Table 4.
Genes under positive selection.
| Gene locus | Gene description (gene symbol) | COG(1) | Recombination(2) | Branch under pos. selection | Q-value | ω(3) | p(4) | BEB (P > 95%)(5) |
|---|---|---|---|---|---|---|---|---|
| Lmo0098 | PTS system, mannose/fructose/sorbose family, IID component (mptD) | NCOG | GCV; MAX | LI/LM | 0.170 | 472.58 | 0.004 | - |
| Lmo0099 | conserved hypothetical protein | NCOG | - | LI/LM | 0.170 | ∞ | 0.009 | - |
| Lmo0139 | conserved hypothetical protein | NCOG | - | LM2A | 0.160 | 56.74 | 0.054 | 95 |
| Lmo0297 | PRD/PTS system IIA 2 domain protein | K; G; T | GCV; MAX; NSS; PHI | LM2A | 0.164 | ∞ | 0.012 | 499 |
| Lmo0397 | conserved hypothetical protein | S | GCV; MAX | LM2A | 0.1264 | ∞ | 0.043 | - |
| Lmo0429 | glycosyl hydrolase, family 38 | G | GCV; MAX; NSS; PHI | LM2A | 0.0325 | 977.51 | 0.008 | 667 |
| Lmo0455 | conserved hypothetical protein | T; Q | GCV; MAX; NSS; PHI | LM2A | 0.1214 | ∞ | 0.004 | - |
| Lmo0653 | conserved hypothetical protein | S | MAX | LM2A | 0.033 | ∞ | 0.012 | 306 |
| Lmo0658 | endonuclease III domain protein | L | MAX; NSS | LM2A | 0.108 | ∞ | 0.023 | 209 |
| Lmo0692 | chemotaxis protein CheA (cheA) | T; N | GCV; MAX; NSS; PHI | LM1A | 0.156 | ∞ | 0.002 | - |
| Lmo0693 | flagellar motor switch domain protein | N; U | - | LM2A | 0.007 | ∞ | 0.022 | - |
| Lmo0695 | conserved hypothetical protein | NCOG | MAX; NSS; PHI | LM1A | 0.175 | ∞ | 0.014 | - |
| Lmo0732 | cell wall surface anchor family protein | NCOG | GCV | LM1A | 0.185 | 6.92 | 0.076 | - |
| Lmo0782 | PTS system, mannose/fructose/sorbose family, IIC component (mpoD) | NCOG | GCV; MAX | Overall; | 0.146; | 88.23; | 0.008; | - |
| LM1A; | 0.052; | ∞; | 0.0001; | - | ||||
| LM2A | 0.098 | ∞ | 0.004 | - | ||||
| Lmo0785 | sigma-54 dependent Kal regulator (manR) | K; T | GCV; MAX | LM2A | 0.129 | 1.00 | 0.000 | - |
| Lmo0872 | major facilitator family transporter | G | GCV; MAX; NSS | LM2A | 0.137 | ∞ | 0.008 | - |
| Lmo0910 | putative membrane protein | R | MAX; NSS | LM1A | 0.019 | ∞ | 0.012 | - |
| Lmo1146 | conserved hypothetical protein | NCOG | GCV; MAX | LI/LM | 0.046 | 223.37 | 0.023 | 169 |
| Lmo1164 | PduO protein (pduO) | S; R | GCV | LI/LM | 0.170 | 195.87 | 0.038 | - |
| Lmo1412 | DNA topology modulation protein FlaR (flaR) | F | - | LM2A | 0.160 | 8.56 | 0.139 | 12; 37; 68 |
| Lmo1424 | transporter, NRAMP family (mntH) | P | GCV | LM1A | 0.185 | 1.00 | 0.000 | - |
| Lmo1523 | GTP pyrophosphokinase (relA) | K; T | - | LM2A | 0.033 | 1.00 | 0.000 | - |
| Lmo1529 | preprotein translocase, YajC subunit | U | - | LI/LM | 0.170 | ∞ | 0.011 | - |
| Lmo2102 | glutamine amidotransferase, SNO family (pdxT) | H | GCV; MAX; NSS; PHI | LM1A | 0.185 | ∞ | 0.017 | 66 |
| Lmo2121 | glycosyl transferase, family 65 | G | GCV; MAX; NSS | LM1A | 7.6E-06 | 35.31 | 0.031 | 722; 723; 725; 729; 730; 744; 752; |
| Lmo2178 | cell wall surface anchor family protein | M | GCV; MAX; NSS; PHI | LI/LM; | 0.193; | 15.92; | 0.001; | - |
| LM2A | 0.137 | 5.34 | 0.025 | 1769 | ||||
| Lmo2215 | ABC transporter, ATP-binding protein | V | MAX; NSS | Overall | 0.188 | 14.23 | 0.008 | - |
| Lmo2222 | Ser/Thr protein phosphatase family protein | L | GCV; MAX | LM2A | 0.160 | ∞ | 0.021 | 253 |
| Lmo2446 | glycosyl hydrolase, family 31 | G | GCV; MAX; NSS; PHI | LM2A | 0.003 | ∞ | 0.0001 | - |
| Lmo2596 | ribosomal protein S9 (rpsI) | NCOG | - | LM2A | 0.021 | ∞ | 0.010 | - |
| Lmo2611 | adenylate kinase (adk) | F | GCV; MAX | LM2A | 0.120 | 24.80 | 0.013 | - |
| Lmo2724 | conserved hypothetical protein | S | NSS | LI/LM | 0.170 | ∞ | 0.008 | - |
| Lmo2802 | glucose-inhibited division protein B (girB) | M | GCV; MAX; NSS; PHI | LM1A | 0.046 | ∞ | 0.013 | - |
| Lmo2804 | conserved hypothetical protein | NCOG | GCV; MAX; NSS; PHI | Overall | 6.5E-17 | 16.53 | 0.044 | - |
| Lmo2824 | D-isomer specific 2- hydroxyacid dehydrogenase family protein | E; H | GCV; MAX; NSS | LM2A | 0.160 | 229.62 | 0.003 | - |
(1) NCOG: Not in COGs; K: Transcription; G: Carbohydrate transport and metabolism; T: Signal transduction mechanisms; S: Function unknown; Q: Secondary metabolites biosynthesis, transport and catabolism; L: Replication, recombination and repair; N: Cell motility; U: Intracellular trafficking and secretion; R: General function prediction only; F: Nucleotide transport and metabolism; P: Inorganic ion transport and metabolism; E: Amino acid transport and metabolism; H: Coenzyme transport and metabolism; M: Cell wall/membrane biogenesis; V: Defense mechanisms
(2) GCV: GENECONV; MAX: Maximum χ2; NSS: Neighbour Similarity Score; PHI: Pairwise Homoplasy Test
(3) ω = dN/dS (Number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous sites); infinite values of ω (∞) indicate that the model did not find synonymous changes for the branches tested (dS = 0; ω ~ ∞). However, this (i.e., ω ~ ∞) does not affect the validity of the Likelihood Ratio Test, which was used to identify the genes under positive selection (Z. Yang, pers. Communication; see http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2079&sid=c4a82e1ca334ca84a00a8b85e0f33c9d and http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2329&sid=c4a82e1ca334ca84a00a8b85e0f33c9d;
(4) Proportion of sites under positive selection
(5) This column lists sites identified using Bayes Empirical Bayes (BEB) as being under positive selection; numbers identify the amino acid sites (in alignments) that are under positive selection