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Table 5 Genes that are conserved in LI and LII but absent or disparately distributed in LIII

From: Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Gene1 Annotation LIII2 L. innocua 3 Operon4
Carbohydrate transport and metabolism
lmo0357 Similar to PTS system, enzyme IIA component IIIA + 059
lmo0358 Similar to PTS system, fructose-specific enzyme IIBC component IIIA + 059
lmo0359 Similar to D-fructose-1,6-biphosphate aldolase" IIIA + -
lmo0631 Similar to PTS system, fructose-specific IIA component IIIA - -
lmo0632 Similar to PTS system, fructose-specific IIC component IIIA + -
lmo0633 Similar to PTS system, fructose-specific IIB component IIIA + -
lmo0735 Similar to ribulose-5-phosphate 3-epimerase IIIA + 119
lmo0736 Similar to ribose 5-phosphate isomerase IIIA + 119
lmo0738 Similar to PTS system, beta-glucoside-specific enzyme IIABC IIIA + 119
lmo0739 Similar to 6-phospho-beta-glucosidase IIIA + 119
lmo0766 Similar to putative sugar ABC transporter, permease protein IIIA + -
lmo0767 Similar to ABC transporter, permease protein IIIA + -
lmo1031 Hypothetical protein IIIA - 166
lmo1032 Similar to transketolase IIIA - 166
lmo1033 Similar to transketolase IIIA - 166
lmo1035 Similar to PTS beta-glucoside-specific enzyme IIABC IIIA + 166
lmo1971 Similar to pentitol PTS system enzyme II C component IIIA + -
lmo1972 Similar to pentitol PTS system enzyme II B component IIIA + -
lmo1973 Similar to PTS system enzyme II A component IIIA + -
lmo2133 Similar to fructose-1,6-biphosphate aldolase type IIIA + -
lmo2134 Similar to fructose-1,6-biphosphate aldolase type II IIIA + -
lmo2135 Similar to PTS system, fructose-specific enzyme IIC component IIIA + -
lmo2136 Similar to PTS system, fructose-specific enzyme IIB component IIIA + -
lmo2137 Similar to PTS system, fructose-specific enzyme IIA component IIIA + -
lmo2143 Similar to mannose-6-phosphate isomerase IIIA - -
lmo2733 Similar to PTS system, fructose-specific IIABC component IIIA + 494
lmo2734 Similar to sugar hydrolase IIIA + 494
lmo2735 Similar to Sucrose phosphorylase IIIA + 494
lmo2736 Hypothetical protein IIIA + 494
lmo2771 Similar to beta-glucosidase IIIA + -
lmo2772 Similar to PTS system, beta-glucoside-specific enzyme IIABC IIIA + -
lmo2847 Similar to rhamnulose-1-phosphate aldolase IIIA + 516
lmo2848 Similar to L-rhamnose isomerase IIIA + 516
lmo2849 Similar to rhamnulokinase IIIA + 516
lmo2850 Similar to sugar transport proteins IIIA + 516
Cell envelope biogenesis, outer membrane
lmo0017 Similar to Bacillus anthracis CapA protein IIIA - -
Cell wall
lmo0933 Similar to sugar transferase IIIA + -
lmo1062 Similar to ABC transporters (permease protein) IIIA + -
lmo1088 TagB, teichoic acid biosynthesis protein B precursor IIIA + 177
lmo1089 TagD, teichoic acid biosynthesis protein D IIIA + 177
lmo0333 Similar to internalin, putative peptidoglycan bound protein IIIA - -
lmo0842 Putative peptidoglycan bound protein (LPXTG motif) IIIA + -
lmo1136 Similar to internalin, putative peptidoglycan bound protein IIIA + -
lmo1289 Similar to internalin, putative peptidoglycan bound protein IIIA + -
lmo1666 Peptidoglycan linked protein (LPXTG motif) IIIA - -
lmo2085 Putative peptidoglycan binding protein (LPXTG motif) IIIA - -
lmo2026 Putative peptidoglycan binding protein (LPXTG motif) IIIA + -
lmo2550 Similar to glycosyl transferases IIIA + -
Energy production and conversion     
lmo0334 Hypothetical protein IIIA - -
lmo1034 Similar to glycerol kinase IIIA + 166
General function prediction only     
lmo0752 Weakly similar to a putative haloacetate dehalogenase IIIA - -
lmo1970 Similar to putative phosphotriesterase related proteins IIIA + -
Phage-related     
lmo2285 Protein gp18, bacteriophage A118 IIIA + -
lmo2286 Protein gp17, bacteriophage A118 IIIA + -
Secondary metabolites biosynthesis     
lmo2157 SepA, required for septum formation IIIA - -
Acid and bile resistance     
lmo0037 Similar to amino acid transporter IIIB - -
lmo0038 Similar to agmatine deiminase IIIB - 008
lmo0039 Similar to carbamate kinase IIIB - 008
lmo0040 Similar to agmatine deiminase IIIB - -
lmo0447 Similar to glutamate decarboxylase IIIA + -
lmo0448 Similar to amino acid antiporter IIIA + -
lmo0446 Similar to penicillin acylase and to conjugated bile acid hydrolase IIIA - -
lmo0754 Weakly similar to a bile acid 7-alpha dehydratase IIIA - -
Transcriptional regulation     
lmo0041 Similar to transcription regulator, RpiR family IIIB - -
lmo0360 Similar to transcriptional regulator, DeoR family IIIA + -
lmo0749 Hypothetical protein IIIA + -
lmo0753 Similar to transcription regulator, Crp/Fnr family IIIA - -
lmo1030 Similar to transcription regulator, BglG family IIIA + -
lmo1060 Similar to 2-component response regulator IIIA + -
lmo2138 Similar to transcription regulator, BglG family IIIA + -
lmo2144 Similar to transcription regulator, GntR family IIIA - -
lmo2408 Similar to repressor protein IIIA + -
lmo2732 Similar to transcription regulator, RpiR family IIIA - -
lmo2773 Similar to transcription antiterminator IIIA + -
lmo2851 Similar to transcription regulator, AraC family IIIA + -
Transport and binding     
Lmo1063 Similar to ABC transporter (ATP binding protein) IIIA + -
Lmo1100 CadA, cadmium resistance protein IIIA + -
Translation     
Lmo0849 Similar to amidases IIIB + -
Function unknown     
lmo0072 Hypothetical protein - - -
lmo0086 Hypothetical protein IIIA + -
lmo0094 Hypothetical protein IIIA + -
lmo0095 Hypothetical protein IIIA + -
lmo2846 Similar to B. subtilis YulD protein IIIA + 516
lmo1036 Hypothetical protein IIIA - 166
lmo0444 Hypothetical protein IIIA + -
lmo0765 Hypothetical protein IIIA + -
  1. 1Genes conserved in all LI and LII genomes but absent in two or more LIII sub-groups (IIIA, IIIB or IIIC). Genes are listed based on their annotation in functional groups.
  2. 2LIII subgroup in which a listed gene is present.
  3. 3Presence "+" or absence "-" of a gene in L. innocua genome.
  4. 4Genes belong to an annotated operon based on [45]; "-", not annotated in operons.