13.59 -13.51 -13.47 -13.39 -13.32

0 0 0 0 0 0 0 0.001 0.001 0.001 0.002 0.002 0.003 0.003 0.003 0.003

17 134 419 387 388 442 379 447 142 53 8 96 308 95 185 384

37 152 434 396 402 456 397 464 156 66 22 111 319 109 202 395

SAUSA300s177

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17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63

crtM SAUSA300_2499 trpB SAUSA300_1267 SAUSA300_0284 SAUSA300_2113 fabF SAUSA300_0886 SAUSA300_1065 gudB SAUSA300_0861 SAUSA300_0132 SAUSA300_0930 SAUSA300_1211 splF SAUSA300_1753 tyrS SAUSA300_1675 SAUSA300_2453 rpsE SAUSA300_2187 SAUSA300_0027 SAUSA300_1218 atpG SAUSA300_2059 SAUSA300_0604 rocD SAUSA300_0860 opp-2B SAUSA300_1276 thrS SAUSA300_1629 SAUSA300_0195 SAUSA300_2404 hemL SAUSA300_1614 folC SAUSA300_1610 pepS SAUSA300_1860 SAUSA300_0901 SAUSA300_1433 SAUSA300_0997 oppF SAUSA300_0893 SAUSA300_1898 SAUSA300_0194 SAUSA300_0681 SAUSA300_1938 holA SAUSA300_1546 SAUSA300_1795 phnE SAUSA300_0143 SAUSA300_1466 SAUSA300_0592 ggt SAUSA300_0204 SAUSA300_1118 rplV SAUSA300_2199 SAUSA300_0417 SAUSA300_1482 SAUSA300_1314 SAUSA300_1129 rimM SAUSA300_1132

-13.31 -13.29 -13.2 -13.13 -13.1 -13.03 -13.02 -12.97 -12.91 -12.69 -12.65 -12.65 -12.6 -12.58 -12.42 -12.38 -12.34 -12.19 -12.16 -12.04 -11.98 -11.73 -11.63 -11.58 -11.52 -11.49 -11.48 -11.43 -11.38 -11.15 -11.09 -11.07 -11.03 -10.97 -10.95 -10.92 -10.88 -10.83 -10.77 -10.75 -10.64 -10.57 -10.54 -10.49 -10.43 -10.4 -10.39

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0.003 0.003 0.003 0.003 0.003 0.004 0.004 0.004 0.004 0.005 0.005 0.005 0.005 0.005 0.006 0.006 0.006 0.007 0.007 0.007 0.008 0.009 0.009 0.01 0.01 0.01 0.01 0.011 0.011 0.013 0.013 0.013 0.014 0.014 0.014 0.014 0.015 0.015 0.016 0.016 0.017 0.017 0.018 0.018 0.019 0.019 0.019

139 21 401 372 391 43 20 205 302 140 40 391 199 389 389 209 197 384 16 388 390 79 382 198 16 389 218 385 81 375 193 389 81 198 13 194 192 391 389 391 389 198 82 397 95 192 286

151 31 421 392 402 55 31 223 319 154 55 403 211 398 401 229 212 396 32 398 402 94 397 208 30 402 232 400 101 391 211 399 100 216 28 212 203 403 402 402 399 212 101 416 110 210 305

64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110

hslO dnaA sucD uvrB int rnr purL purE argC dnaK rpsS cap5F glvC aroK gap topB hemL -

SAUSA300_0490 SAUSA300_0178 SAUSA300_2102 SAUSA300_0001 SAUSA300_0740 SAUSA300_2262 SAUSA300_0688 SAUSA300_0325 SAUSA300_1139 SAUSA300_1792 SAUSA300_0171 SAUSA300_1390 SAUSA300_0413 SAUSA300_0741 SAUSA300_1515 SAUSA300_0211 SAUSA300_0799 SAUSA300_0764 SAUSA300_0971 SAUSA300_0579 SAUSA300_2418 SAUSA300_2215 SAUSA300_0609 SAUSA300_0966 SAUSA300_0231 SAUSA300_2247 SAUSA300_0186 SAUSA300_0010 SAUSA300_1540 SAUSA300_0333 SAUSA300_2200 SAUSA300_0205 SAUSA300_0301 SAUSA300_0157 SAUSA300_2368 SAUSA300_0340 SAUSA300_2270 SAUSA300_1499 SAUSA300_2361 SAUSA300_0756 SAUSA300_2208 SAUSA300_2318 SAUSA300_0294 SAUSA300_2101 SAUSA300_2338 SAUSA300_1845 SAUSA300_0110

-10.36 -10.35 -10.26 -10.23 -10.22 -10.14 -10.12 -10.07 -10.05 -9.92 -9.89 -9.88 -9.88 -9.87 -9.79 -9.77 -9.75 -9.72 -9.64 -9.63 -9.58 -9.53 -9.53 -9.49 -9.47 -9.46 -9.44 -9.39 -9.39 -9.38 -9.35 -9.35 -9.34 -9.33 -9.28 -9.28 -9.19 -9.14 -9.14 -9.09 -9.06 -9.03 -9.02 -8.99 -8.94 -8.91 -8.87

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0.019 0.02 0.02 0.021 0.021 0.022 0.022 0.023 0.023 0.024 0.025 0.025 0.025 0.025 0.026 0.026 0.026 0.027 0.028 0.028 0.029 0.029 0.029 0.03 0.03 0.03 0.031 0.031 0.031 0.031 0.032 0.032 0.032 0.032 0.033 0.033 0.034 0.035 0.035 0.036 0.036 0.037 0.037 0.037 0.038 0.039 0.039

308 162 157 108 385 43 327 68 29 81 141 353 81 349 140 386 388 389 389 313 302 358 383 188 292 267 389 195 18 307 132 202 256 305 202 386 212 140 389 201 419 344 256 96 162 367 383

319 181 170 124 397 60 347 86 49 101 152 364 101 365 151 396 398 404 402 331 319 374 395 205 310 286 403 211 33 320 150 218 275 319 217 402 227 154 398 214 437 364 275 111 176 382 402

111 112 113 114 115 116 117 118

cap5G arcC rpsC lacB -

SAUSA300_0158 SAUSA300_0773 SAUSA300_0565 SAUSA300_1063 SAUSA300_2198 SAUSA300_2154 SAUSA300_0739 SAUSA300_2382

-8.8 -8.78 -8.77 -8.53 -8.37 -8.37 -8.36 -8.35

0.041 0.041 0.041 0.045 0.048 0.048 0.049 0.049

299 17 403 9 389 166 195 70

310 34 417 24 398 180 211 86

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

splA argR ureC rpsK arcA glmM clpP murA hemL folA sbcC rarD

SAUSA300_0010 SAUSA300_1758 SAUSA300_2143 SAUSA300_0066 SAUSA300_0987 SAUSA300_2131 SAUSA300_2240 SAUSA300_2179 SAUSA300_0065 SAUSA300_0880 SAUSA300_1969 SAUSA300_2453 SAUSA300_0295 SAUSA300_1218 SAUSA300_1207 SAUSA300_0212 SAUSA300_2111 SAUSA300_0916 SAUSA300_1453 SAUSA300_0752 SAUSA300_2321 SAUSA300_2078 SAUSA300_1614 SAUSA300_1319 SAUSA300_1243 SAUSA300_2448 SAUSA300_0740 SAUSA300_0610 SAUSA300_0030 SAUSA300_2522 SAUSA300_2402 SAUSA300_0376 SAUSA300_0576 SAUSA300_2628

-16.6 -15.44 -13.88 -13.72 -13.64 -13.26 -12.58 -12.32 -12.32 -11.95 -11.77 -11.67 -11.55 -11.53 -11.47 -11.46 -11.43 -11.35 -11.34 -11.25 -11.24 -11.16 -10.8 -10.74 -10.64 -10.55 -10.5 -10.42 -10.39 -10.34 -10.32 -10.26 -10.26 -10.03

0 0 0.002 0.002 0.002 0.003 0.005 0.006 0.006 0.008 0.009 0.009 0.01 0.01 0.01 0.01 0.011 0.011 0.011 0.012 0.012 0.013 0.015 0.016 0.017 0.018 0.018 0.019 0.019 0.02 0.02 0.021 0.021 0.023

15 12 17 14 19 20 19 19 19 14 16 16 12 20 181 19 16 19 19 5 15 16 21 19 19 20 15 14 12 19 19 158 19 18

32 28 30 28 33 34 28 31 31 28 31 32 28 31 192 31 29 29 31 25 27 32 30 32 31 31 28 29 28 34 29 170 28 31

SAUSA300s182 SAUSA300s186 SAUSA300s193

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35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53

atpD menB scrB malR rumA rocF arcD rplW rpsE

SAUSA300_2058 SAUSA300_2037 SAUSA300_0948 SAUSA300_1929 SAUSA300_2128 SAUSA300_2259 SAUSA300_0409 SAUSA300_1994 SAUSA300_1457 SAUSA300_1099 SAUSA300_2619 SAUSA300_1701 SAUSA300_1878 SAUSA300_2114 SAUSA300_1082 SAUSA300_2568 SAUSA300_1397 SAUSA300_2202 SAUSA300_2187

-9.99 -9.97 -9.91 -9.78 -9.55 -9.43 -9.38 -9.37 -8.8 -8.73 -8.65 -8.54 -8.48 -8.46 -8.43 -8.39 -8.35 -8.34 -8.33

0.023 0.024 0.024 0.026 0.029 0.031 0.031 0.032 0.041 0.042 0.043 0.045 0.046 0.047 0.047 0.048 0.049 0.049 0.049

19 20 19 19 17 14 214 19 15 19 19 23 16 19 13 20 14 17 19

29 34 29 32 28 34 224 28 26 28 28 36 25 31 33 34 27 31 29

1 2 3 4 5 6 7 8 9 10 11

rplQ dltD efb narI

SAUSA300_0671 SAUSA300_0217 SAUSA300_0269 SAUSA300_2384 SAUSA300_2177 SAUSA300_0304 SAUSA300_1324 SAUSA300_0838 SAUSA300_1055 SAUSA300_0982 SAUSA300_2340

-10.01 -9.82 -9.6 -9.28 -9.1 -9.05 -8.91 -8.87 -8.76 -8.66 -8.42

0.023 0.026 0.028 0.033 0.036 0.036 0.039 0.039 0.041 0.043 0.048

112 112 75 1 83 15 85 105 104 74 76

120 120 90 14 97 28 97 117 113 91 84

1 2 3 4 5 6 7 8 9 10 11

rpe birA pyrE -

SAUSA300_0710 SAUSA300_2473 SAUSA300_1115 SAUSA300_0990 SAUSA300_0132 SAUSA300_1347 SAUSA300_1098 SAUSA300_0283 SAUSA300_2097 SAUSA300_2451 SAUSA300_1210

-16.32 -12.57 -10.77 -10.36 -9.51 -9.29 -9.27 -9.22 -9.22 -9.19 -8.71

0 0.005 0.016 0.019 0.03 0.033 0.033 0.034 0.034 0.034 0.042

60 67 46 67 34 35 48 35 32 68 47

80 80 57 76 51 51 57 43 47 76 61

SAUSA300s199 SAUSA300s201

SAUSA300s204

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12 13 14 15 16 17

icaA cap5O -

SAUSA300_2600 SAUSA300_0495 SAUSA300_2337 SAUSA300_0166 SAUSA300_0805 SAUSA300_0679

-8.69 -8.66 -8.63 -8.49 -8.47 -8.36

0.042 0.043 0.044 0.046 0.047 0.049

48 40 1 63 48 48

57 51 12 73 61 59

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

bioA folK gidB rpsT

SAUSA300_2384 SAUSA300_0724 SAUSA300_2490 SAUSA300_2472 SAUSA300_2372 SAUSA300_0428 SAUSA300_0334 SAUSA300_0494 SAUSA300_2644 SAUSA300_0268 SAUSA300_0859 SAUSA300_1963 SAUSA300_1910 SAUSA300_1106 SAUSA300_1545

-12.91 -12.66 -11.63 -10.37 -10.23 -10.13 -9.78 -9.72 -9.43 -8.89 -8.85 -8.52 -8.41 -8.39 -8.39

0.004 0.005 0.009 0.019 0.021 0.022 0.026 0.027 0.031 0.039 0.04 0.046 0.048 0.048 0.048

72 45 69 49 73 46 56 4 72 73 56 50 124 3 60

89 64 84 65 86 60 68 17 86 82 66 65 135 20 73

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

pstA pheA splD panB gltX manA ald fruB modA

SAUSA300_1281 SAUSA300_1896 SAUSA300_0618 SAUSA300_1755 SAUSA300_2534 SAUSA300_2418 SAUSA300_0513 SAUSA300_2577 SAUSA300_2421 SAUSA300_0346 SAUSA300_1930 SAUSA300_1745 SAUSA300_1331 SAUSA300_2579 SAUSA300_2093 SAUSA300_0917 SAUSA300_1354 SAUSA300_0684 SAUSA300_1135 SAUSA300_2320 SAUSA300_1086 SAUSA300_2230

-20.31 -16 -14.21 -12.48 -12.22 -11.43 -10.33 -10.31 -10.3 -10.09 -10 -10 -9.88 -9.77 -9.76 -9.73 -9.47 -9.45 -9.31 -9.27 -9.25 -9.22

0 0 0.001 0.005 0.006 0.011 0.02 0.02 0.02 0.022 0.023 0.023 0.025 0.026 0.026 0.027 0.03 0.03 0.032 0.033 0.033 0.034

103 96 108 38 105 7 39 88 96 144 126 87 7 112 43 114 84 111 87 74 3 42

120 110 123 51 122 21 50 101 106 160 140 101 20 123 57 124 93 123 103 87 21 53

SAUSA300s208

SAUSA300s211

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23 24 25 26 27 28 29 30 31 32 33

epiB spxA atpG nrdR -

SAUSA300_0097 SAUSA300_0128 SAUSA300_1766 SAUSA300_1380 SAUSA300_2311 SAUSA300_0898 SAUSA300_2059 SAUSA300_2381 SAUSA300_2209 SAUSA300_1632 SAUSA300_1068

-9.16 -9.09 -8.73 -8.67 -8.67 -8.66 -8.63 -8.61 -8.54 -8.34 -8.3

0.035 0.036 0.042 0.043 0.043 0.043 0.043 0.044 0.045 0.049 0.05

31 82 106 110 105 104 76 87 86 6 122

47 96 118 122 119 118 87 104 97 18 130

1 2 3 4 5 6 7 8 9 10 11 12 13 14

cls lytN sucC truA coaD fhuG

SAUSA300_2044 SAUSA300_1140 SAUSA300_1060 SAUSA300_2332 SAUSA300_1138 SAUSA300_2290 SAUSA300_1905 SAUSA300_2173 SAUSA300_1220 SAUSA300_1665 SAUSA300_1024 SAUSA300_0314 SAUSA300_1375 SAUSA300_0635

-14.83 -13.6 -13.5 -11.39 -10.72 -9.83 -9.7 -9.36 -9.33 -9 -8.53 -8.42 -8.42 -8.38

0.001 0.002 0.003 0.011 0.016 0.025 0.027 0.032 0.032 0.037 0.045 0.047 0.047 0.048

1 10 16 16 8 27 6 21 21 20 9 28 20 28

20 24 32 30 18 38 26 35 37 34 18 37 35 42

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

fhuB yajC arcA rnc sbcC

SAUSA300_2304 SAUSA300_2423 SAUSA300_0634 SAUSA300_0479 SAUSA300_1335 SAUSA300_0023 SAUSA300_0034 SAUSA300_0135 SAUSA300_1594 SAUSA300_2570 SAUSA300_1944 SAUSA300_1032 SAUSA300_0413 SAUSA300_0519 SAUSA300_1126 SAUSA300_1967 SAUSA300_1637 SAUSA300_1243

-13.4 -12.48 -11.86 -11.59 -11.28 -10.28 -9.89 -9.54 -9.36 -9.34 -9.3 -9.18 -9.17 -8.8 -8.69 -8.66 -8.6 -8.5

0.003 0.005 0.008 0.01 0.012 0.02 0.025 0.029 0.032 0.032 0.033 0.034 0.035 0.041 0.042 0.043 0.044 0.046

50 23 20 5 3 6 63 17 20 1 18 21 4 22 23 28 21 17

65 42 29 15 12 14 70 25 31 13 34 33 14 34 37 43 34 34

SAUSA300s212

SAUSA300s213

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19 -

SAUSA300_1912

-8.36

0.049

20

31

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

fruA arcC arcC dapD cap5J rnc ftsL adh nrdF isaB pdhB pyc ftsK msrA clpC panE -

SAUSA300_0685 SAUSA300_1450 SAUSA300_0484 SAUSA300_2259 SAUSA300_1491 SAUSA300_1063 SAUSA300_0061 SAUSA300_2348 SAUSA300_1926 SAUSA300_1290 SAUSA300_0161 SAUSA300_1947 SAUSA300_0206 SAUSA300_0329 SAUSA300_1126 SAUSA300_1074 SAUSA300_0475 SAUSA300_0589 SAUSA300_0681 SAUSA300_0594 SAUSA300_0717 SAUSA300_2573 SAUSA300_0994 SAUSA300_2137 SAUSA300_1576 SAUSA300_1014 SAUSA300_1169 SAUSA300_0172 SAUSA300_1256 SAUSA300_1050 SAUSA300_0362 SAUSA300_0510 SAUSA300_2535 SAUSA300_1172 SAUSA300_1129 SAUSA300_1703 SAUSA300_1394 SAUSA300_1299

-12.9 -12.87 -12.57 -11.81 -11.62 -11.6 -11.58 -11.52 -11.47 -11.39 -11.3 -10.99 -10.87 -10.82 -10.7 -10.69 -10.43 -10.26 -10.25 -10.18 -10 -9.96 -9.94 -9.86 -9.72 -9.72 -9.71 -9.47 -9.38 -9.36 -9.28 -9.13 -9.11 -8.97 -8.91 -8.66 -8.66 -8.35

0.004 0.004 0.005 0.008 0.01 0.01 0.01 0.01 0.01 0.011 0.012 0.014 0.015 0.015 0.016 0.016 0.019 0.02 0.021 0.021 0.023 0.024 0.024 0.025 0.027 0.027 0.027 0.03 0.031 0.032 0.033 0.035 0.036 0.038 0.039 0.043 0.043 0.049

36 92 88 152 100 153 97 65 27 101 177 152 97 103 100 155 91 153 151 99 86 155 100 60 86 97 65 105 105 104 87 103 82 37 64 33 15 86

55 110 107 168 111 167 112 79 43 109 188 167 108 115 119 170 105 165 165 113 101 167 110 75 106 110 79 117 119 116 107 111 96 50 79 45 27 97

ndk

SAUSA300_0041 SAUSA300_1352 SAUSA300_2433 SAUSA300_1358

-12.01 -10.53 -10 -9.82

0.007 0.018 0.023 0.026

11 20 16 8

19 35 33 20

SAUSA300s214

SAUSA300s215 1 2 3 4

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5 6 7 8 9

scrB spsA

SAUSA300_0508 SAUSA300_0286 SAUSA300_1994 SAUSA300_1050 SAUSA300_0867

-9.09 -8.85 -8.76 -8.67 -8.62

0.036 0.04 0.041 0.043 0.044

11 10 5 8 2

20 23 16 19 17

lysS SAUSA300_0496 SAUSA300_0102 SAUSA300_1530 SAUSA300_0243 SAUSA300_0239 SAUSA300_0012 plsX SAUSA300_1122 SAUSA300_2436 SAUSA300_0147 SAUSA300_0418 priA SAUSA300_1105 glnR SAUSA300_1200 SAUSA300_0574 SAUSA300_1858 cap5P SAUSA300_0167 SAUSA300_1786 SAUSA300_2425 SAUSA300_0030 opp-1ASAUSA300_2411 rplF SAUSA300_2189 SAUSA300_1374 SAUSA300_0072 SAUSA300_1397 crtN SAUSA300_2498 sucD SAUSA300_1139 SAUSA300_1349 SAUSA300_1780 SAUSA300_0681 SAUSA300_1792 SAUSA300_1170 SAUSA300_0979 SAUSA300_2162 folA SAUSA300_1319 SAUSA300_0881 prfC SAUSA300_0921 SAUSA300_1606 SAUSA300_1284 cap5B SAUSA300_0153 gudB SAUSA300_0861 SAUSA300_1981

-17.21 -15.4 -14.02 -14 -13.95 -13.7 -13.7 -13.61 -13.23 -13.07 -13.07 -12.94 -12.92 -12.83 -12.67 -12.66 -12.38 -12.27 -12.12 -12.08 -12.08 -12.05 -11.95 -11.8 -11.76 -11.74 -11.54 -11.19 -11.17 -11.13 -11.11 -10.95 -10.9 -10.85 -10.85 -10.8 -10.69 -10.65 -10.6 -10.58

0 0 0.002 0.002 0.002 0.002 0.002 0.002 0.003 0.004 0.004 0.004 0.004 0.004 0.005 0.005 0.006 0.006 0.007 0.007 0.007 0.007 0.008 0.008 0.009 0.009 0.01 0.012 0.012 0.013 0.013 0.014 0.015 0.015 0.015 0.015 0.016 0.017 0.017 0.017

122 78 127 127 112 116 78 92 77 72 92 124 138 114 115 46 124 126 117 115 128 79 117 117 72 109 127 141 142 114 84 40 128 128 118 123 128 70 113 143

141 88 138 142 127 132 88 106 88 85 103 136 157 128 130 60 142 140 137 127 142 88 132 137 88 126 141 156 160 127 104 52 143 137 138 137 143 84 130 160

SAUSA300s216 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

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41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86

recN lpdA queA murC prmA ptsH engA gltS glpP fruA oppA pbp2 pnpA rex yfiA rpsL arcD -

SAUSA300_0954 SAUSA300_0414 SAUSA300_0170 SAUSA300_1468 SAUSA300_0587 SAUSA300_0996 SAUSA300_1596 SAUSA300_1686 SAUSA300_2279 SAUSA300_0872 SAUSA300_0832 SAUSA300_1538 SAUSA300_0983 SAUSA300_0269 SAUSA300_1364 SAUSA300_0662 SAUSA300_2291 SAUSA300_1190 SAUSA300_0685 SAUSA300_0891 SAUSA300_1341 SAUSA300_1167 SAUSA300_1999 SAUSA300_1977 SAUSA300_2491 SAUSA300_1971 SAUSA300_0736 SAUSA300_2026 SAUSA300_1470 SAUSA300_1303 SAUSA300_0023 SAUSA300_0484 SAUSA300_0530 SAUSA300_0064 SAUSA300_1945 SAUSA300_2386 SAUSA300_0565 SAUSA300_2622 SAUSA300_1952 SAUSA300_1346 SAUSA300_1928 SAUSA300_1584 SAUSA300_2494 SAUSA300_2248 SAUSA300_0139 SAUSA300_2147

-10.58 -10.45 -10.41 -10.4 -10.34 -10.33 -10.24 -10.22 -10.18 -10.16 -10.14 -10.11 -10 -9.96 -9.9 -9.79 -9.72 -9.7 -9.68 -9.6 -9.59 -9.4 -9.38 -9.32 -9.28 -9.19 -9.18 -9.17 -9.13 -9.11 -9.03 -8.98 -8.95 -8.91 -8.83 -8.83 -8.76 -8.66 -8.62 -8.6 -8.57 -8.54 -8.53 -8.48 -8.32 -8.3

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0.017 0.019 0.019 0.019 0.02 0.02 0.021 0.021 0.021 0.022 0.022 0.022 0.023 0.024 0.025 0.026 0.027 0.027 0.027 0.028 0.029 0.031 0.031 0.032 0.033 0.034 0.034 0.035 0.035 0.035 0.037 0.038 0.038 0.039 0.04 0.04 0.041 0.043 0.044 0.044 0.045 0.045 0.045 0.046 0.049 0.05

46 72 127 161 70 69 121 140 68 112 134 42 128 137 118 123 124 77 96 112 135 123 117 110 72 132 127 103 77 79 37 130 123 101 138 43 126 128 116 127 122 91 168 73 120 86

58 85 138 177 84 81 139 154 77 123 149 55 138 152 137 134 136 89 110 127 154 133 137 124 87 151 141 123 88 89 51 144 138 111 152 53 136 137 130 141 137 105 177 87 131 106

SAUSA300s219 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

purR phoB deoC tig oxaA rpsM aldA2 mnhE mraW splA ear dgkA -

SAUSA300_2584 SAUSA300_0473 SAUSA300_1380 SAUSA300_2561 SAUSA300_2099 SAUSA300_0126 SAUSA300_0790 SAUSA300_2090 SAUSA300_1622 SAUSA300_0578 SAUSA300_0646 SAUSA300_1354 SAUSA300_1450 SAUSA300_1648 SAUSA300_2046 SAUSA300_2180 SAUSA300_0274 SAUSA300_0805 SAUSA300_2560 SAUSA300_1463 SAUSA300_1021 SAUSA300_1901 SAUSA300_2433 SAUSA300_1082 SAUSA300_1899 SAUSA300_0851 SAUSA300_1954 SAUSA300_1073 SAUSA300_0618 SAUSA300_1758 SAUSA300_0815 SAUSA300_1328 SAUSA300_1529 SAUSA300_0979 SAUSA300_0302 SAUSA300_0060 SAUSA300_0294 SAUSA300_0372 SAUSA300_0550

-16.8 -15.67 -14.5 -13.3 -12.95 -12.57 -11.83 -11.56 -11.1 -10.67 -10.54 -10.33 -10.29 -10.23 -10.1 -10.05 -10.04 -10 -9.99 -9.9 -9.87 -9.87 -9.73 -9.66 -9.61 -9.56 -9.3 -9.15 -9.14 -9.06 -8.93 -8.86 -8.84 -8.8 -8.72 -8.69 -8.62 -8.58 -8.44

0 0 0.001 0.003 0.004 0.005 0.008 0.01 0.013 0.016 0.018 0.02 0.02 0.021 0.022 0.023 0.023 0.023 0.023 0.025 0.025 0.025 0.027 0.028 0.028 0.029 0.033 0.035 0.035 0.036 0.038 0.04 0.04 0.041 0.042 0.043 0.044 0.044 0.047

199 157 207 225 209 208 152 223 136 219 130 46 204 161 131 50 39 229 130 105 43 232 209 52 132 216 150 78 208 82 134 135 45 44 81 152 81 46 139

215 173 225 239 227 225 166 232 150 239 145 59 214 175 142 60 51 239 142 115 60 248 224 65 146 229 161 93 225 96 146 147 61 57 96 165 96 60 157

1 2 3 4 5

rsbU ansA tdk

SAUSA300_2025 SAUSA300_0597 SAUSA300_1368 SAUSA300_0733 SAUSA300_2073

-13.57 -11.83 -9.63 -9.6 -9.38

0.002 0.008 0.028 0.028 0.031

33 53 52 7 38

47 68 67 22 52

SAUSA300s221

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6 7 8 9 10 11 12

glvC ksgA betB -

SAUSA300_2246 SAUSA300_1374 SAUSA300_2270 SAUSA300_0470 SAUSA300_2546 SAUSA300_0428 SAUSA300_0023

-9.13 -9.08 -8.94 -8.67 -8.56 -8.46 -8.39

0.035 0.036 0.038 0.043 0.045 0.047 0.048

33 4 2 4 52 57 38

51 15 13 13 70 67 52

1 2 3 4 5 6 7 8 9 10 11 12 13

aroK accB -

SAUSA300_1879 SAUSA300_0733 SAUSA300_1274 SAUSA300_2472 SAUSA300_2040 SAUSA300_0234 SAUSA300_0176 SAUSA300_1499 SAUSA300_0232 SAUSA300_2632 SAUSA300_1476 SAUSA300_1665 SAUSA300_0428

-12.3 -12.06 -11.98 -11.78 -11.47 -10.93 -10.27 -10.25 -9.28 -9.09 -8.93 -8.72 -8.4

0.006 0.007 0.008 0.009 0.01 0.014 0.02 0.021 0.033 0.036 0.038 0.042 0.048

34 1 48 38 40 39 36 50 34 22 22 6 9

49 15 63 53 48 55 45 62 51 32 37 25 28

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23

atpH scrR arcC mfd murI sucD -

SAUSA300_0710 SAUSA300_2061 SAUSA300_1129 SAUSA300_1995 SAUSA300_0981 SAUSA300_1418 SAUSA300_1275 SAUSA300_0061 SAUSA300_1952 SAUSA300_0775 SAUSA300_1400 SAUSA300_0481 SAUSA300_2138 SAUSA300_2069 SAUSA300_0254 SAUSA300_2305 SAUSA300_0289 SAUSA300_1049 SAUSA300_1139 SAUSA300_1248 SAUSA300_0251 SAUSA300_0630 SAUSA300_1417

-17.95 -14.01 -11.62 -11.39 -11.21 -11.18 -11.14 -11.07 -10.64 -10.38 -10.22 -10.19 -10.16 -10.13 -9.78 -9.75 -9.57 -9.52 -9.39 -9.38 -9.35 -9.25 -9.22

0 0.002 0.009 0.011 0.012 0.012 0.013 0.013 0.017 0.019 0.021 0.021 0.021 0.022 0.026 0.026 0.029 0.029 0.031 0.031 0.032 0.033 0.034

3 47 49 50 49 51 47 50 51 37 5 26 41 51 27 3 1 51 44 10 50 48 44

18 59 61 58 63 61 58 59 61 49 18 38 55 63 40 11 16 63 62 25 58 61 58

SAUSA300s222

SAUSA300s223

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24 25 26 27 28 29 30 31 32 33 34 35 36

holA rarD murD murC sspB rpe -

SAUSA300_2540 SAUSA300_1546 SAUSA300_1210 SAUSA300_2628 SAUSA300_1077 SAUSA300_2542 SAUSA300_1853 SAUSA300_1686 SAUSA300_0339 SAUSA300_1325 SAUSA300_0950 SAUSA300_1115 SAUSA300_0796

-9.22 -9 -8.87 -8.85 -8.81 -8.7 -8.7 -8.65 -8.63 -8.58 -8.48 -8.41 -8.3

0.034 0.037 0.039 0.04 0.04 0.042 0.042 0.043 0.044 0.044 0.046 0.048 0.05

41 23 43 38 35 36 53 50 50 1 51 21 44

53 40 51 49 49 51 61 62 60 16 61 37 63

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

recN hsdS xerD rpsK sucD purL trmB def rpsM hslV -

SAUSA300_1468 SAUSA300_1961 SAUSA300_0406 SAUSA300_1751 SAUSA300_2559 SAUSA300_1447 SAUSA300_2360 SAUSA300_0646 SAUSA300_1416 SAUSA300_2179 SAUSA300_0567 SAUSA300_1947 SAUSA300_0587 SAUSA300_1139 SAUSA300_0971 SAUSA300_1254 SAUSA300_1350 SAUSA300_1807 SAUSA300_1694 SAUSA300_0991 SAUSA300_2350 SAUSA300_0489 SAUSA300_0924 SAUSA300_2180 SAUSA300_1842 SAUSA300_1934 SAUSA300_1716 SAUSA300_1146 SAUSA300_2145 SAUSA300_2260 SAUSA300_0773 SAUSA300_0939

-17.54 -14.88 -13.82 -13.82 -12.69 -12.55 -11.64 -11.62 -11.48 -11.43 -10.98 -10.97 -10.66 -10.58 -10.54 -10.42 -10 -9.99 -9.96 -9.95 -9.91 -9.85 -9.83 -9.77 -9.75 -9.74 -9.59 -9.59 -9.52 -9.42 -9.35 -9.1

0 0.001 0.002 0.002 0.005 0.005 0.009 0.01 0.01 0.011 0.014 0.014 0.017 0.017 0.018 0.019 0.023 0.023 0.024 0.024 0.024 0.025 0.025 0.026 0.026 0.027 0.028 0.029 0.029 0.031 0.032 0.036

162 172 160 160 76 175 163 169 170 174 157 238 64 172 180 67 243 92 172 160 160 277 177 181 164 63 170 161 89 70 261 177

181 189 175 175 91 187 177 187 187 187 172 252 82 187 192 80 254 105 183 177 175 291 192 192 180 77 184 180 104 82 275 187

SAUSA300s225

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33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

srrA sdhA hutU folA

SAUSA300_2473 SAUSA300_0105 SAUSA300_2524 SAUSA300_1442 SAUSA300_1871 SAUSA300_2552 SAUSA300_0234 SAUSA300_1971 SAUSA300_0579 SAUSA300_0050 SAUSA300_1047 SAUSA300_0899 SAUSA300_1399 SAUSA300_2278 SAUSA300_1319

-9.07 -9.05 -8.97 -8.86 -8.84 -8.83 -8.81 -8.8 -8.77 -8.64 -8.64 -8.6 -8.57 -8.54 -8.31

0.036 0.036 0.038 0.04 0.04 0.04 0.04 0.041 0.041 0.043 0.043 0.044 0.045 0.045 0.05

66 172 163 58 159 70 159 172 161 73 41 238 70 76 81

77 187 177 76 174 87 175 191 176 87 54 252 82 96 94

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

ansA tnp rplT sgtB mecA rpsS aroK sucB

SAUSA300_0809 SAUSA300_1368 SAUSA300_2300 SAUSA300_1810 SAUSA300_2115 SAUSA300_2043 SAUSA300_1625 SAUSA300_0509 SAUSA300_2160 SAUSA300_1086 SAUSA300_0519 SAUSA300_0565 SAUSA300_1855 SAUSA300_0652 SAUSA300_1877 SAUSA300_1734 SAUSA300_0356 SAUSA300_2206 SAUSA300_1971 SAUSA300_2563 SAUSA300_1033 SAUSA300_1802 SAUSA300_0032 SAUSA300_2200 SAUSA300_1499 SAUSA300_1305

-14.1 -12.72 -12.62 -11.86 -11.86 -11.47 -11.15 -10.58 -10.19 -9.91 -9.79 -9.53 -9.41 -9.09 -9.08 -9.06 -9.04 -8.98 -8.95 -8.94 -8.93 -8.75 -8.71 -8.71 -8.6 -8.6

0.002 0.005 0.005 0.008 0.008 0.01 0.013 0.017 0.021 0.024 0.026 0.029 0.031 0.036 0.036 0.036 0.037 0.037 0.038 0.038 0.038 0.041 0.042 0.042 0.044 0.044

1 52 40 40 40 32 17 28 43 31 57 29 24 26 26 38 34 45 28 46 18 33 15 20 27 20

18 68 54 56 56 44 35 41 54 43 67 38 43 39 40 46 52 53 41 57 38 46 30 35 43 38

SAUSA300_2406 SAUSA300_1424

-14.53 -13.58

0.001 0.002

154 94

167 112

SAUSA300s226

SAUSA300s230 12-

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3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49

SAUSA300_0934 ipdC SAUSA300_0190 rplL SAUSA300_0525 SAUSA300_1183 SAUSA300_0206 SAUSA300_0215 rnc SAUSA300_1126 SAUSA300_0438 SAUSA300_0608 SAUSA300_0716 gltD SAUSA300_0446 SAUSA300_0936 sucB SAUSA300_1305 SAUSA300_0252 SAUSA300_2087 SAUSA300_0214 SAUSA300_2259 acpP SAUSA300_1125 SAUSA300_0632 hisS SAUSA300_1587 SAUSA300_1161 SAUSA300_0285 rnpA SAUSA300_2647 SAUSA300_0589 sbcD SAUSA300_1242 SAUSA300_0545 SAUSA300_1397 opp-1ASAUSA300_2411 rpsM SAUSA300_2180 murA SAUSA300_2078 def SAUSA300_0991 parC SAUSA300_1251 SAUSA300_1902 SAUSA300_2232 SAUSA300_0735 SAUSA300_0953 agrB SAUSA300_1989 oppB SAUSA300_0895 accC SAUSA300_1563 SAUSA300_1173 tgt SAUSA300_1595 oppF SAUSA300_0890 proC SAUSA300_1452 SAUSA300_1932 SAUSA300_0575 SAUSA300_1407 SAUSA300_0797

-12.73 -12.17 -11.88 -11.8 -11.66 -11.47 -11.38 -11.32 -11.32 -11.32 -11.27 -11.23 -11.06 -11.05 -11.02 -10.75 -10.72 -10.65 -10.61 -10.53 -10.24 -10.23 -10.07 -10.01 -9.91 -9.89 -9.82 -9.72 -9.69 -9.65 -9.64 -9.58 -9.54 -9.48 -9.45 -9.27 -9.23 -9.19 -9.12 -9.11 -9.05 -8.98 -8.93 -8.9 -8.66 -8.63 -8.62

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0.005 0.007 0.008 0.008 0.009 0.01 0.011 0.011 0.011 0.011 0.012 0.012 0.013 0.013 0.014 0.016 0.016 0.017 0.017 0.018 0.021 0.021 0.023 0.023 0.024 0.025 0.026 0.027 0.027 0.028 0.028 0.029 0.029 0.03 0.03 0.033 0.034 0.034 0.035 0.035 0.036 0.037 0.038 0.039 0.043 0.044 0.044

30 7 145 163 94 80 166 6 18 71 80 167 20 1 100 116 163 140 164 190 136 170 145 113 206 68 163 97 107 4 157 1 102 200 201 166 106 163 203 92 206 112 112 53 66 6 129

50 22 159 178 108 93 179 15 32 79 93 179 36 15 119 125 182 152 179 203 149 184 158 123 219 79 181 111 121 20 173 17 119 215 215 184 121 177 215 105 215 121 122 68 79 22 145

50 51 52 53 54 55

trpC fhuG -

SAUSA300_2464 SAUSA300_2446 SAUSA300_2542 SAUSA300_1265 SAUSA300_0635 SAUSA300_1898

-8.5 -8.5 -8.46 -8.36 -8.35 -8.34

0.046 0.046 0.047 0.049 0.049 0.049

176 1 93 145 158 15

187 18 113 159 168 30

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

argH SAUSA300_0863 SAUSA300_0283 SAUSA300_1470 SAUSA300_0299 SAUSA300_1492 SAUSA300_2578 SAUSA300_1352 SAUSA300_0296 nrdD SAUSA300_2551 atpG SAUSA300_2059 SAUSA300_0126 SAUSA300_0695 SAUSA300_0939 SAUSA300_0565 gltX SAUSA300_0513 SAUSA300_1946 oppC SAUSA300_0888 SAUSA300_1008 mqo SAUSA300_2312 SAUSA300_1656 SAUSA300_0335 splA SAUSA300_1758 SAUSA300_1354 SAUSA300_0215 SAUSA300_0059 opp-1ASAUSA300_2411 SAUSA300_2369 purC SAUSA300_0968 SAUSA300_2218 SAUSA300_0775 SAUSA300_2626 SAUSA300_1418 SAUSA300_0664 SAUSA300_0937 SAUSA300_0057 SAUSA300_2298 SAUSA300_0462 ftsL SAUSA300_1074 ilvA SAUSA300_1330

-13.55 -13.12 -12.54 -12.43 -12.24 -12.24 -12.14 -11.96 -11.81 -11.77 -11.51 -11.2 -11.17 -11.1 -11.04 -11.01 -10.71 -10.61 -10.51 -10.48 -10.21 -10.21 -10.16 -10.14 -10.05 -9.92 -9.89 -9.75 -9.67 -9.64 -9.62 -9.5 -9.43 -9.42 -9.41 -9.41 -9.38 -9.19 -9.18

0.002 0.003 0.005 0.006 0.006 0.006 0.007 0.008 0.008 0.009 0.01 0.012 0.012 0.013 0.013 0.014 0.016 0.017 0.018 0.018 0.021 0.021 0.022 0.022 0.023 0.024 0.025 0.026 0.027 0.028 0.028 0.03 0.031 0.031 0.031 0.031 0.031 0.034 0.034

54 117 107 134 141 88 89 134 98 26 86 68 100 58 25 111 99 108 140 113 114 102 119 121 120 24 119 119 138 23 33 128 119 36 108 96 92 20 35

68 127 122 149 155 101 100 149 116 40 102 81 114 69 44 128 112 126 156 127 134 116 137 131 139 44 131 130 151 38 45 139 131 50 127 115 104 35 49

SAUSA300s231

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40 41 42 43 44 45 46 47 48 49 50 51

alaS hisD sdhB gnd ychF

SAUSA300_2556 SAUSA300_1112 SAUSA300_1575 SAUSA300_1259 SAUSA300_2318 SAUSA300_2611 SAUSA300_1048 SAUSA300_1160 SAUSA300_1952 SAUSA300_1459 SAUSA300_1299 SAUSA300_0364

-9.16 -9.15 -9.11 -9.09 -9.01 -8.84 -8.82 -8.74 -8.72 -8.6 -8.54 -8.33

0.035 0.035 0.036 0.036 0.037 0.04 0.04 0.042 0.042 0.044 0.045 0.049

20 101 29 4 130 129 2 99 128 99 123 29

40 112 46 16 148 140 13 112 139 117 137 47

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

trpB rpmE2 gcvT tyrS splA sucD trpE gap purS ksgA rpe hisH -

SAUSA300_1267 SAUSA300_2074 SAUSA300_1498 SAUSA300_1785 SAUSA300_1082 SAUSA300_1675 SAUSA300_2423 SAUSA300_0177 SAUSA300_1758 SAUSA300_0578 SAUSA300_1963 SAUSA300_1877 SAUSA300_1393 SAUSA300_1139 SAUSA300_2138 SAUSA300_1194 SAUSA300_0289 SAUSA300_0630 SAUSA300_1433 SAUSA300_0418 SAUSA300_1977 SAUSA300_0483 SAUSA300_1262 SAUSA300_1633 SAUSA300_0969 SAUSA300_0060 SAUSA300_1349 SAUSA300_0470 SAUSA300_0276 SAUSA300_1115 SAUSA300_2608 SAUSA300_0056 SAUSA300_1327

-15.9 -14.42 -13.54 -13.53 -13.05 -12.89 -12.83 -12.81 -12.41 -12.31 -12 -11.89 -11.75 -11.73 -11.69 -11.44 -11.3 -11.3 -11.16 -11.15 -11.02 -10.92 -10.91 -10.8 -10.74 -10.73 -10.7 -10.68 -10.64 -10.55 -10.53 -10.46 -10.32

0 0.001 0.002 0.002 0.004 0.004 0.004 0.004 0.006 0.006 0.007 0.008 0.009 0.009 0.009 0.011 0.012 0.012 0.013 0.013 0.014 0.014 0.014 0.015 0.016 0.016 0.016 0.016 0.017 0.018 0.018 0.018 0.02

53 62 105 240 58 275 155 165 119 262 60 95 116 57 81 165 117 65 117 164 189 113 114 249 228 116 115 278 55 250 187 168 234

72 76 122 253 74 289 172 182 133 276 74 106 127 74 99 183 135 77 128 183 205 127 130 260 246 127 127 294 75 261 199 182 247

SAUSA300s233

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73

SAUSA300_2406 SAUSA300_1112 ftsK SAUSA300_1169 SAUSA300_0683 SAUSA300_1805 rimM SAUSA300_1132 SAUSA300_0871 arcC SAUSA300_0061 SAUSA300_0582 SAUSA300_1725 SAUSA300_0712 SAUSA300_1945 SAUSA300_0509 ebpS SAUSA300_1370 SAUSA300_0031 SAUSA300_1656 opp-1ASAUSA300_2411 SAUSA300_1637 SAUSA300_2480 SAUSA300_2361 SAUSA300_1879 SAUSA300_0745 SAUSA300_1170 SAUSA300_1397 SAUSA300_1277 SAUSA300_1084 cmk SAUSA300_1367 dut SAUSA300_1949 coaE SAUSA300_1634 SAUSA300_1437 SAUSA300_1930 SAUSA300_2542 pyrP SAUSA300_1092 SAUSA300_1799 SAUSA300_2289 SAUSA300_2051 SAUSA300_1842 crtN SAUSA300_2498 SAUSA300_1346 SAUSA300_1297

-10.26 -10.24 -10.2 -10.12 -10.1 -10.08 -10.08 -10.06 -10.04 -10.01 -9.94 -9.81 -9.75 -9.55 -9.38 -9.38 -9.38 -9.28 -9.27 -9.25 -9.11 -9.01 -8.87 -8.86 -8.85 -8.85 -8.84 -8.78 -8.67 -8.61 -8.6 -8.55 -8.55 -8.48 -8.45 -8.44 -8.44 -8.43 -8.35 -8.33

0.021 0.021 0.021 0.022 0.022 0.022 0.022 0.023 0.023 0.023 0.024 0.026 0.026 0.029 0.031 0.031 0.031 0.033 0.033 0.033 0.035 0.037 0.039 0.039 0.04 0.04 0.04 0.041 0.043 0.044 0.044 0.045 0.045 0.046 0.047 0.047 0.047 0.047 0.049 0.049

115 50 101 169 58 86 242 117 167 52 246 164 278 117 237 57 56 283 166 24 279 280 115 278 60 109 58 57 263 100 115 116 192 282 271 149 162 56 50 235

128 70 113 182 74 99 253 128 182 70 263 178 294 127 247 73 73 294 178 39 294 296 126 289 76 123 72 74 275 114 127 128 202 300 287 168 175 74 64 248

coa -

-13.01 -12.35 -11.31 -11.25 -11.22

0.004 0.006 0.011 0.012 0.012

104 82 92 42 127

121 96 107 58 140

SAUSA300s234 1 2 3 4 5

SAUSA300_0516 SAUSA300_2332 SAUSA300_1734 SAUSA300_0224 SAUSA300_1932

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

murA moaC cdr splA guaA thrC tuf phoU -

SAUSA300_2472 SAUSA300_0769 SAUSA300_1023 SAUSA300_2078 SAUSA300_1207 SAUSA300_0378 SAUSA300_0206 SAUSA300_0918 SAUSA300_2225 SAUSA300_1248 SAUSA300_2260 SAUSA300_1741 SAUSA300_2167 SAUSA300_0873 SAUSA300_0365 SAUSA300_2529 SAUSA300_1758 SAUSA300_0608 SAUSA300_1212 SAUSA300_0349 SAUSA300_0351 SAUSA300_0389 SAUSA300_1227 SAUSA300_0533 SAUSA300_1279 SAUSA300_2374 SAUSA300_1386 SAUSA300_1247 SAUSA300_1199

-11.19 -11.06 -10.91 -10.54 -10.52 -10.39 -10.14 -10.12 -10.12 -10.05 -9.98 -9.94 -9.86 -9.48 -9.37 -9.34 -9.11 -9.07 -9.02 -8.83 -8.82 -8.75 -8.67 -8.63 -8.6 -8.51 -8.49 -8.49 -8.43

0.012 0.013 0.014 0.018 0.018 0.019 0.022 0.022 0.022 0.023 0.024 0.024 0.025 0.03 0.032 0.032 0.035 0.036 0.037 0.04 0.04 0.041 0.043 0.044 0.044 0.046 0.046 0.046 0.047

78 131 84 129 118 117 129 71 82 108 106 105 133 142 142 120 133 101 128 93 1 129 129 129 127 93 129 46 105

92 142 96 142 126 130 140 89 96 122 121 120 147 158 159 129 144 116 142 112 11 144 140 141 145 112 141 58 121

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

bccT moeB ssb ccpA -

SAUSA300_1894 SAUSA300_1396 SAUSA300_1743 SAUSA300_2549 SAUSA300_2227 SAUSA300_0293 SAUSA300_1847 SAUSA300_1118 SAUSA300_1437 SAUSA300_0367 SAUSA300_1682 SAUSA300_1740 SAUSA300_2451 SAUSA300_1673 SAUSA300_0544 SAUSA300_0070

-19.54 -12.31 -12.13 -12.05 -12.01 -11.72 -11.45 -11.2 -11.12 -11.06 -10.64 -10.2 -10.08 -9.86 -9.53 -9.31

0 0.006 0.007 0.007 0.007 0.009 0.011 0.012 0.013 0.013 0.017 0.021 0.022 0.025 0.029 0.032

205 211 214 215 214 214 83 84 214 215 199 216 199 86 21 214

221 222 220 228 223 222 93 96 222 231 213 231 209 96 35 225

SAUSA300s237

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

17 18 19 20 21 22 23 24 25 26

purR rplQ -

SAUSA300_1503 SAUSA300_0298 SAUSA300_0281 SAUSA300_1942 SAUSA300_1249 SAUSA300_0473 SAUSA300_0183 SAUSA300_1086 SAUSA300_2177 SAUSA300_0296

-9.27 -9.16 -8.84 -8.67 -8.55 -8.42 -8.41 -8.35 -8.35 -8.34

0.033 0.035 0.04 0.043 0.045 0.047 0.048 0.049 0.049 0.049

39 214 207 213 35 201 217 63 85 214

47 222 222 221 45 211 231 71 99 222

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

recG menA mtlD phnE modB rpsP acpS glmM birA hemX glpQ argF -

SAUSA300_1120 SAUSA300_0261 SAUSA300_0944 SAUSA300_0425 SAUSA300_1224 SAUSA300_2108 SAUSA300_0281 SAUSA300_1707 SAUSA300_0142 SAUSA300_2229 SAUSA300_1131 SAUSA300_1902 SAUSA300_0423 SAUSA300_2028 SAUSA300_2111 SAUSA300_2126 SAUSA300_1347 SAUSA300_0549 SAUSA300_1618 SAUSA300_0862 SAUSA300_1668 SAUSA300_1862 SAUSA300_1062 SAUSA300_1069 SAUSA300_0341 SAUSA300_1786 SAUSA300_1036

-14.14 -13.15 -12.91 -10.74 -10.42 -10.36 -10.35 -9.87 -9.77 -9.67 -9.65 -9.58 -9.54 -9.51 -9.5 -9.2 -9.1 -8.97 -8.94 -8.56 -8.54 -8.52 -8.39 -8.36 -8.33 -8.33 -8.31

0.002 0.003 0.004 0.016 0.019 0.019 0.02 0.025 0.026 0.027 0.028 0.029 0.029 0.03 0.03 0.034 0.036 0.038 0.038 0.045 0.045 0.045 0.048 0.049 0.049 0.049 0.05

95 24 26 23 96 131 2 1 82 96 139 35 12 1 96 95 96 114 138 35 138 7 71 24 45 97 83

110 38 41 38 115 139 15 15 98 115 148 49 29 10 110 114 111 128 151 50 151 18 87 34 58 109 101

1 2 3 4

sarX ansA

SAUSA300_2406 SAUSA300_2076 SAUSA300_0654 SAUSA300_1368

-14.63 -12.86 -12.3 -12.18

0.001 0.004 0.006 0.007

37 186 31 146

52 205 51 159

SAUSA300s241 SAUSA300s242

SAUSA300s247

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34

oppA holA feoA lpdA coaA pyrF ureA rpe comK glk phoB acnA -

SAUSA300_0891 SAUSA300_1397 SAUSA300_1546 SAUSA300_2235 SAUSA300_1867 SAUSA300_2383 SAUSA300_1532 SAUSA300_2575 SAUSA300_2522 SAUSA300_2379 SAUSA300_2488 SAUSA300_1334 SAUSA300_0996 SAUSA300_2084 SAUSA300_1097 SAUSA300_2238 SAUSA300_2410 SAUSA300_1115 SAUSA300_1327 SAUSA300_0338 SAUSA300_1059 SAUSA300_0254 SAUSA300_1684 SAUSA300_0928 SAUSA300_2468 SAUSA300_1507 SAUSA300_2561 SAUSA300_0055 SAUSA300_1246 SAUSA300_2543

-12.09 -11.91 -11.61 -11.42 -11.3 -11.17 -11.08 -11.01 -10.66 -10.51 -10.44 -10.4 -10.36 -10.26 -10.08 -9.93 -9.88 -9.85 -9.59 -9.46 -9.41 -9.36 -9.26 -9.14 -9.03 -8.89 -8.67 -8.42 -8.42 -8.33

0.007 0.008 0.01 0.011 0.012 0.012 0.013 0.014 0.017 0.018 0.019 0.019 0.019 0.021 0.022 0.024 0.025 0.025 0.028 0.03 0.031 0.032 0.033 0.035 0.037 0.039 0.043 0.047 0.047 0.049

36 31 37 7 181 55 40 55 38 181 148 108 34 1 211 1 40 151 187 35 216 50 181 60 59 194 213 38 193 38

54 46 51 19 197 65 51 65 51 196 164 121 50 21 223 14 52 164 201 46 228 64 199 71 68 206 226 52 210 52

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

rex tnp rexA trmD -

SAUSA300_2483 SAUSA300_2426 SAUSA300_2436 SAUSA300_1999 SAUSA300_1551 SAUSA300_2160 SAUSA300_2136 SAUSA300_1859 SAUSA300_2115 SAUSA300_1810 SAUSA300_1944 SAUSA300_0012 SAUSA300_0870 SAUSA300_1133 SAUSA300_0688

-13.95 -13.59 -13.17 -12.6 -12.2 -12.17 -12.13 -12.04 -11.76 -11.76 -11.38 -11.26 -11.23 -11.1 -11.05

0.002 0.002 0.003 0.005 0.007 0.007 0.007 0.007 0.009 0.009 0.011 0.012 0.012 0.013 0.013

68 59 38 59 68 63 59 17 61 61 18 26 22 81 75

81 75 52 78 84 72 72 31 75 75 30 40 35 95 90

SAUSA300s248

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55

qoxD acpS mqo moaD rpsM hslO lgt mutM recN rplD uvrA tyrS tagA rbgA -

SAUSA300_0331 SAUSA300_1934 SAUSA300_0430 SAUSA300_1566 SAUSA300_1879 SAUSA300_0960 SAUSA300_0394 SAUSA300_0915 SAUSA300_1456 SAUSA300_2028 SAUSA300_2541 SAUSA300_2221 SAUSA300_1942 SAUSA300_0485 SAUSA300_2180 SAUSA300_2464 SAUSA300_2451 SAUSA300_0490 SAUSA300_0365 SAUSA300_0744 SAUSA300_2559 SAUSA300_1349 SAUSA300_1561 SAUSA300_1635 SAUSA300_2465 SAUSA300_1858 SAUSA300_1468 SAUSA300_1435 SAUSA300_1873 SAUSA300_2203 SAUSA300_0420 SAUSA300_0742 SAUSA300_1955 SAUSA300_1675 SAUSA300_0623 SAUSA300_0194 SAUSA300_1136 SAUSA300_2435 SAUSA300_0508 SAUSA300_0071

-10.98 -10.59 -10.36 -10.27 -10.26 -10.13 -10.11 -10.06 -10.03 -9.96 -9.92 -9.81 -9.8 -9.77 -9.74 -9.62 -9.6 -9.49 -9.46 -9.33 -9.32 -9.3 -9.25 -9.24 -9.19 -9.11 -9.07 -8.97 -8.93 -8.92 -8.81 -8.79 -8.73 -8.58 -8.57 -8.54 -8.53 -8.45 -8.41 -8.4

0.014 0.017 0.019 0.02 0.02 0.022 0.022 0.023 0.023 0.024 0.024 0.026 0.026 0.026 0.027 0.028 0.028 0.03 0.03 0.032 0.032 0.033 0.033 0.034 0.034 0.035 0.036 0.038 0.038 0.039 0.04 0.041 0.042 0.045 0.045 0.045 0.045 0.047 0.048 0.048

63 128 111 5 37 26 120 110 112 22 51 70 72 81 44 86 130 75 102 77 30 11 11 86 129 69 121 17 18 40 76 112 27 65 31 64 43 90 109 63

77 143 123 25 50 37 136 130 128 37 70 85 86 96 61 95 144 90 118 93 49 31 25 98 144 85 136 30 33 56 96 128 43 84 41 79 58 98 125 76

rnc

SAUSA300_1508 SAUSA300_1229 SAUSA300_1081 SAUSA300_1141 SAUSA300_1126

-12.53 -12.09 -11.83 -11.59 -11.28

0.005 0.007 0.008 0.01 0.012

147 53 96 164 61

158 65 113 176 69

SAUSA300s249 1 2 3 4 5

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

cobI pth aldA2 cbiO clpC opuCb qoxB lysS -

SAUSA300_2323 SAUSA300_0480 SAUSA300_1576 SAUSA300_1033 SAUSA300_0550 SAUSA300_1241 SAUSA300_1984 SAUSA300_1901 SAUSA300_1674 SAUSA300_2176 SAUSA300_1798 SAUSA300_1107 SAUSA300_0510 SAUSA300_0090 SAUSA300_2392 SAUSA300_0707 SAUSA300_1706 SAUSA300_0962 SAUSA300_0496 SAUSA300_1977

-11.21 -11.04 -10.77 -10.44 -10.38 -10.08 -9.95 -9.95 -9.6 -9.35 -9.25 -9.09 -9.08 -8.79 -8.73 -8.71 -8.69 -8.57 -8.41 -8.4

0.012 0.013 0.016 0.019 0.019 0.022 0.024 0.024 0.028 0.032 0.033 0.036 0.036 0.041 0.042 0.042 0.042 0.045 0.048 0.048

190 174 147 1 110 178 44 192 200 94 187 59 62 61 61 151 183 163 98 59

203 188 161 14 124 188 57 207 211 106 202 67 71 69 71 160 194 174 110 71

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

pstA ansA rpsH pyrP alr2 ybaK -

SAUSA300_1745 SAUSA300_1867 SAUSA300_2295 SAUSA300_1198 SAUSA300_0068 SAUSA300_1184 SAUSA300_0661 SAUSA300_2422 SAUSA300_1667 SAUSA300_1281 SAUSA300_2475 SAUSA300_0136 SAUSA300_1205 SAUSA300_1368 SAUSA300_2190 SAUSA300_1092 SAUSA300_1517 SAUSA300_1292 SAUSA300_1059 SAUSA300_0682 SAUSA300_0425 SAUSA300_0423 SAUSA300_2336 SAUSA300_0797 SAUSA300_1042

-14.19 -13.17 -12.95 -12.23 -11.87 -11.71 -11.4 -11.28 -11.09 -11.04 -11.02 -10.92 -10.8 -10.75 -10.58 -10.28 -10.04 -9.73 -9.72 -9.63 -9.54 -9.53 -9.43 -9.35 -9.28

0.001 0.003 0.004 0.006 0.008 0.009 0.011 0.012 0.013 0.013 0.014 0.014 0.015 0.016 0.017 0.02 0.023 0.027 0.027 0.028 0.029 0.029 0.031 0.032 0.033

113 140 53 137 137 137 56 139 23 116 134 141 62 32 137 138 142 136 108 53 71 6 105 66 72

126 151 70 150 149 148 70 153 37 126 148 151 71 46 147 152 156 150 122 64 85 18 123 82 86

SAUSA300s250

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

26 27 28 29 30 31 32 33 34 35 36 37 38 39

nixA hslU gap ltrA -

SAUSA300_2630 SAUSA300_2511 SAUSA300_1147 SAUSA300_1933 SAUSA300_0756 SAUSA300_1327 SAUSA300_0608 SAUSA300_0647 SAUSA300_1912 SAUSA300_1975 SAUSA300_0354 SAUSA300_1669 SAUSA300_0780 SAUSA300_0809

-9.22 -9.19 -9.16 -9.15 -9.1 -8.84 -8.81 -8.8 -8.72 -8.66 -8.65 -8.55 -8.42 -8.33

0.034 0.034 0.035 0.035 0.036 0.04 0.04 0.04 0.042 0.043 0.043 0.045 0.048 0.049

102 53 56 138 143 137 53 71 69 81 6 52 30 53

115 71 70 148 153 148 66 82 84 94 18 61 45 68

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

sufD agrB galM srrB secG glmM gltS rpmA rplX queA narH fnbA sdrE

SAUSA300_0484 SAUSA300_0796 SAUSA300_0819 SAUSA300_0241 SAUSA300_1989 SAUSA300_2414 SAUSA300_0308 SAUSA300_1407 SAUSA300_2087 SAUSA300_2285 SAUSA300_2552 SAUSA300_1441 SAUSA300_0762 SAUSA300_0930 SAUSA300_0252 SAUSA300_1932 SAUSA300_1700 SAUSA300_2423 SAUSA300_2111 SAUSA300_0344 SAUSA300_1902 SAUSA300_2291 SAUSA300_0718 SAUSA300_1601 SAUSA300_1057 SAUSA300_2193 SAUSA300_2037 SAUSA300_1596 SAUSA300_2342 SAUSA300_2441 SAUSA300_0548

-14.59 -14.23 -13.16 -13.07 -12.45 -12.14 -12.13 -12.01 -11.83 -11.7 -11.37 -11.13 -11 -10.76 -10.71 -10.62 -10.62 -10.41 -10.15 -9.98 -9.96 -9.71 -9.69 -9.68 -9.55 -9.54 -9.52 -9.39 -9.35 -9.34 -9.28

0.001 0.001 0.003 0.004 0.006 0.007 0.007 0.007 0.008 0.009 0.011 0.013 0.014 0.016 0.016 0.017 0.017 0.019 0.022 0.024 0.024 0.027 0.027 0.027 0.029 0.029 0.029 0.031 0.032 0.032 0.033

292 294 301 291 286 346 293 325 294 292 294 287 342 290 293 292 294 300 292 301 325 288 294 258 299 342 298 256 340 294 296

306 309 321 310 304 362 303 344 302 302 302 300 356 302 307 306 306 315 300 318 338 307 302 269 316 351 309 274 355 302 310

SAUSA300s255

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

32 33 34 35 36 37 38 39 40 41 42 43 44 45

lysS argR arcC nsaS splA

SAUSA300_2531 SAUSA300_1426 SAUSA300_0496 SAUSA300_2031 SAUSA300_2248 SAUSA300_1053 SAUSA300_2310 SAUSA300_0653 SAUSA300_2571 SAUSA300_0061 SAUSA300_2558 SAUSA300_1435 SAUSA300_1321 SAUSA300_1758

-9.18 -9.08 -9.02 -8.9 -8.89 -8.86 -8.81 -8.64 -8.56 -8.53 -8.5 -8.43 -8.42 -8.41

0.034 0.036 0.037 0.039 0.039 0.04 0.04 0.043 0.045 0.045 0.046 0.047 0.047 0.048

299 257 304 287 295 294 257 301 342 292 332 259 299 263

309 275 321 302 309 304 276 321 351 305 348 273 310 277

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

saeR sarU ureC hisS ftsL argR holA hisC epiP -

SAUSA300_0338 SAUSA300_0691 SAUSA300_1450 SAUSA300_1891 SAUSA300_2400 SAUSA300_0485 SAUSA300_1961 SAUSA300_1129 SAUSA300_2438 SAUSA300_0212 SAUSA300_2240 SAUSA300_1587 SAUSA300_2262 SAUSA300_1074 SAUSA300_1469 SAUSA300_0035 SAUSA300_1971 SAUSA300_1483 SAUSA300_2146 SAUSA300_0790 SAUSA300_0293 SAUSA300_1939 SAUSA300_0312 SAUSA300_1375 SAUSA300_1546 SAUSA300_2206 SAUSA300_1959 SAUSA300_0708 SAUSA300_1763 SAUSA300_1786 SAUSA300_1181

-19.1 -16.06 -15.66 -14.75 -12.72 -12.33 -11.7 -11.47 -11.24 -11.02 -10.82 -10.62 -10.58 -10.57 -10.35 -10.28 -10.23 -10.19 -10 -9.79 -9.79 -9.78 -9.7 -9.69 -9.47 -9.38 -9.23 -9.22 -9.19 -9.18 -9.08

0 0 0 0.001 0.005 0.006 0.009 0.01 0.012 0.014 0.015 0.017 0.017 0.017 0.02 0.02 0.021 0.021 0.023 0.026 0.026 0.026 0.027 0.027 0.03 0.031 0.034 0.034 0.034 0.034 0.036

86 34 25 82 56 87 80 70 87 50 75 16 78 47 15 51 62 86 75 17 59 75 75 45 62 78 64 60 75 87 80

105 48 39 100 68 102 94 86 103 70 89 27 95 62 33 71 74 103 92 28 69 87 87 59 74 93 83 69 95 97 92

SAUSA300s256

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

32 33 34 35 36 37 38 39 40 41 42 43

mtlA moeA rplL hemE -

SAUSA300_0439 SAUSA300_2107 SAUSA300_2224 SAUSA300_2635 SAUSA300_2348 SAUSA300_0026 SAUSA300_0525 SAUSA300_1424 SAUSA300_2640 SAUSA300_2494 SAUSA300_1783 SAUSA300_0880

-9.07 -9.05 -9.02 -8.93 -8.82 -8.79 -8.77 -8.73 -8.63 -8.44 -8.43 -8.37

0.036 0.036 0.037 0.038 0.04 0.041 0.041 0.042 0.043 0.047 0.047 0.048

29 62 22 33 73 80 70 80 3 34 55 49

43 75 35 47 90 92 84 92 16 46 70 69

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

splA betB cdsA recF ggt def thiD cap1C putP nusG -

SAUSA300_1758 SAUSA300_2472 SAUSA300_2169 SAUSA300_0643 SAUSA300_2546 SAUSA300_1451 SAUSA300_1284 SAUSA300_0428 SAUSA300_1154 SAUSA300_1930 SAUSA300_0414 SAUSA300_1483 SAUSA300_1733 SAUSA300_2262 SAUSA300_0718 SAUSA300_0004 SAUSA300_1876 SAUSA300_1969 SAUSA300_0204 SAUSA300_1873 SAUSA300_0991 SAUSA300_2049 SAUSA300_1656 SAUSA300_2320 SAUSA300_2596 SAUSA300_0332 SAUSA300_1883 SAUSA300_2552 SAUSA300_0521 SAUSA300_0721 SAUSA300_1028 SAUSA300_2267 SAUSA300_0176

-16.13 -14.59 -14.36 -13.83 -12.93 -12.67 -12.5 -12.04 -12 -11.83 -11.66 -11.49 -11.2 -11.17 -11.05 -10.73 -10.64 -10.57 -10.52 -10.47 -10.34 -10.28 -10.21 -10.13 -10.08 -10.05 -9.94 -9.86 -9.85 -9.83 -9.76 -9.65 -9.58

0 0.001 0.001 0.002 0.004 0.005 0.005 0.007 0.007 0.008 0.009 0.01 0.012 0.012 0.013 0.016 0.017 0.017 0.018 0.018 0.02 0.02 0.021 0.022 0.022 0.023 0.024 0.025 0.025 0.025 0.026 0.028 0.029

235 72 47 133 65 40 144 98 46 38 195 145 223 221 236 136 262 153 148 267 164 279 39 246 147 33 188 155 33 205 36 282 99

251 88 61 149 85 54 164 118 60 52 213 165 239 231 256 152 273 170 164 276 180 295 52 257 158 47 203 172 48 216 48 295 113

SAUSA300s258

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52

trmB acsA tagG uvrA rplO eno recQ -

SAUSA300_0146 SAUSA300_1694 SAUSA300_1679 SAUSA300_2318 SAUSA300_0625 SAUSA300_0479 SAUSA300_0742 SAUSA300_2509 SAUSA300_1807 SAUSA300_0088 SAUSA300_0859 SAUSA300_2185 SAUSA300_2580 SAUSA300_0760 SAUSA300_2423 SAUSA300_0012 SAUSA300_0343 SAUSA300_0705 SAUSA300_2308

-9.51 -9.51 -9.47 -9.4 -9.36 -9.32 -9.2 -9.1 -9.03 -8.99 -8.92 -8.73 -8.58 -8.51 -8.49 -8.39 -8.38 -8.32 -8.31

0.03 0.03 0.03 0.031 0.032 0.032 0.034 0.036 0.037 0.037 0.038 0.042 0.044 0.046 0.046 0.048 0.048 0.049 0.05

144 158 231 284 156 284 43 283 34 179 280 152 219 41 264 36 236 39 158

157 173 244 299 170 298 58 298 47 192 299 164 228 54 273 56 248 54 170

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

atl SAUSA300_0955 menA SAUSA300_0944 SAUSA300_0653 SAUSA300_0495 ruvB SAUSA300_1597 opp-1ASAUSA300_2411 SAUSA300_0509 rarD SAUSA300_2628 SAUSA300_2423 SAUSA300_1021 SAUSA300_1780 nirR SAUSA300_2347 priA SAUSA300_1105 holA SAUSA300_1546 nth SAUSA300_1343 SAUSA300_0827 SAUSA300_1665 norA SAUSA300_0680 SAUSA300_0936 SAUSA300_2164 oppB SAUSA300_0887 SAUSA300_1944 hisS SAUSA300_1587 ackA SAUSA300_1657 thiI SAUSA300_1661 SAUSA300_0578

-13.08 -12.25 -12.06 -11.14 -10.86 -10.83 -10.81 -10.67 -10.65 -10.5 -10.36 -10.34 -10.26 -10.19 -10.15 -10.02 -10.01 -9.98 -9.89 -9.82 -9.8 -9.68 -9.66 -9.64 -9.59 -9.52

0.004 0.006 0.007 0.013 0.015 0.015 0.015 0.016 0.017 0.018 0.019 0.02 0.021 0.021 0.022 0.023 0.023 0.024 0.025 0.026 0.026 0.027 0.027 0.028 0.029 0.029

6 39 28 41 8 76 119 141 119 142 76 4 76 7 77 110 42 50 70 51 122 49 66 26 142 97

17 56 48 55 25 89 131 155 133 161 90 20 89 23 92 124 57 63 88 64 136 62 80 39 156 111

SAUSA300s259

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27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46

trpB rocD rplO hsdR tcaB moaB ggt -

SAUSA300_1267 SAUSA300_0860 SAUSA300_2328 SAUSA300_1606 SAUSA300_2185 SAUSA300_1513 SAUSA300_2360 SAUSA300_2586 SAUSA300_0042 SAUSA300_0196 SAUSA300_2301 SAUSA300_2226 SAUSA300_1204 SAUSA300_1656 SAUSA300_0266 SAUSA300_0204 SAUSA300_1858 SAUSA300_2350 SAUSA300_1326 SAUSA300_0067

-9.44 -9.35 -9.12 -9.03 -9.02 -8.92 -8.9 -8.9 -8.78 -8.75 -8.73 -8.63 -8.53 -8.53 -8.48 -8.36 -8.35 -8.34 -8.31 -8.3

0.031 0.032 0.035 0.037 0.037 0.038 0.039 0.039 0.041 0.041 0.042 0.044 0.045 0.045 0.046 0.049 0.049 0.049 0.05 0.05

121 52 105 1 79 106 108 35 151 45 72 4 76 1 104 77 118 116 6 74

134 62 122 18 92 120 125 55 163 62 86 20 88 17 124 96 132 128 15 88

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

smpB nrdG ipk ctpA sarU rsbU rnc hisZ atpG gltA sbcD pyk cinA

SAUSA300_0765 SAUSA300_2550 SAUSA300_1911 SAUSA300_0472 SAUSA300_1313 SAUSA300_0505 SAUSA300_0302 SAUSA300_0637 SAUSA300_0035 SAUSA300_2438 SAUSA300_1961 SAUSA300_2025 SAUSA300_1126 SAUSA300_0740 SAUSA300_2613 SAUSA300_0565 SAUSA300_0901 SAUSA300_2059 SAUSA300_1198 SAUSA300_1641 SAUSA300_1242 SAUSA300_1867 SAUSA300_1644 SAUSA300_0796 SAUSA300_1177

-15.1 -14.69 -14.16 -13.65 -13.53 -13.29 -13.23 -13.21 -12.74 -12.38 -12.14 -12.12 -12.1 -12.03 -11.86 -11.85 -11.8 -11.71 -11.66 -11.63 -11.57 -11.47 -11.34 -11.26 -11.23

0.001 0.001 0.001 0.002 0.002 0.003 0.003 0.003 0.005 0.006 0.007 0.007 0.007 0.007 0.008 0.008 0.008 0.009 0.009 0.009 0.01 0.01 0.011 0.012 0.012

49 32 44 245 240 62 43 67 246 57 64 204 240 47 267 50 237 238 242 287 51 76 155 238 282

65 50 64 262 255 76 62 82 257 71 80 217 253 62 281 65 257 256 256 302 65 90 175 250 295

SAUSA300s260

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72

acuC oppF glnR arcA lysS leuD adh gatB kdpB groES epiC oppD alr2 queA dnaI hsdR rplL ccrB tmk -

SAUSA300_0239 SAUSA300_2624 SAUSA300_1422 SAUSA300_0833 SAUSA300_1681 SAUSA300_0090 SAUSA300_1400 SAUSA300_2576 SAUSA300_2318 SAUSA300_1945 SAUSA300_0893 SAUSA300_1200 SAUSA300_0065 SAUSA300_0916 SAUSA300_0496 SAUSA300_0353 SAUSA300_1548 SAUSA300_2013 SAUSA300_1416 SAUSA300_0432 SAUSA300_2522 SAUSA300_0564 SAUSA300_1919 SAUSA300_1012 SAUSA300_0594 SAUSA300_0301 SAUSA300_1880 SAUSA300_2033 SAUSA300_1983 SAUSA300_1385 SAUSA300_1765 SAUSA300_1101 SAUSA300_2232 SAUSA300_1220 SAUSA300_0894 SAUSA300_1292 SAUSA300_1596 SAUSA300_0997 SAUSA300_2493 SAUSA300_1630 SAUSA300_1879 SAUSA300_0196 SAUSA300_0525 SAUSA300_0037 SAUSA300_1435 SAUSA300_0459 SAUSA300_1318

-11.21 -11.15 -11.03 -11 -10.81 -10.68 -10.58 -10.51 -10.45 -10.41 -10.4 -10.36 -10.23 -10.21 -10.15 -10.07 -10 -9.92 -9.85 -9.84 -9.72 -9.72 -9.69 -9.57 -9.56 -9.55 -9.55 -9.51 -9.47 -9.43 -9.42 -9.4 -9.27 -9.03 -8.99 -8.98 -8.93 -8.93 -8.9 -8.89 -8.81 -8.75 -8.73 -8.72 -8.71 -8.69 -8.69

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0.012 0.013 0.013 0.014 0.015 0.016 0.017 0.018 0.019 0.019 0.019 0.019 0.021 0.021 0.022 0.023 0.023 0.024 0.025 0.025 0.027 0.027 0.027 0.029 0.029 0.029 0.029 0.03 0.03 0.031 0.031 0.031 0.033 0.037 0.037 0.037 0.038 0.038 0.039 0.039 0.04 0.041 0.042 0.042 0.042 0.042 0.043

243 285 116 245 242 238 49 58 199 203 169 41 157 159 163 218 2 51 240 66 287 3 152 242 55 43 242 285 211 172 63 65 267 2 276 239 241 44 246 136 279 278 155 278 288 156 287

257 299 133 257 254 253 63 77 215 218 182 56 173 173 181 230 17 69 257 85 304 20 167 255 71 62 258 300 226 191 82 80 280 20 294 253 255 62 263 150 299 295 172 291 303 176 301

73 74 75 76 77 78

udk -

SAUSA300_0882 SAUSA300_0205 SAUSA300_2146 SAUSA300_0508 SAUSA300_1568 SAUSA300_1013

-8.64 -8.55 -8.43 -8.38 -8.34 -8.29

0.043 0.045 0.047 0.048 0.049 0.05

238 245 60 172 96 254

255 263 76 192 108 270

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

recF prmA clpP ksgA acpP rplN ctpA gid ggt oppD nirB oppB carA isaB -

SAUSA300_1387 SAUSA300_1805 SAUSA300_0901 SAUSA300_0288 SAUSA300_0004 SAUSA300_1538 SAUSA300_0645 SAUSA300_0752 SAUSA300_0470 SAUSA300_0907 SAUSA300_1125 SAUSA300_1997 SAUSA300_1936 SAUSA300_2453 SAUSA300_2194 SAUSA300_2382 SAUSA300_1872 SAUSA300_1313 SAUSA300_2320 SAUSA300_2604 SAUSA300_1413 SAUSA300_1144 SAUSA300_2423 SAUSA300_1461 SAUSA300_0204 SAUSA300_1031 SAUSA300_0894 SAUSA300_1701 SAUSA300_2346 SAUSA300_0287 SAUSA300_2592 SAUSA300_1734 SAUSA300_0887 SAUSA300_0232 SAUSA300_1071 SAUSA300_1095 SAUSA300_0585 SAUSA300_2573 SAUSA300_2637

-14.38 -12.71 -12.16 -11.93 -11.64 -11.61 -11.56 -11.4 -11.4 -11.4 -11.28 -11.22 -11.16 -11.05 -10.88 -10.8 -10.78 -10.55 -10.53 -10.52 -10.5 -10.35 -10.2 -10.17 -10.13 -10.06 -9.95 -9.89 -9.89 -9.84 -9.78 -9.62 -9.62 -9.6 -9.5 -9.28 -9.14 -9.09 -9.07

0.001 0.005 0.007 0.008 0.009 0.01 0.01 0.011 0.011 0.011 0.012 0.012 0.013 0.013 0.015 0.015 0.016 0.018 0.018 0.018 0.018 0.02 0.021 0.021 0.022 0.023 0.024 0.025 0.025 0.025 0.026 0.028 0.028 0.028 0.03 0.033 0.035 0.036 0.036

179 11 278 2 152 267 9 172 179 80 176 79 82 306 207 281 78 278 56 79 186 64 280 279 58 166 172 308 307 305 206 154 177 4 269 307 85 82 188

194 21 290 15 163 286 22 189 193 99 192 99 97 319 222 299 91 290 72 93 199 82 295 293 74 181 188 320 320 317 218 169 191 17 280 320 103 99 202

SAUSA300s261

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

arcB thrC folA glmM truA comK

SAUSA300_2569 SAUSA300_0688 SAUSA300_0749 SAUSA300_1227 SAUSA300_0509 SAUSA300_1319 SAUSA300_0912 SAUSA300_2111 SAUSA300_2173 SAUSA300_2137 SAUSA300_1112 SAUSA300_1369 SAUSA300_2468 SAUSA300_2522 SAUSA300_0928

-9.05 -9.02 -9.01 -8.97 -8.96 -8.92 -8.87 -8.77 -8.71 -8.67 -8.62 -8.58 -8.43 -8.39 -8.32

0.036 0.037 0.037 0.038 0.038 0.038 0.039 0.041 0.042 0.043 0.044 0.045 0.047 0.048 0.049

204 166 175 179 278 82 161 173 153 179 204 109 279 106 273

218 184 189 197 292 99 176 192 167 196 218 126 292 119 293

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27

aldA2 mnhG mobB cysS hfq icaB yfiA -

SAUSA300_0031 SAUSA300_1901 SAUSA300_2287 SAUSA300_0849 SAUSA300_2076 SAUSA300_0781 SAUSA300_2314 SAUSA300_2223 SAUSA300_2099 SAUSA300_2326 SAUSA300_1059 SAUSA300_0515 SAUSA300_1394 SAUSA300_1974 SAUSA300_1196 SAUSA300_0233 SAUSA300_2431 SAUSA300_0618 SAUSA300_2601 SAUSA300_2112 SAUSA300_1248 SAUSA300_0126 SAUSA300_0736 SAUSA300_1484 SAUSA300_1461 SAUSA300_2158 SAUSA300_0906

-11.89 -11.79 -11.4 -11.15 -11.02 -10.33 -10.26 -10.23 -10.22 -10.13 -9.71 -9.59 -9.52 -9.49 -9.49 -9.28 -9.2 -9.14 -9.13 -8.82 -8.82 -8.74 -8.55 -8.45 -8.43 -8.42 -8.29

0.008 0.009 0.011 0.013 0.014 0.02 0.021 0.021 0.021 0.022 0.027 0.028 0.029 0.03 0.03 0.033 0.034 0.035 0.035 0.04 0.04 0.042 0.045 0.047 0.047 0.048 0.05

466 41 402 469 12 465 471 380 439 464 397 23 12 471 463 474 471 37 431 461 45 44 473 99 469 395 12

480 52 415 483 22 479 486 393 448 482 411 34 30 490 477 488 490 51 444 473 54 62 488 113 481 405 31

SAUSA300_0118

-10.72

0.016

27

38

SAUSA300s265

SAUSA300s266 1-

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

lysS gatA murQ agrA ffh folP qoxD

SAUSA300_2523 SAUSA300_0516 SAUSA300_0328 SAUSA300_0052 SAUSA300_0496 SAUSA300_1941 SAUSA300_0010 SAUSA300_1129 SAUSA300_1881 SAUSA300_0441 SAUSA300_0309 SAUSA300_0193 SAUSA300_1992 SAUSA300_1938 SAUSA300_0615 SAUSA300_0508 SAUSA300_1853 SAUSA300_1130 SAUSA300_0370 SAUSA300_1669 SAUSA300_0492 SAUSA300_2578 SAUSA300_0960

-10.61 -10.19 -10.09 -9.77 -9.66 -9.6 -9.24 -9 -8.94 -8.93 -8.92 -8.9 -8.88 -8.87 -8.77 -8.69 -8.64 -8.64 -8.62 -8.6 -8.6 -8.34 -8.3

0.017 0.021 0.022 0.026 0.027 0.028 0.034 0.037 0.038 0.038 0.038 0.039 0.039 0.039 0.041 0.043 0.043 0.043 0.044 0.044 0.044 0.049 0.05

47 6 4 21 3 6 20 5 5 46 20 6 5 43 1 7 3 6 28 25 51 28 50

59 17 15 38 21 14 32 15 15 60 30 14 13 58 10 15 15 18 42 37 61 41 59

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

aroK cbf1 ureF gltX icd agrA queA arcB

SAUSA300_1059 SAUSA300_1419 SAUSA300_1499 SAUSA300_1607 SAUSA300_1791 SAUSA300_2242 SAUSA300_0513 SAUSA300_1640 SAUSA300_0675 SAUSA300_2160 SAUSA300_0103 SAUSA300_1992 SAUSA300_1596 SAUSA300_1483 SAUSA300_1274 SAUSA300_0082 SAUSA300_0101 SAUSA300_0428 SAUSA300_0289 SAUSA300_1912 SAUSA300_2515 SAUSA300_0062

-13.33 -13.06 -12.71 -12.62 -12.36 -12.29 -12.04 -11.67 -11.34 -11.2 -10.98 -10.73 -10.71 -10.66 -10.39 -10.13 -10.12 -10.04 -10.03 -10 -9.75 -9.74

0.003 0.004 0.005 0.005 0.006 0.006 0.007 0.009 0.011 0.012 0.014 0.016 0.016 0.017 0.019 0.022 0.022 0.023 0.023 0.023 0.026 0.027

76 54 55 90 29 107 64 55 65 64 5 103 135 89 55 56 106 73 91 130 28 1

88 74 69 109 40 122 80 70 75 75 20 115 151 103 67 68 120 81 110 145 43 20

SAUSA300s267

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

rnhC menC rpsL rplC mraW nrdD cap5O alaS fnbA pstA rimM -

SAUSA300_2237 SAUSA300_0646 SAUSA300_0938 SAUSA300_1039 SAUSA300_2095 SAUSA300_2635 SAUSA300_0285 SAUSA300_1735 SAUSA300_0530 SAUSA300_1734 SAUSA300_2204 SAUSA300_1073 SAUSA300_2551 SAUSA300_0947 SAUSA300_0166 SAUSA300_1575 SAUSA300_2441 SAUSA300_1281 SAUSA300_1132 SAUSA300_1416 SAUSA300_1101 SAUSA300_0376

-9.71 -9.55 -9.27 -9.26 -9.09 -9.08 -9.06 -9.03 -9.01 -8.96 -8.81 -8.74 -8.71 -8.6 -8.59 -8.56 -8.52 -8.47 -8.46 -8.4 -8.4 -8.34

0.027 0.029 0.033 0.033 0.036 0.036 0.036 0.037 0.037 0.038 0.04 0.042 0.042 0.044 0.044 0.045 0.046 0.047 0.047 0.048 0.048 0.049

97 152 155 76 97 30 107 89 107 107 28 131 68 59 89 89 130 11 93 152 60 143

107 163 163 92 109 42 120 107 122 115 41 146 82 77 103 103 146 23 109 163 77 156

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

epiD rexA pstA cbiO fruB tyrS efb rplO rpmC -

SAUSA300_1764 SAUSA300_0126 SAUSA300_0077 SAUSA300_0437 SAUSA300_2472 SAUSA300_0870 SAUSA300_1281 SAUSA300_2176 SAUSA300_1980 SAUSA300_1008 SAUSA300_0684 SAUSA300_1675 SAUSA300_0240 SAUSA300_2215 SAUSA300_1055 SAUSA300_2185 SAUSA300_0246 SAUSA300_0989 SAUSA300_2584 SAUSA300_2196 SAUSA300_2406

-12.19 -12.04 -11.76 -11.23 -11.19 -10.86 -10.54 -10 -9.83 -9.8 -9.79 -9.7 -9.64 -9.49 -9.33 -9.28 -9.2 -9.1 -8.91 -8.88 -8.66

0.007 0.007 0.009 0.012 0.012 0.015 0.018 0.023 0.025 0.026 0.026 0.027 0.028 0.03 0.032 0.033 0.034 0.036 0.039 0.039 0.043

16 27 78 67 26 89 26 49 76 89 15 3 89 79 78 78 4 83 86 89 4

34 39 96 81 39 99 35 63 95 99 34 17 99 94 97 89 19 98 98 100 20

SAUSA300s270

SAUSA300s273 Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

purH fhuA nirD folA queA oppB nusA aur rplQ prmA eno lctP argR scrR pepT atpA ilvA -

SAUSA300_0808 SAUSA300_2452 SAUSA300_0295 SAUSA300_0750 SAUSA300_0975 SAUSA300_1033 SAUSA300_2087 SAUSA300_1207 SAUSA300_0875 SAUSA300_0495 SAUSA300_0579 SAUSA300_0633 SAUSA300_0600 SAUSA300_0072 SAUSA300_2345 SAUSA300_1319 SAUSA300_2029 SAUSA300_1596 SAUSA300_0887 SAUSA300_0424 SAUSA300_1159 SAUSA300_2436 SAUSA300_2572 SAUSA300_0792 SAUSA300_2177 SAUSA300_1538 SAUSA300_0992 SAUSA300_0733 SAUSA300_0760 SAUSA300_1351 SAUSA300_1325 SAUSA300_0432 SAUSA300_1426 SAUSA300_1482 SAUSA300_1693 SAUSA300_0112 SAUSA300_1224 SAUSA300_1469 SAUSA300_1554 SAUSA300_1995 SAUSA300_2493 SAUSA300_0727 SAUSA300_2060 SAUSA300_2509 SAUSA300_1330 SAUSA300_0409 SAUSA300_2483

-15.4 -13.91 -13.35 -13.22 -12.78 -12.69 -12.19 -12.16 -12.1 -12.04 -11.99 -11.94 -11.92 -11.86 -11.26 -11 -10.97 -10.81 -10.75 -10.55 -10.47 -10.46 -10.46 -10.38 -9.9 -9.88 -9.75 -9.75 -9.74 -9.65 -9.63 -9.59 -9.31 -9.2 -9.19 -9.18 -8.98 -8.95 -8.92 -8.92 -8.89 -8.67 -8.61 -8.53 -8.5 -8.48 -8.45

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0 0.002 0.003 0.003 0.004 0.005 0.007 0.007 0.007 0.007 0.008 0.008 0.008 0.008 0.012 0.014 0.014 0.015 0.016 0.018 0.018 0.018 0.018 0.019 0.025 0.025 0.026 0.026 0.026 0.028 0.028 0.029 0.032 0.034 0.034 0.034 0.038 0.038 0.039 0.039 0.039 0.043 0.044 0.045 0.046 0.046 0.047

157 256 156 362 181 84 85 353 257 173 171 240 186 254 157 87 153 162 344 157 126 185 253 256 148 332 125 241 173 77 354 258 158 324 262 186 254 195 99 72 181 162 330 338 254 255 248

174 274 167 373 200 104 105 366 273 185 183 253 202 265 174 107 167 177 355 170 144 198 265 271 162 347 144 253 182 91 365 270 175 339 274 203 270 215 114 83 198 177 344 357 266 273 267

48 moaE SAUSA300_2222 49 SAUSA300_0235

-8.38 -8.33

0.048 0.049

367 173

379 182

SAUSA300s274 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

rpmE2 recF thiD ribF splA apt rplR epiE guaB acpS

SAUSA300_1220 SAUSA300_2637 SAUSA300_0673 SAUSA300_2074 SAUSA300_1602 SAUSA300_0004 SAUSA300_2624 SAUSA300_2049 SAUSA300_1361 SAUSA300_0030 SAUSA300_1386 SAUSA300_2289 SAUSA300_0293 SAUSA300_1165 SAUSA300_1758 SAUSA300_1967 SAUSA300_2505 SAUSA300_2234 SAUSA300_0334 SAUSA300_0695 SAUSA300_1404 SAUSA300_1352 SAUSA300_1591 SAUSA300_2635 SAUSA300_2188 SAUSA300_1761 SAUSA300_0388 SAUSA300_2410 SAUSA300_0622 SAUSA300_2028

-13.87 -12.29 -12.11 -11.59 -10.69 -10.64 -10.47 -10.37 -10.27 -10.06 -9.95 -9.92 -9.76 -9.59 -9.58 -9.5 -9.47 -8.88 -8.84 -8.84 -8.76 -8.74 -8.69 -8.68 -8.53 -8.51 -8.49 -8.44 -8.41 -8.38

0.002 0.006 0.007 0.01 0.016 0.017 0.018 0.019 0.02 0.023 0.024 0.024 0.026 0.028 0.029 0.03 0.03 0.039 0.04 0.04 0.041 0.042 0.042 0.043 0.045 0.046 0.046 0.047 0.048 0.048

98 41 92 93 113 115 102 121 153 102 110 107 77 121 100 105 113 54 69 95 92 115 103 146 22 94 102 43 135 70

116 51 107 113 128 130 113 133 164 118 125 120 89 133 113 119 127 65 83 115 107 128 121 162 34 112 117 52 155 84

1 2 3 4 5 6 7 8 9 10 11

trpB moaB dnaJ oppA rumA rpe

SAUSA300_1961 SAUSA300_1267 SAUSA300_2226 SAUSA300_0709 SAUSA300_1407 SAUSA300_1539 SAUSA300_0892 SAUSA300_1878 SAUSA300_0767 SAUSA300_1121 SAUSA300_1115

-13.2 -12.5 -11.57 -11.45 -10.73 -10.65 -10.5 -10.46 -10.38 -10.29 -10.25

0.003 0.005 0.01 0.011 0.016 0.017 0.018 0.018 0.019 0.02 0.021

4 51 51 71 1 60 58 15 56 16 42

14 63 60 80 20 74 78 31 68 36 53

SAUSA300s275

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12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

rplO pyrH hisA arcB fruA rpsJ -

SAUSA300_2185 SAUSA300_2452 SAUSA300_1554 SAUSA300_1151 SAUSA300_2138 SAUSA300_2607 SAUSA300_0062 SAUSA300_1739 SAUSA300_2552 SAUSA300_1607 SAUSA300_0687 SAUSA300_0206 SAUSA300_0907 SAUSA300_2029 SAUSA300_0128 SAUSA300_0685 SAUSA300_1019 SAUSA300_1480 SAUSA300_2205 SAUSA300_0906 SAUSA300_2077

-10 -9.68 -9.56 -9.48 -9.32 -9.32 -9.23 -9.23 -9.02 -8.95 -8.86 -8.84 -8.78 -8.71 -8.65 -8.64 -8.6 -8.42 -8.41 -8.38 -8.31

0.023 0.027 0.029 0.03 0.032 0.032 0.034 0.034 0.037 0.038 0.04 0.04 0.041 0.042 0.043 0.043 0.044 0.047 0.048 0.048 0.05

5 12 2 30 45 58 6 8 6 17 3 6 41 10 45 7 4 54 20 52 18

20 30 20 37 53 75 19 21 23 30 16 20 53 23 53 23 24 64 36 67 32

1 2 3 4 5 6 7 8 9 10 11

glnR -

SAUSA300_1739 SAUSA300_1422 SAUSA300_2633 SAUSA300_0719 SAUSA300_0212 SAUSA300_0602 SAUSA300_2232 SAUSA300_1200 SAUSA300_0276 SAUSA300_0575 SAUSA300_1031

-10.79 -10.39 -10.29 -10.02 -10.01 -9.63 -9.57 -9.5 -9.33 -9.09 -8.82

0.015 0.019 0.02 0.023 0.023 0.028 0.029 0.03 0.032 0.036 0.04

38 41 51 12 47 52 20 43 43 48 36

47 54 62 27 62 61 34 62 58 62 48

1 2 3 4 5 6 7 8 9 10 11

rplB oppB clpC -

SAUSA300_2201 SAUSA300_0194 SAUSA300_0887 SAUSA300_2206 SAUSA300_2160 SAUSA300_1413 SAUSA300_1547 SAUSA300_0510 SAUSA300_0681 SAUSA300_2552 SAUSA300_0300

-17.92 -15.66 -14.53 -14.21 -14.18 -14.08 -13.46 -13.36 -13.26 -13.09 -12.91

0 0 0.001 0.001 0.001 0.002 0.003 0.003 0.003 0.003 0.004

124 296 362 308 274 268 232 274 364 363 315

141 310 378 323 286 286 245 285 381 378 328

SAUSA300s276

SAUSA300s281

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12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

SAUSA300_0110 nuc SAUSA300_1222 SAUSA300_2053 thrC SAUSA300_1227 rocD SAUSA300_0860 fumC SAUSA300_1801 atpC SAUSA300_2057 SAUSA300_0056 purR SAUSA300_0473 lacF SAUSA300_2151 SAUSA300_2350 SAUSA300_1377 SAUSA300_0239 bccT SAUSA300_2549 SAUSA300_2590 hsdR SAUSA300_0196 cap5M SAUSA300_0164 SAUSA300_2321 oppA SAUSA300_0891 mnhD SAUSA300_0852 SAUSA300_2234 SAUSA300_1879 SAUSA300_1172 SAUSA300_0745 SAUSA300_2147 SAUSA300_0610 SAUSA300_2584 SAUSA300_1955 SAUSA300_2383 SAUSA300_1284 argR SAUSA300_0066 uvrB SAUSA300_0741 modB SAUSA300_2229 ptsI SAUSA300_0984 hpt SAUSA300_0488 SAUSA300_0036 hisC SAUSA300_0708 SAUSA300_2486 SAUSA300_1797 lgt SAUSA300_0744 guaB SAUSA300_0388 SAUSA300_1599 hslV SAUSA300_1146 SAUSA300_2485 ribH SAUSA300_1712 SAUSA300_1318 hlgA SAUSA300_2365

-12.44 -12.36 -12.12 -12.11 -12.06 -12.02 -11.88 -11.8 -11.52 -11.36 -11.35 -11.31 -11.29 -11.19 -11.08 -10.98 -10.87 -10.69 -10.65 -10.58 -10.46 -10.45 -10.45 -10.4 -10.4 -10.35 -10.28 -10.26 -10.25 -10.24 -10.14 -10.12 -10.1 -10.07 -10.01 -9.9 -9.86 -9.8 -9.79 -9.76 -9.71 -9.69 -9.65 -9.45 -9.4 -9.31 -9.29

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

0.006 0.006 0.007 0.007 0.007 0.007 0.008 0.008 0.01 0.011 0.011 0.011 0.012 0.012 0.013 0.014 0.015 0.016 0.017 0.017 0.018 0.018 0.019 0.019 0.019 0.02 0.02 0.02 0.021 0.021 0.022 0.022 0.022 0.023 0.023 0.025 0.025 0.026 0.026 0.026 0.027 0.027 0.028 0.03 0.031 0.032 0.033

275 129 251 274 370 370 310 273 313 367 274 276 308 372 137 369 174 48 370 270 362 1 369 137 172 344 168 297 34 137 371 144 9 79 307 273 164 21 296 312 311 312 168 362 306 370 305

285 146 268 285 384 384 322 285 327 378 285 288 322 387 152 378 192 62 379 285 378 15 378 152 190 362 182 311 48 153 384 158 23 92 321 286 179 39 308 329 324 326 182 378 321 381 319

59 60 61 62 63 64 65 66 67 68 69 70

gcvT ftsA trxB glcU saeR -

SAUSA300_2448 SAUSA300_1498 SAUSA300_1079 SAUSA300_1950 SAUSA300_0901 SAUSA300_1298 SAUSA300_0747 SAUSA300_2210 SAUSA300_2296 SAUSA300_0376 SAUSA300_0691 SAUSA300_0718

-9.11 -9.11 -9.09 -9.06 -9.04 -8.93 -8.72 -8.69 -8.68 -8.62 -8.53 -8.35

0.035 0.036 0.036 0.036 0.037 0.038 0.042 0.043 0.043 0.044 0.045 0.049

186 369 79 318 297 269 373 370 296 40 44 138

201 385 92 328 308 285 387 379 307 60 57 158

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

icd ung oppF gltC rexB pheS epiP -

SAUSA300_1974 SAUSA300_2304 SAUSA300_2320 SAUSA300_1052 SAUSA300_1640 SAUSA300_0841 SAUSA300_0563 SAUSA300_0890 SAUSA300_0942 SAUSA300_0444 SAUSA300_0266 SAUSA300_0869 SAUSA300_0304 SAUSA300_0857 SAUSA300_1037 SAUSA300_2289 SAUSA300_1763 SAUSA300_1663

-15.65 -11.4 -10.82 -10.79 -10 -9.93 -9.77 -9.75 -9.61 -9.28 -9.07 -8.92 -8.89 -8.54 -8.47 -8.4 -8.38 -8.31

0 0.011 0.015 0.015 0.023 0.024 0.026 0.026 0.028 0.033 0.036 0.038 0.039 0.045 0.047 0.048 0.048 0.05

24 40 19 1 25 12 52 25 14 27 23 20 54 39 29 54 45 25

42 56 28 14 37 27 65 43 25 41 33 30 63 48 43 68 58 43

1 2 3 4 5 6 7 8 9 10 11

guaA cysK pckA nupC -

SAUSA300_0389 SAUSA300_0342 SAUSA300_0491 SAUSA300_0430 SAUSA300_1731 SAUSA300_0373 SAUSA300_0917 SAUSA300_0506 SAUSA300_0126 SAUSA300_1035 SAUSA300_0328

-13.05 -12.06 -11.56 -11.47 -11.44 -11.42 -10.84 -10.71 -10.64 -10.45 -10.42

0.004 0.007 0.01 0.01 0.011 0.011 0.015 0.016 0.017 0.019 0.019

74 70 244 304 86 121 49 121 74 307 14

83 82 264 322 102 135 59 135 83 321 29

SAUSA300s283

SAUSA300s285 SAUSA300s286

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12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

cap5J brnQ hsdS betA fmtC lacA ilvC ptsI

SAUSA300_0825 SAUSA300_1785 SAUSA300_2308 SAUSA300_0161 SAUSA300_1374 SAUSA300_0306 SAUSA300_0406 SAUSA300_1751 SAUSA300_1059 SAUSA300_2263 SAUSA300_2332 SAUSA300_0578 SAUSA300_2545 SAUSA300_1663 SAUSA300_0826 SAUSA300_2501 SAUSA300_2426 SAUSA300_0376 SAUSA300_1255 SAUSA300_2155 SAUSA300_0924 SAUSA300_2009 SAUSA300_0725 SAUSA300_0984

-10.35 -10.3 -10.12 -10.09 -10.01 -9.93 -9.74 -9.74 -9.62 -9.46 -9.29 -9.24 -9.14 -9.07 -9.04 -8.93 -8.91 -8.86 -8.82 -8.82 -8.76 -8.73 -8.43 -8.37

0.02 0.02 0.022 0.022 0.023 0.024 0.027 0.027 0.028 0.03 0.033 0.033 0.035 0.036 0.037 0.038 0.039 0.039 0.04 0.04 0.041 0.042 0.047 0.048

9 174 76 222 247 54 314 314 5 328 126 87 175 54 244 124 126 121 54 50 13 148 42 323

22 188 92 234 265 68 328 328 19 337 141 102 189 68 258 138 144 136 70 63 24 162 56 337

SAUSA300_0728 SAUSA300_1865 SAUSA300_0856

-9.75 -9.14 -8.9

0.026 0.035 0.039

9 4 16

25 20 25

SAUSA300_2439 SAUSA300_0023 SAUSA300_2581 SAUSA300_1242 SAUSA300_2346 SAUSA300_2196 SAUSA300_1930 SAUSA300_0685 SAUSA300_1344 SAUSA300_0048 SAUSA300_1305 SAUSA300_0865 SAUSA300_2438 SAUSA300_0332 SAUSA300_0568 SAUSA300_2324

-13.8 -12.39 -11.76 -11.72 -11.45 -11.08 -11.06 -10.95 -10.85 -10.83 -10.63 -10.51 -10.47 -10.46 -10.35 -10.25

0.002 0.006 0.009 0.009 0.011 0.013 0.013 0.014 0.015 0.015 0.017 0.018 0.018 0.018 0.02 0.021

97 105 78 115 1 98 106 1 115 93 62 104 1 113 87 114

113 122 88 122 16 118 121 16 122 108 77 122 14 122 100 122

SAUSA300s287 12 vraR 3SAUSA300s290 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

galU sbcD nirB rpmC fruA sucB pgi sarU -

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17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

SAUSA300_1106 cidC SAUSA300_2477 SAUSA300_1428 SAUSA300_1537 SAUSA300_1725 SAUSA300_2131 SAUSA300_0209 SAUSA300_0610 SAUSA300_0340 rpiA SAUSA300_2283 SAUSA300_2350 guaB SAUSA300_0388 lytN SAUSA300_1140 SAUSA300_0696 SAUSA300_2130 rarD SAUSA300_2628 frr SAUSA300_1152 empbp SAUSA300_0774 SAUSA300_0359 ureC SAUSA300_2240 cbiO SAUSA300_2176 SAUSA300_2029 xerD SAUSA300_1447 gatC SAUSA300_1882 ahpF SAUSA300_0379 SAUSA300_1135 gudB SAUSA300_0861 frp SAUSA300_2462

-10.17 -10.16 -10.03 -9.87 -9.79 -9.59 -9.53 -9.44 -9.42 -9.31 -9.22 -9.12 -8.99 -8.94 -8.91 -8.91 -8.85 -8.82 -8.82 -8.82 -8.7 -8.69 -8.5 -8.41 -8.38 -8.3 -8.3 -8.29

0.021 0.022 0.023 0.025 0.026 0.029 0.029 0.031 0.031 0.032 0.034 0.035 0.037 0.038 0.039 0.039 0.04 0.04 0.04 0.04 0.042 0.042 0.046 0.048 0.048 0.05 0.05 0.05

59 114 83 107 114 55 17 98 82 114 81 114 100 107 1 16 80 60 85 2 26 1 30 112 106 67 103 114

69 122 100 122 122 66 28 113 102 122 93 122 118 122 15 30 95 78 99 16 42 16 40 122 120 83 120 122

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

hisD hlgC alaS msrB cobI purH

-15.32 -12.64 -11.19 -10.99 -10.66 -10.28 -10.15 -10.02 -9.77 -9.75 -9.59 -9.33 -9.3 -9.26 -9.11 -8.91 -8.86

0.001 0.005 0.012 0.014 0.017 0.02 0.022 0.023 0.026 0.026 0.028 0.032 0.033 0.033 0.036 0.039 0.04

43 67 55 21 93 27 43 47 1 5 12 48 87 40 43 7 2

63 87 64 34 104 36 51 61 8 15 24 62 97 54 55 19 17

SAUSA300s291 SAUSA300_2611 SAUSA300_2539 SAUSA300_2366 SAUSA300_1879 SAUSA300_2547 SAUSA300_1492 SAUSA300_1086 SAUSA300_2426 SAUSA300_0917 SAUSA300_1575 SAUSA300_0349 SAUSA300_1316 SAUSA300_2323 SAUSA300_0126 SAUSA300_1366 SAUSA300_2468 SAUSA300_0975

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

18 19 20 21

betB -

SAUSA300_2546 SAUSA300_1275 SAUSA300_1502 SAUSA300_0558

-8.82 -8.53 -8.49 -8.44

0.04 0.045 0.046 0.047

21 91 68 38

38 104 77 52

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

sarX pyrR groEL argR trmB guaC icaA -

SAUSA300_0654 SAUSA300_1584 SAUSA300_1091 SAUSA300_0505 SAUSA300_1642 SAUSA300_1982 SAUSA300_2471 SAUSA300_0537 SAUSA300_2571 SAUSA300_1694 SAUSA300_0784 SAUSA300_1235 SAUSA300_2600 SAUSA300_1013 SAUSA300_1958 SAUSA300_0395 SAUSA300_1158 SAUSA300_0068 SAUSA300_1425 SAUSA300_1057 SAUSA300_0180

-13.82 -12.8 -11.62 -9.89 -9.81 -9.8 -9.71 -9.14 -9.09 -9.09 -9.02 -8.89 -8.88 -8.87 -8.64 -8.61 -8.6 -8.5 -8.46 -8.35 -8.32

0.002 0.004 0.01 0.025 0.026 0.026 0.027 0.035 0.036 0.036 0.037 0.039 0.039 0.039 0.043 0.044 0.044 0.046 0.047 0.049 0.049

40 65 34 20 40 64 26 57 54 42 10 35 46 46 66 12 66 64 57 44 18

53 75 47 34 48 75 35 74 70 53 25 45 66 64 74 25 76 74 71 63 32

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

ptsI splD isaA cap5H fruB uvrA rpmI

SAUSA300_0128 SAUSA300_1086 SAUSA300_1461 SAUSA300_0984 SAUSA300_1755 SAUSA300_2506 SAUSA300_0917 SAUSA300_0159 SAUSA300_2578 SAUSA300_0638 SAUSA300_2206 SAUSA300_0125 SAUSA300_1965 SAUSA300_0684 SAUSA300_1741 SAUSA300_0742 SAUSA300_0126 SAUSA300_1626

-13.82 -12.69 -12.47 -12.31 -12.07 -11.79 -11.72 -11.32 -11.03 -10.86 -10.84 -10.39 -10.35 -10.29 -9.96 -9.94 -9.62 -9.27

0.002 0.005 0.005 0.006 0.007 0.009 0.009 0.011 0.014 0.015 0.015 0.019 0.02 0.02 0.024 0.024 0.028 0.033

4 3 9 27 27 38 112 103 113 3 65 27 49 23 108 104 66 108

20 17 23 42 41 48 125 119 126 17 79 43 64 37 119 117 79 123

SAUSA300s292

SAUSA300s293

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19 20 21 22 23 24 25 26 27 28 29 30

arcA murF epiE modB ald plsX glpP cap5O

SAUSA300_1118 SAUSA300_2570 SAUSA300_2101 SAUSA300_2038 SAUSA300_1761 SAUSA300_2229 SAUSA300_1331 SAUSA300_1122 SAUSA300_1190 SAUSA300_1859 SAUSA300_2643 SAUSA300_0166

-9.24 -9.1 -8.99 -8.95 -8.92 -8.86 -8.8 -8.69 -8.65 -8.58 -8.37 -8.34

0.034 0.036 0.037 0.038 0.039 0.04 0.041 0.043 0.043 0.045 0.049 0.049

5 6 36 71 4 103 106 4 61 5 41 5

18 20 44 85 18 122 126 18 75 20 54 19

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33

rplO hpt folE gap rpmI aroD

SAUSA300_0671 SAUSA300_1955 SAUSA300_1942 SAUSA300_1742 SAUSA300_1210 SAUSA300_2493 SAUSA300_0024 SAUSA300_2289 SAUSA300_1948 SAUSA300_2206 SAUSA300_2185 SAUSA300_0907 SAUSA300_0230 SAUSA300_0102 SAUSA300_0924 SAUSA300_1745 SAUSA300_1349 SAUSA300_0264 SAUSA300_0488 SAUSA300_0713 SAUSA300_1229 SAUSA300_0565 SAUSA300_0590 SAUSA300_1599 SAUSA300_0277 SAUSA300_0756 SAUSA300_1626 SAUSA300_1508 SAUSA300_0476 SAUSA300_1348 SAUSA300_2457 SAUSA300_1430 SAUSA300_0787

-12.99 -12.71 -11.86 -11.72 -11.13 -11.02 -10.96 -10.69 -10.6 -10.42 -10.3 -10.29 -10.21 -10.2 -10.14 -10.1 -10.02 -9.95 -9.84 -9.82 -9.69 -9.63 -9.55 -9.35 -9.34 -9.2 -9.14 -9.03 -8.85 -8.83 -8.82 -8.58 -8.56

0.004 0.005 0.008 0.009 0.013 0.014 0.014 0.016 0.017 0.019 0.02 0.02 0.021 0.021 0.022 0.022 0.023 0.024 0.025 0.026 0.027 0.028 0.029 0.032 0.032 0.034 0.035 0.037 0.04 0.04 0.04 0.045 0.045

35 58 38 102 38 83 8 58 102 41 54 33 86 9 34 70 9 35 35 81 27 102 34 37 49 9 37 85 25 8 51 83 10

53 71 53 112 53 93 21 71 112 54 73 51 97 20 51 84 21 51 55 90 41 110 44 51 69 25 54 97 41 18 65 95 23

SAUSA300s294

Downloaded from www.microbiologyresearch.org by IP: 107.174.36.110 On: Sat, 30 Jul 2016 03:17:03

34 35 36 37 38

argH cap1B fabF -

SAUSA300_0863 SAUSA300_2597 SAUSA300_0886 SAUSA300_0587 SAUSA300_1551

-8.53 -8.49 -8.45 -8.34 -8.3

0.045 0.046 0.047 0.049 0.05

98 26 32 35 11

110 42 44 50 22

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

alsS rpoA narI guaA ilvA hemH mnhE pdhB msrA agrA

SAUSA300_2436 SAUSA300_0761 SAUSA300_0394 SAUSA300_2166 SAUSA300_1684 SAUSA300_2178 SAUSA300_2340 SAUSA300_1207 SAUSA300_2300 SAUSA300_0389 SAUSA300_2014 SAUSA300_1007 SAUSA300_1782 SAUSA300_0851 SAUSA300_2286 SAUSA300_1979 SAUSA300_1277 SAUSA300_0994 SAUSA300_1960 SAUSA300_1256 SAUSA300_1992

-14.17 -13.72 -12.46 -12.31 -11.96 -10.83 -10.25 -10.12 -9.6 -9.44 -9.35 -9.29 -9.23 -9.23 -9.21 -9.08 -9.07 -8.88 -8.6 -8.59 -8.29

0.001 0.002 0.006 0.006 0.008 0.015 0.021 0.022 0.028 0.031 0.032 0.033 0.034 0.034 0.034 0.036 0.036 0.039 0.044 0.044 0.05

77 74 120 74 76 78 53 95 45 53 124 36 49 52 73 51 77 48 74 81 48

90 90 139 88 89 96 63 109 62 66 137 51 63 68 91 65 93 62 89 95 61

1 2 3 4 5 6 7 8 9 10 11 12

ear truA ureC nrdI

SAUSA300_1352 SAUSA300_0734 SAUSA300_1930 SAUSA300_0023 SAUSA300_1879 SAUSA300_2413 SAUSA300_0815 SAUSA300_2173 SAUSA300_2332 SAUSA300_2240 SAUSA300_1021 SAUSA300_0715

-11.67 -11.47 -11.18 -9.94 -9.79 -9.74 -9.44 -9.02 -8.86 -8.86 -8.47 -8.4

0.009 0.01 0.012 0.024 0.026 0.027 0.031 0.037 0.04 0.04 0.047 0.048

53 51 57 2 19 1 2 15 62 11 11 52

68 64 74 18 31 14 16 25 78 22 23 67

1 cysS 23-

SAUSA300_0515 SAUSA300_0681 SAUSA300_0646

-13.87 -13.36 -12.22

0.002 0.003 0.006

23 20 38

36 33 49

SAUSA300s296

SAUSA300s297

SAUSA300s298

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4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

hisD pyrH rpsS murA rplM gid hisZ treP ribF modB nuc

SAUSA300_0943 SAUSA300_2611 SAUSA300_1229 SAUSA300_1151 SAUSA300_2200 SAUSA300_0034 SAUSA300_2078 SAUSA300_2172 SAUSA300_2132 SAUSA300_2261 SAUSA300_1198 SAUSA300_1144 SAUSA300_1112 SAUSA300_0749 SAUSA300_2613 SAUSA300_0448 SAUSA300_1165 SAUSA300_1383 SAUSA300_1792 SAUSA300_0753 SAUSA300_2229 SAUSA300_1065 SAUSA300_1222

-12.14 -11.17 -11.13 -11.08 -10.8 -10.46 -10.38 -10.1 -10.06 -9.9 -9.86 -9.84 -9.84 -9.82 -9.66 -9.57 -9.43 -9.3 -9.17 -9.15 -8.87 -8.43 -8.35

0.007 0.012 0.013 0.013 0.015 0.018 0.019 0.022 0.023 0.025 0.025 0.025 0.025 0.026 0.027 0.029 0.031 0.033 0.034 0.035 0.039 0.047 0.049

37 1 19 38 36 39 38 24 20 6 38 4 20 6 2 36 38 23 48 4 6 4 39

51 18 33 46 46 53 48 38 34 20 46 20 33 25 16 49 55 32 61 18 20 18 48

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

moaD asnC ggt ssb fruB atpC -

SAUSA300_2221 SAUSA300_2452 SAUSA300_0110 SAUSA300_2552 SAUSA300_2234 SAUSA300_2589 SAUSA300_2300 SAUSA300_1345 SAUSA300_0979 SAUSA300_0204 SAUSA300_2453 SAUSA300_0367 SAUSA300_0684 SAUSA300_2057 SAUSA300_2626 SAUSA300_0516 SAUSA300_0012 SAUSA300_0408 SAUSA300_1219 SAUSA300_1942

-24.98 -18.28 -15.44 -15.11 -14.78 -14.3 -14.26 -14.11 -13.43 -13.16 -13.02 -12.99 -12.98 -12.91 -12.73 -12.66 -12.61 -12.54 -12.52 -12.5

0 0 0 0.001 0.001 0.001 0.001 0.002 0.003 0.003 0.004 0.004 0.004 0.004 0.005 0.005 0.005 0.005 0.005 0.005

359 356 254 367 236 230 44 257 180 309 266 367 218 360 358 417 358 341 354 232

376 376 272 377 252 248 59 273 198 325 279 384 232 372 375 433 372 357 374 246

SAUSA300s299 SAUSA300s300

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21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67

oppB SAUSA300_0887 SAUSA300_1956 SAUSA300_1312 srtB SAUSA300_1034 SAUSA300_0550 clfA SAUSA300_0772 SAUSA300_0284 SAUSA300_1556 mnhF SAUSA300_0850 SAUSA300_1413 SAUSA300_0243 SAUSA300_1462 SAUSA300_2237 SAUSA300_0796 fmhA SAUSA300_2356 gudB SAUSA300_0861 SAUSA300_1394 SAUSA300_2213 SAUSA300_1314 SAUSA300_0283 SAUSA300_0105 SAUSA300_1934 oppA SAUSA300_0891 SAUSA300_1369 mqo SAUSA300_2541 rplQ SAUSA300_2177 hslU SAUSA300_1147 smpB SAUSA300_0765 crr SAUSA300_1315 SAUSA300_2050 SAUSA300_0079 lctP SAUSA300_0112 gidB SAUSA300_2644 SAUSA300_2629 rpmE2 SAUSA300_2074 SAUSA300_0239 SAUSA300_0555 SAUSA300_0924 opp-1ASAUSA300_2411 SAUSA300_0604 SAUSA300_0900 SAUSA300_1218 SAUSA300_1022 SAUSA300_0276 grpE SAUSA300_1541 SAUSA300_1397 thiD SAUSA300_2049

-12.5 -12.48 -12.41 -12.39 -12.1 -12.01 -11.97 -11.89 -11.83 -11.5 -11.49 -11.48 -11.47 -11.38 -11.27 -11.24 -11.2 -11.13 -11.11 -11.05 -10.88 -10.77 -10.76 -10.72 -10.72 -10.61 -10.46 -10.31 -10.26 -10.17 -10.04 -10.02 -10.01 -10 -9.98 -9.97 -9.96 -9.9 -9.87 -9.77 -9.69 -9.69 -9.65 -9.62 -9.45 -9.44 -9.42

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0.005 0.005 0.006 0.006 0.007 0.007 0.008 0.008 0.008 0.01 0.01 0.01 0.01 0.011 0.012 0.012 0.012 0.013 0.013 0.013 0.015 0.016 0.016 0.016 0.016 0.017 0.018 0.02 0.02 0.021 0.023 0.023 0.023 0.023 0.024 0.024 0.024 0.024 0.025 0.026 0.027 0.027 0.028 0.028 0.03 0.031 0.031

365 232 147 78 16 357 362 364 316 253 82 232 283 358 362 261 232 256 395 223 81 361 261 225 256 319 358 257 315 365 483 367 48 237 224 82 232 275 232 366 220 266 152 83 310 358 339

384 251 161 96 30 374 376 373 330 268 99 250 295 374 376 278 246 276 408 239 95 375 278 240 268 338 376 269 329 374 497 376 58 250 238 101 247 291 247 375 237 278 166 95 329 372 355

68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98

phnE fni ureC pheA cap1B cap5F atpA nupC hisB deoD sdrE tmk

SAUSA300_1470 SAUSA300_1577 SAUSA300_0143 SAUSA300_1012 SAUSA300_2292 SAUSA300_0701 SAUSA300_2240 SAUSA300_1896 SAUSA300_0809 SAUSA300_0225 SAUSA300_1032 SAUSA300_2232 SAUSA300_1802 SAUSA300_1259 SAUSA300_2597 SAUSA300_0925 SAUSA300_0157 SAUSA300_2060 SAUSA300_0558 SAUSA300_0592 SAUSA300_0506 SAUSA300_2609 SAUSA300_0138 SAUSA300_0517 SAUSA300_0548 SAUSA300_0696 SAUSA300_2146 SAUSA300_0307 SAUSA300_1021 SAUSA300_1466 SAUSA300_0459

-9.4 -9.31 -9.24 -9.2 -9.18 -9.11 -9.09 -9.04 -9.01 -8.98 -8.98 -8.98 -8.94 -8.93 -8.88 -8.88 -8.84 -8.79 -8.78 -8.72 -8.69 -8.68 -8.56 -8.52 -8.5 -8.49 -8.46 -8.43 -8.42 -8.41 -8.34

0.031 0.032 0.033 0.034 0.034 0.035 0.036 0.037 0.037 0.037 0.038 0.038 0.038 0.038 0.039 0.039 0.04 0.041 0.041 0.042 0.042 0.043 0.045 0.046 0.046 0.046 0.047 0.047 0.047 0.048 0.049

221 488 224 332 341 308 342 172 366 319 234 251 368 361 155 41 374 224 367 358 172 178 362 370 368 308 81 339 39 312 356

238 507 243 347 352 323 352 186 380 337 248 266 384 374 168 57 389 241 376 374 183 198 373 384 388 323 101 352 55 331 372

1 2 3 4 5 6 7 8 9 10 11 12 13 14

trpB trpE rocD hutU ddh -

SAUSA300_0694 SAUSA300_1267 SAUSA300_1262 SAUSA300_0860 SAUSA300_0029 SAUSA300_1548 SAUSA300_1446 SAUSA300_1858 SAUSA300_1483 SAUSA300_1012 SAUSA300_0707 SAUSA300_2278 SAUSA300_2463 SAUSA300_0301

-15.63 -14.88 -14.61 -14.1 -14.05 -13.8 -13.53 -13.23 -13.18 -12.89 -12.71 -12.62 -12.29 -12.16

0 0.001 0.001 0.002 0.002 0.002 0.002 0.003 0.003 0.004 0.005 0.005 0.006 0.007

203 237 196 271 185 235 80 268 228 199 270 202 28 272

216 255 214 285 200 255 94 283 241 214 283 214 42 290

SAUSA300s301

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15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61

moaD lgt ahpF rpe aroC ksgA sarT dltB recO agrB tagA metS ispD murE pgi -

SAUSA300_2221 SAUSA300_0302 SAUSA300_0744 SAUSA300_0658 SAUSA300_0379 SAUSA300_1115 SAUSA300_1357 SAUSA300_0470 SAUSA300_0704 SAUSA300_2437 SAUSA300_1426 SAUSA300_1400 SAUSA300_0245 SAUSA300_0836 SAUSA300_1729 SAUSA300_1344 SAUSA300_0414 SAUSA300_0418 SAUSA300_1352 SAUSA300_1326 SAUSA300_1526 SAUSA300_1101 SAUSA300_1421 SAUSA300_1479 SAUSA300_1961 SAUSA300_0585 SAUSA300_2307 SAUSA300_1506 SAUSA300_1194 SAUSA300_1702 SAUSA300_0646 SAUSA300_2505 SAUSA300_1989 SAUSA300_0569 SAUSA300_1503 SAUSA300_2168 SAUSA300_0177 SAUSA300_0623 SAUSA300_1353 SAUSA300_0467 SAUSA300_0249 SAUSA300_0919 SAUSA300_2425 SAUSA300_0865 SAUSA300_2077 SAUSA300_2093 SAUSA300_2468

-11.98 -11.87 -11.65 -11.57 -11.52 -11.47 -11.26 -11.16 -11.15 -11.14 -10.82 -10.74 -10.66 -10.62 -10.54 -10.46 -10.46 -10.44 -10.41 -10.36 -10.28 -10.21 -10.18 -10.16 -10.14 -10.08 -10 -9.97 -9.96 -9.87 -9.86 -9.83 -9.82 -9.78 -9.78 -9.75 -9.73 -9.7 -9.7 -9.65 -9.59 -9.55 -9.52 -9.51 -9.48 -9.4 -9.3

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0.008 0.008 0.009 0.01 0.01 0.01 0.012 0.013 0.013 0.013 0.015 0.016 0.017 0.017 0.018 0.018 0.018 0.019 0.019 0.019 0.02 0.021 0.021 0.021 0.022 0.022 0.023 0.024 0.024 0.025 0.025 0.025 0.025 0.026 0.026 0.026 0.027 0.027 0.027 0.028 0.028 0.029 0.029 0.03 0.03 0.031 0.033

273 272 287 273 181 83 198 270 271 237 203 140 286 288 201 205 141 141 316 152 81 146 222 53 72 120 176 203 143 193 146 272 58 196 27 243 143 234 119 151 288 202 230 204 142 196 181

291 290 303 291 194 95 216 284 283 246 216 156 295 303 210 219 152 152 329 166 95 166 236 71 86 131 191 217 156 210 159 285 78 214 38 259 156 249 129 163 304 214 246 216 156 210 195

62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80

tagH dnaB sarA est nsaS rpoE udk -

SAUSA300_0624 SAUSA300_0016 SAUSA300_0383 SAUSA300_0605 SAUSA300_0763 SAUSA300_1581 SAUSA300_0252 SAUSA300_2558 SAUSA300_2082 SAUSA300_0719 SAUSA300_0925 SAUSA300_0553 SAUSA300_2343 SAUSA300_1568 SAUSA300_0483 SAUSA300_2248 SAUSA300_0761 SAUSA300_0659 SAUSA300_0881

-9.11 -9.11 -9.05 -9.03 -8.98 -8.95 -8.93 -8.8 -8.78 -8.75 -8.71 -8.69 -8.68 -8.67 -8.65 -8.59 -8.51 -8.41 -8.32

0.035 0.035 0.036 0.037 0.037 0.038 0.038 0.04 0.041 0.041 0.042 0.043 0.043 0.043 0.043 0.044 0.046 0.048 0.049

271 39 130 263 195 202 37 112 190 116 74 120 189 272 88 203 146 279 34

285 54 146 279 210 213 51 125 208 133 89 131 209 285 104 216 163 295 51

1 2 3 4 5 6 7 8 9 10 11 12 13 14

hsdM moaD argR msrA fhs rplL cdr

SAUSA300_0232 SAUSA300_0176 SAUSA300_0285 SAUSA300_1879 SAUSA300_1752 SAUSA300_2221 SAUSA300_1469 SAUSA300_1212 SAUSA300_1256 SAUSA300_1678 SAUSA300_0525 SAUSA300_1065 SAUSA300_0283 SAUSA300_0873

-14.23 -10.07 -10.03 -9.88 -9.87 -9.4 -9.4 -9.31 -8.94 -8.79 -8.51 -8.47 -8.38 -8.36

0.001 0.023 0.023 0.025 0.025 0.031 0.031 0.032 0.038 0.041 0.046 0.046 0.048 0.049

67 72 9 69 64 11 12 9 10 19 11 10 11 10

83 81 21 86 78 24 22 19 21 25 25 21 22 25

1 2 3 4 5 6 7 8 9 10

manA cysK fruB gntK -

SAUSA300_0856 SAUSA300_1057 SAUSA300_2577 SAUSA300_0491 SAUSA300_0684 SAUSA300_2510 SAUSA300_0618 SAUSA300_2450 SAUSA300_2443 SAUSA300_1673

-14.47 -11.69 -10.83 -9.89 -9.63 -9.58 -9.53 -9.53 -9.24 -8.52

0.001 0.009 0.015 0.025 0.028 0.029 0.029 0.029 0.033 0.046

16 4 37 19 43 22 43 35 1 3

30 19 49 34 51 33 51 49 12 18

SAUSA300s302

SAUSA300s303

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11 mnhG SAUSA300_0849

-8.32

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0.049

3

12

mRNA_start mRNA_stop 2 1 -75 10 -65 -54 5 11 -50 -11 -23 6 -75 8 -80 -62 -20 9 1

20 14 -62 20 -52 -40 20 20 -35 5 -13 18 -55 20 -68 -50 -9 17 18

-69 -72 -4 -69 -68 11 -72 -5 -80 -76 -29 -58 7 -12 -70 -80 -75 -1 -5

-49 -61 8 -60 -54 19 -60 12 -67 -61 -12 -50 18 4 -55 -68 -66 13 7

-11 -12

9 7

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-16 -16 -22 -14 -18 -15 -69 -26 -80 -78 -17 -67 -22 -14 -15 -14 -66 -44 -20 -16 -18 -64 -13 -21 -8 3 -69 -67 -80 -67 -57 -8 -50 -18 -19 -24 -13 10 -13 -53 -73 -22 -39 -79

2 -6 -6 -3 -2 -5 -54 -7 -71 -66 -4 -57 -4 -5 -1 -1 -52 -30 -8 -1 -2 -49 7 -5 13 18 -54 -51 -66 -56 -39 8 -37 3 -7 -12 8 19 -1 -42 -58 -11 -24 -70

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-73

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**************************************** PROGRAM PARAMETERS TargetRNA version: Replicon: NTs before start codon: NTs after start codon: Seed length: sRNA conservation and accessibility: sRNA window size: mRNA structural accessibility: Interaction region: Filter size: Single target: File of candidate targets: p-value: ****************************************

TRUE

sRNAs predicted to regulate at least one virulence factor sRNAs not predicted to regulate any virulence factor Transcripts where predictions using TargetRNA2 were not possible due to size-restrictions Known virulence factors of S. aureus

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TRUE

-

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2.01 Staphylococcus aureus subsp. aureus USA300_FPR3757 chromosome 80 20 7 13 20 400 0.05 http://tempest.wellesley.edu/~btjaden/TargetRNA2/index.html

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