Table 2 Gene-ontology (GO) terms of intragenic and non-homoplastic variants (SNPs and InDels) fixed in Salmonella enterica subsp. enterica serovars Dublin versus all the others genomes (Ontology 1 called ‘Dub_All’), Pullorum/Gallinarum versus Enteritidis (Ontology 2 called ‘Ent_Pull/Gall’), Pullorum versus Gallinarum (Ontology 3 called ‘Pull_Gall’), and Gallinarum versus Pullorum (Ontology 4 called ‘Gall_Pull’)
Gene-ontology enrichment analysis | GO ID | GO-term | Number of hits | Expected number of hits | GO-level | p-value | Corrected p-value | Ontology |
|---|---|---|---|---|---|---|---|---|
1 | GO:0006105 | succinate metabolic process | 36 | 14.692 | 8 | 5.8×10−13 | 8.1×10−10 | BP |
|  | GO:0006307 | DNA dealkylation involved in DNA repair | 4 | 1.433 | 9 | 1.0×10−42 | 1.0×10−39 | BP |
|  | GO:0006468 | protein phosphorylation | 61 | 40.850 | 8 | 3.9×10−05 | 5.5×10−02 | BP |
|  | GO:0006520 | cellular amino acid metabolic process | 533 | 445.766 | 7 | 6.4×10−08 | 9.0×10−05 | BP |
|  | GO:0006525 | arginine metabolic process | 104 | 53.392 | 10 | 8.4×10−18 | 1.1×10−14 | BP |
|  | GO:0006527 | arginine catabolic process | 62 | 25.800 | 11 | 1.3×10−19 | 1.9×10−16 | BP |
|  | GO:0006545 | glycine biosynthetic process | 5 | 1.792 | 11 | 1.0×10−42 | 1.0×10−39 | BP |
|  | GO:0006560 | proline metabolic process | 81 | 46.583 | 10 | 2.4×10−10 | 3.4×10−07 | BP |
|  | GO:0006562 | proline catabolic process | 27 | 12.183 | 11 | 3.4×10−08 | 4.9×10−05 | BP |
|  | GO:0009064 | glutamine family amino acid metabolic process | 190 | 116.817 | 9 | 4.6×10−17 | 6.5×10−14 | BP |
|  | GO:0009065 | glutamine family amino acid catabolic process | 89 | 37.983 | 10 | 2.4×10−25 | 3.4×10−22 | BP |
|  | GO:0009233 | menaquinone metabolic process | 27 | 13.258 | 6 | 9.0×10−07 | 1.2×10−03 | BP |
|  | GO:0009234 | menaquinone biosynthetic process | 27 | 13.258 | 7 | 9.0×10−07 | 1.2×10−03 | BP |
|  | GO:0010133 | proline catabolic process to glutamate | 27 | 12.183 | 11 | 3.4×10−08 | 4.9×10−05 | BP |
|  | GO:0019544 | arginine catabolic process to glutamate | 10 | 3.942 | 12 | 1.2×10−05 | 1.7×10−02 | BP |
|  | GO:0019545 | arginine catabolic process to succinate | 36 | 14.692 | 9 | 5.8×10−13 | 8.1×10−10 | BP |
|  | GO:0035510 | DNA dealkylation | 4 | 1.433 | 8 | 1.0×10−42 | 1.0×10−39 | BP |
|  | GO:1,901,565 | organonitrogen compound catabolic process | 162 | 112.517 | 5 | 3.8×10−09 | 5.3×10−06 | BP |
|  | GO:1,901,605 | alpha-amino acid metabolic process | 320 | 240.441 | 8 | 8.0×10−11 | 1.1×10−07 | BP |
|  | GO:1,901,606 | alpha-amino acid catabolic process | 100 | 62.350 | 9 | 1.9×10−09 | 2.7×10−06 | BP |
|  | GO:0009379 | Holliday junction helicase complex | 4 | 1.408 | 5 | 1.0×10−42 | 1.0×10−39 | CC |
|  | GO:0003842 | 1-pyrroline-5-carboxylate dehydrogenase activity | 27 | 12.957 | 6 | 1.5×10−07 | 1.8×10−04 | MF |
|  | GO:0003908 | methylated-DNA-[protein]-cysteine S-methyltransferase activity | 4 | 1.524 | 7 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004020 | adenylylsulfate kinase activity | 4 | 1.524 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004072 | aspartate kinase activity | 6 | 2.286 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004372 | glycine hydroxymethyltransferase activity | 5 | 1.905 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004412 | homoserine dehydrogenase activity | 6 | 2.286 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004657 | proline dehydrogenase activity | 27 | 12.957 | 5 | 1.5×10−07 | 1.8×10−04 | MF |
|  | GO:0004743 | pyruvate kinase activity | 10 | 3.811 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0004815 | aspartate-tRNA ligase activity | 5 | 1.905 | 7 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0008770 | [acyl-carrier-protein] phosphodiesterase activity | 4 | 1.524 | 7 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0009015 | N-succinylarginine dihydrolase activity | 12 | 4.954 | 6 | 3.5×10−06 | 4.1×10−03 | MF |
|  | GO:0009017 | succinylglutamate desuccinylase activity | 10 | 4.192 | 6 | 2.4×10−05 | 2.8×10−02 | MF |
|  | GO:0015166 | polyol transmembrane transporter activity | 12 | 4.573 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0015169 | glycerol-3-phosphate transmembrane transporter activity | 12 | 4.573 | 8 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0015430 | glycerol-3-phosphate-transporting ATPase activity | 6 | 2.286 | 9 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0015605 | organophosphate ester transmembrane transporter activity | 12 | 4.573 | 5 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0016749 | N-succinyltransferase activity | 5 | 1.905 | 7 | 1.0×10−42 | 1.0×10−39 | MF |
|  | GO:0018480 | 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase activity | 8 | 3.049 | 6 | 1.0×10−42 | 1.0×10−39 | MF |
2 | GO:0003973 | (S)-2-hydroxy-acid oxidase activity | 4 | 0.013 | 6 | 1.1×10−12 | 1.3×10−09 | MF |
|  | GO:0016899 | oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor | 4 | 0.013 | 5 | 1.1×10−12 | 1.3×10−09 | MF |
3 | GO:0043603 | cellular amide metabolic process | 36 | 17.451 | 5 | 1.9×10−05 | 2.7×10−02 | BP |
|  | GO:0006428 | isoleucyl-tRNA aminoacylation | 4 | 0.445 | 11 | 4.7×10−05 | 6.7×10−02 | BP |
|  | GO:0006522 | alanine metabolic process | 4 | 0.376 | 10 | 1.8×10−05 | 2.5×10−02 | BP |
|  | GO:0009078 | pyruvate family amino acid metabolic process | 4 | 0.376 | 9 | 1.8×10−05 | 2.5×10−02 | BP |
|  | GO:0004822 | isoleucine-tRNA ligase activity | 4 | 0.475 | 7 | 6.5×10−05 | 7.5×10−02 | MF |
|  | GO:0015079 | potassium ion transmembrane transporter activity | 8 | 1.680 | 9 | 3.7×10−05 | 4.2×10−02 | MF |
|  | GO:0008079 | translation termination factor activity | 5 | 0.657 | 7 | 3.0×10−05 | 3.4×10−02 | MF |
|  | GO:0003747 | translation release factor activity | 5 | 0.657 | 8 | 3.0×10−05 | 3.4×10−02 | MF |
4 | GO:0043603 | cellular amide metabolic process | 36 | 17.473 | 5 | 2.0×10−05 | 2.8×10−02 | BP |
|  | GO:0006428 | isoleucyl-tRNA aminoacylation | 4 | 0.445 | 11 | 4.8×10−05 | 6.7×10−02 | BP |
|  | GO:0006522 | alanine metabolic process | 4 | 0.377 | 10 | 1.8×10−05 | 2.5×10−02 | BP |
|  | GO:0009078 | pyruvate family amino acid metabolic process | 4 | 0.377 | 9 | 1.8×10−05 | 2.5×10−02 | BP |
|  | GO:0004822 | isoleucine-tRNA ligase activity | 4 | 0.475 | 7 | 6.5×10−05 | 7.5×10−02 | MF |
|  | GO:0015079 | potassium ion transmembrane transporter activity | 8 | 1.681 | 9 | 3.7×10−05 | 4.2×10−02 | MF |
|  | GO:0008079 | translation termination factor activity | 5 | 0.658 | 7 | 3.0×10−05 | 3.4×10−02 | MF |
|  | GO:0003747 | translation release factor activity | 5 | 0.658 | 8 | 3.0×10−05 | 3.4×10−02 | MF |