Table 1 Putative genes, domains, and their proposed functions deduced from 41 potential coding regions
Gene | Codon | No. of amino acids | Best homologb [organism (no. of strains), GenBank accession no.] | % Identity (no. of amino acids overlapping) | Conserved domain (accession no.) | Proposed function | |
|---|---|---|---|---|---|---|---|
Start | Stopa | ||||||
repA | 1 | 1122 | 373 | Rep protein [L. gasseri, WP_049160251.1] | 99 (373) | RepA_N (pfam06970) | Plasmid replication |
relB | 1382 | 1663 | 93 | DinJ [Lactobacillaceae multispecies (24), WP_003646131.1] | 99 (93) | RelB_DinJ (TIGR02384) | Plasmid stabilization |
orf3 | 1710 | 1895 | 61 | CHP [Lactobacillaceae multispecies (42), WP_010620892] | 100 (61) | – | – |
orf4 | 1892 | 2572 | 226 | ATPase [Lactobacillus multispecies (3), WP_007124583.1] | 98 (226) | P-loop_NTPase (cl21455) | Conjugative transfer |
orf5 | 2562 | 2840 C | 92 | CHP [L. versmoldensis, WP_010625587.1) | 98 (92) | DUF3847 (cl15196) | – |
orf6 | 2863 | 3090 C | 75 | CHP [Lactobacillaceae multispecies (6), WP_003555660.1] | 95 (75) | – | – |
orf7 | 3343 | 5406 | 687 | Nickase, TraA-like [L. plantarum, WP_063733792.1] | 99 (687) | MobA_MobL (pfam03389) | Conjugative transfer |
orf8 | 5490 | 5801 | 103 | CHP [Lactobacillus multispecies (7), WP_003712158.1] | 100 (103) | – | – |
orf9 | 5838 | 6452 | 204 | CHP (L. casei, WP_012552809.1) | 98 (204) | – | – |
trsB | 6454 | 6789 | 111 | TraB protein [Lactobacillus multispecies (5), WP_003590767.1) | 100 (111) | T4SS_CagC (pfam16943) | Conjugative transfer |
trsC | 6810 | 7172 | 120 | TraC protein [Lactobacillus multispecies (15), WP_003590770.1] | 100 (120) | T7_EssCb_Firm (TIGR03928) | Conjugative transfer |
trsD | 7141 | 7800 | 219 | TraD protein [Lactobacillus multispecies (3), WP_003712179.1] | 100 (219) | VirB4_CagE (TIGR00929) | Conjugative transfer |
trsE | 7812 | 9830 | 672 | Protein TrsE [L. paracasei, WP_016370338.1] | 99 (672) | CagE_TrbE_VirB (pfam03135), VirB4 (COG3451) | Conjugative transfer |
trsF | 9823 | 11241 | 472 | TraF protein [L. casei WP_003590776.1] | 97 (472) | T7_EssB (TIGR03926) | Conjugative transfer |
orf15 | 11242 | 12399 | 385 | Peptidoglycan hydrolase [Lactobacillus multispecies (2), WP_049170325.1] | 99 (385) | Spr (COG0791) | Conjugative transfer |
orf16 | 12413 | 13030 | 205 | CHP [L. oris, WP_003712154.1] | 98 (205) | GH18_chitinase-like (cl10447) | – |
orf17 | 13017 | 13385 | 122 | Thioredoxin [Lactobacillus multispecies (3), WP_016370342.1) | 99 (122) | TRX_family (cd02947) | Conjugative transfer |
trsJ | 13386 | 13856 | 156 | TraJ protein [L. helveticus (5), WP_003625649.1] | 97 (156) | – | Conjugative transfer |
orf19 | 13853 | 14089 | 78 | HP [L. pentosus MP-10, CCB82908.1] | 94 (78) | – | – |
trsK | 14086 | 15636 | 516 | TraK protein [L. paralimentarius, WP_056955663.1) | 99 (516) | TraG_VirD4 (cd01126) | Conjugative transfer |
orf21 | 15651 | 16040 | 129 | CHP [Lactobacillus multispecies (6), WP_003712166.1] | 98 (129) | – | – |
trsL | 16059 | 16898 | 279 | TraL protein [L. gasseri, WP_012621107.1] | 99 (279) | – | Conjugative transfer |
orf23 | 16913 | 17323 | 136 | CHP [L. plantarum, WP_016511108.1] | 98 (136) | – | – |
trsI | 17330 | 19465 | 711 | DNA topoisomerase III [L. plantarum, WP_062688604.1] | 98 (711) | TOP1Ac (cd00186) | Conjugative transfer |
orf25 | 19585 | 19800 | 71 | CHP [Lactobacillaceae multispecies (17), WP_003713050.1] | 99 (71) | – | – |
ltrC | 19803 | 20927 | 374 | LtrC-like protein [L. curvatus, WP_039098912.1] | 94 (374) | ArdC (COG4227) | Conjugative transfer |
orf27 | 21127 | 21306 | 59 | CHP LRH_03875 [L. rhamnosus HN001, ACH91653.1] | 98 (59) | – | – |
orf28 | 21637 | 22986 | 449 | Pyridine nucleotide-disulfide oxidoreductase [L. casei, WP_012552825.1] | 99 (449) | Pyr_redox (pfam00070) Pyr_redox_dim (pfam02852) | – |
orf29 | 23139 | 23504 | 121 | HNH endonuclease [L. salivarius, WP_047036278.1] | 97 (305)c | HNHc (cd00085) | Phage DNA packaging |
orf30 | 23517 | 24020 | 167 | SMI1/KNR4 family protein [Lactobacillus multispecies (4), WP_011241750.1] | 99 (167) | SMI1_KNR4 (pfam09346) | – |
orf31 | 24312 | 27482 C | 1056 | Collagen-binding protein [L. fermentum, WP_048340564.1] | 95 (1055) | Cna_B (pfam05738) CollagenBindB (cd00222) | Bacterial adhesion |
orf32 | 27508 | 27648 | 46 | HP LBGG_02325 [L. gasseri MV-22, EFQ45516.1] | 93 (60)c | – | – |
orf33 | 27775 | 27954 C | 59 | HP [Lactobacillus multispecies (1), WP_032954691.1] | 100 (59) | – | – |
orf34 | 28034 | 28618 | 194 | α/β hydrolase [L. oris (2), WP_056984888.1] | 99 (194) | Abhydrolase_5 (pfam12695) | – |
orf35 | 28739 | 29323 | 194 | Putative resolvase [Lactobacillus multispecies (3), WP_056984887.1] | 100 (194) | Resolvase (pfam00239) | Recombination |
orf36 | 29343 | 29525 C | 60 | CHP [Lactobacillus multispecies (4), WP_016370330.1] | 100 (60) | – | – |
orf37 | 29610 | 30062 C | 150 | CHP [Lactobacillus multispecies (6), WP_003590731.1] | 100 (150) | – | – |
orf38 | 30323 | 30793 | 156 | HP [L. paracasei subsp. Paracasei, ABA12837.1] | 100 (156) | – | – |
orf39 | 31103 | 31273 C | 56 | DinJ damage inducible [Lactobacillaceae multispecies (9), WP_003590736.1] | 100 (56) | RelB (pfam04221) | Plasmid stabilization |
orf40 | 31754 | 32545 | 263 | Peptide transporter [Lactobacillus multispecies (6), WP_003712521.1] | 99 (263) | BcsQ (COG1192) | Plasmid replication |
orf41 | 32617 | 32856 | 79 | CHP [Lactobacillus multispecies (5), WP_016370331.1] | 100 (79) | – | – |