Spreadsheet: 2e07fc45-b92f-43c2-9ee6-46aab4709b02
Sheet: Sheet1

Table S3. ORFs containing sequence changes in comparison of the Mexico A genome with the [NAME] genome. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5
ORF annotated in the [NAME] genome (GenBank acc. no. AE000520.1) | ORF annotated in the Mexico A genome | Changes found in comparison the Mexico A genome with the [NAME] genome (GenBank acc. no. AE000520.1) | Changes found in comparison the Mexico A genome with the revised [NAME] genome (Pospíšilová, unpublished) | Predicted function | Functional category
TP_0005 | TPAMA_0005 | sub | sub | cDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | DNA Replication, Repair, Recombination
TP_0006 | TPAMA_0006 | sub | no change | conserved hypothetical protein | Unknown
TP_0007 | TPAMA_0006 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0009 | TPAMA_0009 | sub | sub | [NAME] protein A | Virulence
TP_0012 | - | del (1 bp) | del (1 bp) | hypothetical protein | Unknown
TP_0013 | TPAMA_0013 | in (2 bp) | no change | conserved hypothetical protein | Unknown
TP_0018 | TPAMA_0018 | sub, 3 in (1 bp) | sub | transcription elongation factor GreA | Transcription
TP_0020 | TPAMA_0020 | sub | no change | hypothetical membrane protein | Unknown
TP_0040 | TPAMA_0040 | del (1 bp) | del (1 bp) | probable methyl-accepting chemotaxis protein | Cell processes
TP_0049 | TPAMA_0049 | sub, in (1 bp) | in (1 bp) | hypothetical protein | General metabolism
TP_0051 | TPAMA_0051 | sub | sub | peptide chain release factor RF1 | Translation
TP_0065 | TPAMA_0065 | in (1 bp) | no change | probable SAM dependent methyltransferase | General metabolism
TP_0067 | - | in (1 bp), sub | in (1 bp), sub | conserved hypothetical protein | Unknown
TP_0073 | TPAMA_0073 | sub | sub | conserved hypothetical protein | Unknown
TP_0076 | TPAMA_0076 | sub, in (1 bp) | no change | sugar ABC superfamily ATP binding cassette transporter, membrane protein | Transport
TP_0077 | TPAMA_0077 | sub | sub | capsular polysaccharide biosynthesis protein CapD | Cell structure
TP_0079 | TPAMA_0079 | sub | sub | bifunctional aldehyde oxidase/xanthine dehydrogenase | General metabolism
TP_0082 | TPAMA_0082 | in (1 bp) | no change | sigma-54 dependent transcriptional regulator | Regulation
TP_0083 | TPAMA_0083 | sub, in (1 bp) | sub | conserved hypothetical protein | Unknown
TP_0098 | TPAMA_0098 | del (1 bp) | no change | [NAME] | Cell processes
TP_0106 | TPAMA_0106 | 2 sub | no change | BCCT family betaine/carnitine/choline transporter | Transport
TP_0117 | TPAMA_0117 | 20 sub | 20 sub | [NAME] protein C | Virulence
TP_0126 | TPAMA_0126 | del (1 bp) |  | hypothetical protein | Unknown
TP_0127 | [NAME] | del (1 bp) | no change | hypothetical protein | Unknown
TP_0131 | TPAMA_0131 | MSC |  | [NAME] protein D | Virulence
TP_0134 | TPAMA_0134 | sub |  | hypothetical outer membrane protein | Unknown
TP_0135 | TPAMA_0135 | 2 sub, 1 in (1 bp) | partial data | hypothetical protein | Unknown
TP_0136 | TPAMA_0136 | 50 sub, 2 del (3 bp, 6 bp) | 50 sub, 2 del (3 bp, 6 bp) | hypothetical outer membrane protein | Virulence
TP_0137 | - | sub | sub | hypothetical protein | Unknown
TP_0147 | TPAMA_0147 | sub | sub | glycosyl hydrolase family protein | General metabolism
TP_0154 | TPAMA_0154 | 4 sub | no change | pseudouridylate synthase | Translation
TP_0172 | TPAMA_0172 | in (1 bp) | no change | conserved hypothetical membrane protein | Unknown
TP_0173 | TPAMA_0172 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0174 | TPAMA_0174 | del (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0175 | TPAMA_0174 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0176 | TPAMA_0174 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0177 | TPAMA_0177 | del (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0178 | TPAMA_0178 | sub | sub | hypothetical protein | Unknown
TP_0179 | TPAMA_0179 | 8 sub | 8 sub | hypothetical protein | Unknown
TP_0180 | TPAMA_0179 | in (2 bp) | in (2 bp) | conserved hypothetical protein | Unknown
TP_0208 | TPAMA_0208 | in (1 bp) | no change | [NAME] family Type I general secretory pathway protein SecY | Transport
TP_0217 | TPAMA_0217 | in (1 bp) | no change | [NAME] | Cell processes
TP_0221 | TPAMA_0221 | in (1 bp) | no change | serine-type D-Ala-D-Ala carboxypeptidase | Cell structure
TP_r01 | TPAMA_r0001 | in (1 bp) | no change | 16S ribosomal RNA | RNA
TP_0230 | [NAME] | sub | sub | DNA replication factor Y | DNA Replication, Repair, Recombination
TP_0233 | TPAMA_0233 | sub | sub | anti sigma factor antagonist | Regulation
TP_0245 | [NAME] | sub | sub | conserved hypothetical protein | Unknown
TP_0248 | - | del (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0252 | TPAMA_0252 | sub | sub | apolipoprotein N-acyltransferase | Cell structure
TP_0254 | TPAMA_0254 | sub | sub | transcription termination factor [NAME] | Transcription
TP_0258 | TPAMA_0258 | 2 sub | 2 sub | conserved hypothetical protein | Unknown
TP_0263 | TPAMA_0263 | in (1 bp) | no change | conserved hypothetical protein | Virulence
TP_0265 | TPAMA_0265 | sub | sub | LIVCS family branched chain amino acid:cation symporter | Transport
TP_0279 | TPAMA_0279 | in (2 bp) | in (2 bp) | bifunctional cytidylate kinase/ribosomal protein S1 | Translation
TP_0284 | TPAMA_0284 | in (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0286 | TPAMA_0286 | in (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0287 | TPAMA_0286 | sub | sub | hypothetical protein | Unknown
TP_0288 | TPAMA_0288 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0297 | TPAMA_0297 | 2 sub | 2 sub | conserved hypothetical protein | Unknown
TP_0299 | TPAMA_0299 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0300 | TPAMA_0299 | sub | sub | sugar ABC superfamily ATP binding cassette transporter, ABC protein | Transport
TP_0304 | TPAMA_0304 | 4 sub, del (3 bp) | 4 sub, del (3 bp) | hypothetical protein | Unknown
TP_0309 | TPAMA_0309 | sub | sub | probable polar amino acid ABC superfamily ATP binding cassette transporter, binding protein | Transport
TP_0310 | TPAMA_0310 | 2 sub | 2 sub | probable single-stranded DNA-binding protein | DNA Replication, Repair, Recombination
TP_0313 | TPAMA_0313 | sub | sub | [NAME] protein E | Virulence
TP_0314 | - | 2 sub |  | hypothetical protein | Unknown
TP_0317 | TPAMA_0317 | 40 sub |  | [NAME] protein G | Virulence
TP_0319 | TPAMA_0319 | sub | sub | sugar ABC superfamily ATP binding cassette transporter, membrane protein | Transport
TP_0324 | TPAMA_0324 | in (1 bp) | no change | hypothetical outer membrane protein | Unknown
TP_0326 | TPAMA_0326 | 4 sub, del (15 bp) | 4 sub, del (15 bp) | outer membrane protein | Virulence
TP_0329 | TPAMA_0329 | del (1 bp) | no change | glycine hydroxymethyltransferase | General metabolism
TP_0330 | TPAMA_0330 | sub | sub | AAA family ATPase | General metabolism
TP_0344 | TPAMA_0344 | sub | sub | transcription-repair coupling factor | Transcription
TP_0346 | TPAMA_0346 | 2 sub | 2 sub | conserved hypothetical protein | Unknown
TP_0347 | - | del (4 bp) | del (4 bp) | hypothetical membrane protein | Unknown
TP_0348 | TPAMA_0348 | 2 in (1 bp) | in (1 bp) | hypothetical membrane protein | Unknown
TP_0350 | TPAMA_0350 | sub | no change | glutamate-5-semialdehyde dehydrogenase | General metabolism
TP_0376 | - | in (1 bp) | no change | hypothetical membrane protein | Unknown
TP_0377 | TPAMA_0377 | in (1 bp) | no change | flagellar basal body-associated protein FliL | Cell processes
TP_0379 | TPAMA_0379 | 2 sub | no change | [NAME] family Type I general secretory pathway protein SecA | Transport
TP_0387 | TPAMA_0387 | sub | sub | cell division protein FtsW | Cell processes
TP_0389 | TPAMA_0389 | sub | sub | cell division protein FtsA | Cell processes
TP_0394 | TPAMA_0394 | sub | sub | DNA topoisomerase TopA | DNA Replication, Repair, Recombination
TP_0402 | TPAMA_0402 | sub | sub | IIISP family [NAME] (virulence-related) secretory pathway protein | Virulence
TP_0407 | TPAMA_0407 | del (1 bp) | no change | HAD family hydrolase | General metabolism
TP_0408 | TPAMA_0408 | sub | sub | conserved hypothetical protein | Unknown
TP_0414 | TPAMA_0414 | sub | sub | AGCS family alanine or glycine:sodium (Na+) or proton (H+) symporter | Transport
TP_0415 | TPAMA_0415 | in (1 bp) | no change | hypothetical protein | Unknown
[NAME] | TPAMA_0419 | del (1 bp) | no change | acid phosphatase | Cell processes
TP_0424 | TPAMA_0424 | in (1 bp) | no change | two-sector ATPase, V(1) subunit E | Transport
TP_0425 | TPAMA_0425 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0430 | TPAMA_0430 | sub | sub | two-sector ATPase, V(0) subunit K | Transport
TP_0431 | TPAMA_0431 | sub | sub | probable [NAME] family transcriptional regulator | Regulation
TP_0433 | TPAMA_0433 | in (120 bp) | in (120 bp) | hypothetical protein | Unknown
TP_0443 | TPAMA_0443 | sub | sub | conserved hypothetical protein | Unknown
TP_0449 | TPAMA_0449 | sub | sub | hypothetical protein | Unknown
TP_0461 | TPAMA_0461 | del (1 bp) | del (1 bp) | probable transcriptional regulator | Regulation
TP_0462 | TPAMA_0462 | 7 sub, del (1 bp) | 7 sub | conserved hypothetical protein | Unknown
TP_0463 | TPAMA_0462 | sub | sub | hypothetical protein | Unknown
TP_0469 | - | 2 sub, in (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0470 | TPAMA_0470 | in (216 bp) | in (216 bp) | conserved hypothetical protein | Unknown
TP_0471 | TPAMA_0471 | sub | sub | conserved hypothetical protein | Unknown
TP_0473 | TPAMA_0473 | sub | sub | hypothetical membrane protein | Unknown
TP_0477 | TPAMA_0477 | in (1 bp) | no change | 6-phosphogluconolactonase | General metabolism
TP_0481 | TPAMA_0481 | sub, in (1 bp) | partial data | hypothetical protein | Unknown
TP_0485 | TPAMA_0485 | sub | sub | probable adenylate cyclase | General metabolism
TP_0486 | TPAMA_0486 | del (1 bp) | no change | Borrelia-like antigen p83/100 | Unknown
TP_0487 | TPAMA_0487 | 2 sub, in (1 bp) | partial data | hypothetical protein | Unknown
TP_0488 | TPAMA_0488 | 27 sub | 27 sub | methyl-accepting chemotaxis protein | Cell processes
TP_0491 | TPAMA_0491 | in (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0493 | TPAMA_0493 | sub | sub | DNA-directed [NAME] polymerase sigma subunit RpoD | Transcription
TP_0512 | TPAMA_0512 | sub | sub | bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | General metabolism
TP_0515 | TPAMA_0515 | 12 sub | 12 sub | conserved hypothetical outer membrane protein | Unknown
TP_0520 | TPAMA_0520 | in (1 bp) | no change | sensor histidine kinase | Regulation
TP_0529 | TPAMA_0529 | sub | sub | two-sector ATPase, V(1) subunit A | Transport
TP_0533 | TPAMA_0533 | in (1 bp) | no change | two-sector ATPase, V(0) subunit I | Transport
TP_0536 | TPAMA_0536 | 2 in (1 bp) | no change | hypothetical protein | Unknown
TP_0544 | TPAMA_0544 | in (6 bp) | in (6 bp) | conserved hypothetical protein | Unknown
TP_0547 | TPAMA_0547 | 2 sub | 2 sub | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | General metabolism
TP_0548 | TPAMA_0548 | 32 sub, 2 in (3 bp, 9 bp) | partial data | hypothetical membrane protein | Unknown
TP_0554 | TPAMA_0554 | sub | sub | phosphoglycolate phosphatase | General metabolism
TP_0555 | TPAMA_0555 | in (1 bp) | no change | [NAME] family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter | Transport
TP_0558 | TPAMA_0558 | 5 sub | 5 sub | probable NiCoT family nickel (Ni2+)-cobalt (Co2+) transporter | Transport
TP_0559 | TPAMA_0559 | 2 sub | 2 sub | thiamine biosynthesis ATP pyrophosphatase | General metabolism
TP_0560 | TPAMA_0560 | sub | sub | transketolase | General metabolism
TP_0569 | TPAMA_0569 | sub | sub | Xaa-Pro aminopeptidase | General metabolism
TP_0571 | [NAME] | sub | sub | [NAME] family protein | Cell structure
TP_0574 | TPAMA_0574 | sub | sub | [NAME] | Virulence
TP_0575 | TPAMA_0575 | in (1 bp) | no change | EI family phosphotransferase system enzyme I | Transport
TP_0583 | - | sub | no change | hypothetical protein | Unknown
TP_0584 | TPAMA_0584 | sub | sub | hypothetical protein | Unknown
TP_0588 | TPAMA_0587 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0591 | TPAMA_0591 | 4 sub | sub | bifunctional Hpr kinase/phosphatase | General metabolism
TP_0594 | TPAMA_0594 | sub, del (1 bp) | sub | conserved hypothetical protein | Unknown
TP_0598 | TPAMA_0598 | 2 sub, 3 in (1 bp, 2 bp, 1 bp) | sub | hypothetical protein | Unknown
TP_0610 | TPAMA_0610 | sub |  | [NAME] protein H | Virulence
TP_0612 | TPAMA_0612 | sub | sub | ABC superfamily ATP binding cassette transporter, membrane protein | Transport
TP_0618 | TPAMA_0618 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0619 | TPAMA_0619 | 13 sub | 13 sub | hypothetical protein | Unknown
TP_0620 | TPAMA_0620 | 5 sub | 5 sub | [NAME] protein I | Virulence
TP_0621 | TPAMA_0621 | 6 sub | 6 sub | [NAME] protein J | Virulence
TP_0630 | TPAMA_0630 | sub | sub | protein-glutamate O-methyltransferase | Cell processes
TP_0633 | TPAMA_0633 | sub | no change | bifunctional peptide-methionine (S)-S-oxide reductase/peptide-methionine (R)-S-oxide reductase | Cell processes
TP_0640 | TPAMA_0640 | sub | sub | methyl-accepting chemotaxis protein | Cell processes
TP_0644 | TPAMA_0644 | sub | sub | lysine--tRNA ligase | Translation
TP_0651 | - | in (1 bp) | no change | conserved hypothetical membrane protein | Unknown
TP_0665 | TPAMA_0665 | sub | sub | conserved hypothetical protein | Unknown
TP_0667 | TPAMA_0667 | sub | sub | bifunctional phosphoribulokinase/uridine kinase | General metabolism
TP_0668 | TPAMA_0668 | del (6 bp) | del (6 bp) | hypothetical membrane protein | Unknown
TP_0697 | - | in (1 bp) | in (1 bp) | hypothetical membrane protein | Unknown
TP_0699 | - | sub | sub | hypothetical protein | Unknown
TP_0703 | TPAMA_0702 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0721 | TPAMA_0721 | sub | sub | flagellar motor switch protein FliM | Cell structure
TP_0731 | TPAMA_0731 | in (1 bp) | no change | ADP-ribose diphosphatase | General metabolism
[NAME] | TPAMA_0736 | sub | sub | [NAME]) reductase, subunit alpha | General metabolism
TP_0737 | TPAMA_0737 | sub | sub | sugar ABC superfamily ATP binding cassette transporter, binding protein | Transport
TP_0746 | TPAMA_0746 | sub | sub | pyruvate, phosphate dikinase | General metabolism
TP_0748 | [NAME] | sub | sub | cytoplasmic filament protein A | Cell processes
TP_0756 | TPAMA_0756 | sub | sub | methionyl-tRNA formyltransferase | Translation
TP_0762 | TPAMA_0762 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0770 | TPAMA_0770 | sub | sub | probable ATP-dependent RNA helicase | Translation
TP_0782 | TPAMA_0781 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0790 | TPAMA_0790 | sub | sub | probable RND superfamily resistance-nodulation-cell division antibiotic:proton (H+) antiporter | Transport
TP_0792 | TPAMA_0791 | sub | sub | hypothetical protein | Unknown
TP_0804 | TPAMA_0804 | sub | sub | sugar ABC superfamily ATP binding cassette transporter, ABC protein | Transport
TP_0805 | TPAMA_0805 | 2 sub | no change | probable exoribonuclease II | Transcription
TP_0813 | TPAMA_0813 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0820 | TPAMA_0820 | sub | sub | conserved hypothetical protein | Unknown
TP_0830 | TPAMA_0830 | in (1 bp) | no change | tRNA-pseudouridine synthase I | Translation
TP_0841 | TPAMA_0841 | sub | sub | S1 family peptidase Do | General metabolism
TP_0854 | TPAMA_0854 | sub | sub | conserved hypothetical membrane protein | Unknown
TP_0856 | TPAMA_0856 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0858 | TPAMA_0858 | 3 sub | 3 sub | hypothetical protein | Unknown
TP_0859 | TPAMA_0859 | del (1 bp) | no change | hypothetical protein | Unknown
TP_0865 | TPAMA_0865 | 2 sub, in (3 bp) | 2 sub, in (3 bp) | hypothetical outer membrane protein | Unknown
TP_0866 | TPAMA_0866 | in (1 bp) | no change | conserved hypothetical protein | Unknown
TP_0867 | TPAMA_0867 | sub | sub | hypothetical protein | Unknown
TP_0872 | TPAMA_0872 | sub | sub | flagellar hook-associated protein FliD | Cell structure
TP_0877 | TPAMA_0877 | 2 sub | 2 sub | conserved hypothetical protein | Unknown
TP_0885 | TPAMA_0885 | sub | sub | dUTP diphosphatase | General metabolism
TP_0896 | TPAMA_0896 | 2 sub |  | hypothetical protein | Unknown
TP_0897 | TPAMA_0897 | MSC | MSC | [NAME] protein K | Virulence
TP_0898 | TPAMA_0898 | 2 sub | partial data | exodeoxyribonuclease V beta subunit | DNA Replication, Repair, Recombination
TP_0899 | TPAMA_0899 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0912 | TPAMA_0912 | 2 sub | 2 sub | conserved hypothetical protein | Unknown
TP_0915 | TPAMA_0915 | sub | sub | conserved hypothetical protein | Unknown
TP_0921 | TPAMA_0921 | 2 in (1 bp, 2 bp) | partial data | NADH dehydrogenase | General metabolism
TP_0923 | TPAMA_0923 | 2 in (2 bp, 1 bp) | no change | hypothetical outer membrane protein | Unknown
TP_0924 | TPAMA_0924 | sub | sub | transcriptional accessory protein | Transcription
TP_0928 | TPAMA_0928 | in (1 bp) | no change | hypothetical protein | Unknown
TP_0950 | - | in (1 bp) | no change | hypothetical protein | Unknown
TP_0952 | TPAMA_0952 | sub | sub | probable lipase/esterase | General metabolism
TP_0958 | TPAMA_0958 | sub | sub | TRAP-T family tripartite ATP-independent periplasmic transporter, membrane protein | Transport
TP_0966 | TPAMA_0966 | 4 sub | 4 sub | hypothetical protein | Unknown
TP_0967 | TPAMA_0967 | in (9 bp) | in (9 bp) | hypothetical protein | Unknown
TP_0968 | TPAMA_0968 | 3 sub | 3 sub | hypothetical protein | Unknown
TP_0973 | TPAMA_0973 | sub | sub | phenylalanine--tRNA ligase alpha subunit | Translation
TP_0976 | TPAMA_0976 | sub | sub | hypothetical membrane protein | Unknown
TP_0978 | TPAMA_0978 | sub | sub | signal peptidase II | Cell processes
TP_0983 | TPAMA_0983 | sub | no change | hypothetical protein | Unknown
TP_0993 | TPAMA_0993 | in (1 bp) | no change | probable rare lipoprotein A | Unknown
TP_0995 | TPAMA_0995 | sub, in (1 bp) | sub | probable [NAME] family transcription factor | Regulation
TP_1028 | TPAMA_1028 | sub | sub | excision endonuclease subunit UvrD | DNA Replication, Repair, Recombination
TP_1029 | TPAMA_1029 | sub | sub | hypothetical protein | Unknown
TP_1030 | TPAMA_1030 | 7 sub, 2 in (1 bp) | partial data | hypothetical protein | Unknown
TP_1031 | TPAMA_1031 | 31 sub | 31 sub | [NAME] protein L | Virulence