Table 3. Homologues of YgcA(RumA) and YbjF(RumB).
| Identity/similarity score |
||||
|---|---|---|---|---|
| Bacteria | Gene | GenBank accession no. | YgcA(RumA) | YbjF(RumB) |
| Shigella flexneri | ygcA | AE015293 | 99/99 | – |
| Shigella flexneri | ybjF | AE015110 | – | 98/99 |
| Salmonella enterica | ygcA | AE016843 | 84/91 | – |
| Salmonella enterica | ybjF | AE016840 | – | 88/92 |
| Salmonella typhimurium | ygcA | AE008835 | 84/91 | – |
| Salmonella typhimurium | ybjF | AE008737 | – | 87/92 |
| Shewanella oneidensis | SO3456 | AE015782 | 44/62 | – |
| Shewanella oneidensis | SO0980 | AE015542 | – | 56/73 |
| Haemophilus influenzae | HI0333 | U32718 | 46/65 | – |
| Haemophilus influenzae | HI0958 | U32777 | – | 54/70 |
| Pasteurella multocida | PM1866 | AE006224 | 44/62 | – |
| Pasteurella multocida | PM0070 | AE006042 | – | 56/70 |
| Vibrio cholerae | VC2452 | AE004315 | 48/63 | – |
| Vibrio cholerae | VCA0929 | AE004420 | – | 54/68 |
| Yersinia pestis | YPO1336 | AJ414147 | – | 74/83 |
| Haemophilus somnus | Hsom1363 | NZ_AABO02000010 | 46/62 | – |
| Pseudomonas fluorescens | Pflu2080 | NZ_AAAT02000042 | 42/57 | – |
| Pseudomonas syringae | Psyr2664 | NZ_AABP02000005 | 40/56 | – |
|
Azotobacter vinelandii |
Avin0974 |
NZ_AAAU02000022 |
40/57 |
– |
| Archaea | ||||
| Pyrococcus abyssi | PAB0719 | AJ248286 | 26/44 | 27/45 |
| Pyrococcus abyssi | PAB0760 | AJ248286 | 26/44 | 25/41 |
| Pyrococcus horikoshii | PH1137 | AP000005 | 28/46 | 27/47 |
| Pyrococcus horikoshii | PH1259 | AP000005 | 25/44 | 24/42 |
| Pyrococcus furiosus | PF1172 | AE010226 | 27/43 | 27/45 |
| Pyrococcus furiosus | PF0827 | AE010198 | 27/43 | 26/43 |
Homologues of E.coli YgcA(RumA) and YbjF(RumB) revealed in a BLASTp database search. Regions of similarity were found in 57 bacterial species, but only those with identities of >40% and which fulfilled the four criteria described in Materials and Methods are shown in the table. A dash (–) indicates an identity score of <25% compared to the other methyltransferase. Three species of the archaeon Pyrococcus are also listed with sequences similar to both RumA and RumB. These have a lower identity score than many of the bacteria and probably have a comparable, but not identical, function to the E.coli methyltransferases. The Pyrococcus PAB0719, PH1137 and PF1172 genes show >95% identity to each other, as do the PAB0760, PH1259 and PF0827 genes, but there is low similarity between the two groups. No clear homologues were found in other archaea or amongst eukaryotes.