Table 4.
The σ factors of Rlv3841
| Gene and name (if known)a | GC3s, quartopb | Closest homologsc | ||
| Species | Gene | BLAST e value | ||
| RL0422 (RpoN, used for N assimilation) | 0.791 Y | S. meliloti | SMc01139 | 0.0 |
| A. tumefaciens | AGR_C_581 | 0.0 | ||
| M. loti | mll3196 | 2E-161 | ||
| Brucella suis | BR0158 | 3E-156 | ||
| RL0788 | 0.732 N | Pseudomonas fluorescens | Pflu02001224 | 9E-56 |
| Erwinia carotovora | ECA2017 | E-43 | ||
| Burkholderia ambifaria | BambDRAFT_3017 | 9E-30 | ||
| S. meliloti | SMa01432 | 2E-27 | ||
| A.tumefaciens | AGR_C_2739 | 2E-16 | ||
| M.loti | mlr77732 | E-16 | ||
| RL1138 | 0.714 N | Ralstonia eutropha | Reut_B3794 | E-47 |
| Bradyrhizobium japonicum | bll6484 | 2E-44 | ||
| Silicibacter pomeroyi | SPO31254 | E-29 | ||
| M. loti | mlr7773 | 7E-29 | ||
| A. tumefaciens | AGR_C_2739 | 2E-28 | ||
| S. meliloti | SMc01419 | 9E-23 | ||
| RL3020 | 0.749 Y | A. tumefaciens | AGR_C_4121 | 6E-56 |
| B. suis | BRA0021 | 2E-32 | ||
| Burkholderia fungorum | Bcep02004893 | 7E-32 | ||
| Caulobacter crescentus | CC3253 | 2E-30 | ||
| M. loti | mll3493 | 4E-25 | ||
| S. meliloti | SMb20531 | 2E-18 | ||
| RL3235 | 0.777 N | S. meliloti | SMc01419 | E-48 |
| A. tumefaciens | AGR_C_3679p | 9E-44 | ||
| Sphingopyxis alaskensis | SalaDRAFT_1954 | 5E-23 | ||
| B. japonicum | bll2628 | 6E-23 | ||
| M. loti | mlr04075 | E-18 | ||
| RL3402 (RpoD, 'housekeeping' σ) | 0.823 Y | A. tumefaciens | AGR_C_3929p | 0.0 |
| S. meliloti | SMc01563 | 0.0 | ||
| B. suis | BR1479 | 0.0 | ||
| M. loti | mll2466 | 0.0 | ||
| RL3509 | 0.758 N | S. meliloti | SMc02713 | 2E-38 |
| S. alaskensis | SalaDRAFT_1954 | 4E-18 | ||
| Burkholderia cepacia | Bcepa03005434 | 5E-18 | ||
| Novosphingobium aromaticivorans | DSM 12444 | 2E-17 | ||
| A. tumefaciens | AGR_C_3679 | E-14 | ||
| M. loti | mlr7773 | 5E-12 | ||
| RL3703 (RpoZ) | 0.790 Y | S. meliloti | SMc01506 | 5E-84 |
| B. suis | BR1658 | 3E-80 | ||
| Bartonella henselae | BH13830 | 5E-73 | ||
| A. tumefaciens | AGR_L_1386p | 5E-68 | ||
| M. loti | mll3697 | 7E-68 | ||
| RL3766 (RpoH, heat shock σ) | 0.794 Y | A. tumefaciens | AGR_C_4439p | 2E-155 |
| S. meliloti | SMc00646 | 3E-148 | ||
| M. loti | mlr3741 | 5E-138 | ||
| B. suis | BR1650 | E-133 | ||
| RL4524 | 0.780 N | M. loti | mlr8088 | 5E-38 |
| Rhodospirillum rubrum | Rrub02003750 | 3E-37 | ||
| Rhodobacter sphaeroides | 'rpoE' | 3E-34 | ||
| Magnetospirillum magnetotacticum | Magn03011107 | E-33 | ||
| S. meliloti | None listed in top 50 matches | |||
| A. tumefaciens | None listed in top 50 matches | |||
| RL4614 (RpoH2, heat shock σ) | 0.771 N | S. meliloti | SMc03873 | 5E-118 |
| M. loti | mlr3862 | 2E-98 | ||
| B. suis | BR1763 | 5E-97 | ||
| B. henselae | BH15210 | 3E-95 | ||
| A. tumefaciens | AGR_C_4439pd | 7E-58 | ||
| pRL10385 | 0.720 N | M. loti | mll1224 | 2E-52 |
| Microbulbifer degradans | Mdeg02003584 | E-28 | ||
| R. sphaeroides | Rsph03003515 | E-27 | ||
| Solibacter usitatus | AcidDRAFT_4778 | 6E-22 | ||
| S. meliloti | None listed in top 50 matches | |||
| A. tumefaciens | None listed in top 50 matches | |||
| pRL11007 (EcfR) | 0.778 N | M. loti | mlr0407 | 4E-57 |
| R. sphaeroides | Rsph03002607 | E-45 | ||
| M. magnetotacticum | Magn03006880 | 8E-39 | ||
| Bordetella parapertussis | BPP1584 | 4E-37 | ||
| A. tumefaciens | AGR_L_1386p | 3E-24 | ||
| S. meliloti | SMa0143 | 2E-22 | ||
| pRL110418 | 0.794 N | B. japonicum | blr7812 | 2E-83 |
| Streptomyces avermitilis | SAV7424 | 7E-74 | ||
| Nocardia farcina | nfa4970 | 3E-73 | ||
| Frankia sp. | Francci3DRAFT_3517 | 7E-66 | ||
| M. loti | mll6869 | 8E-33 | ||
| S. meliloti | None listed in top 50 matches | |||
| A. tumefaciens | None listed in top 50 matches | |||
| pRL120319 (RpoI, iron uptake sigma) | 0.640 N | Azotobacter vinelandii | AvinDRAFT_4065 | 4E-20 |
| Pseudomonas aeruginosa | 'pvdS'e | 3E-18 | ||
| S. meliloti | SMc04203 | 8E-09 | ||
| A. tumefaciens | AGR_pAT_442 | 2E-08 | ||
| pRL120580 | 0.587 N | Rhodopseudomonas palustris | RPA0550 | 4E-40 |
| R. rubrum | Rrub02003750 | 8E-38 | ||
| M. magnetotacticum | Magn03011107 | 5E-37 | ||
| Pseudomonas syringae | PSPTO1043 | 3E-28 | ||
| M. loti | mlr8088 | 4E-26 | ||
| A. tumefaciens | AGR_C_3605 | 6E-14 | ||
| S. meliloti | None listed in top 50 matches | |||
aRhizobium leguminosarum biovar viciae 3841 (Rlv3841) locus tags are shown and, if the gene has been named in R. leguminosarum, this name is shown. bGC3s (G+C content of silent third positions of codons), member of quartop (yes [Y]/no [N]). cEach of the Rlv3841 sigma factors was used in BLASTP searches (maximum of 50 matches). The sequences and the locus tag numbers, together with the 'e' values, are shown for the top four matches. In those genera (Brucella, Pseudomonas, Streptomyces, Burkholderia) with more than one sequenced species, only one example is shown for each genus. In those cases in which one or more of the species used in the quartop analysis is not in the top four matches, these are also included. dA. tumefaciens has only one rpoH gene (AGR_C_4439p) whereas R. leguminosarum, M. loti, and S. meliloti have two. AGR_C_4439p is more closely related to Rlv3841 RpoH1 (RL3766) than to Rlv3841 RpoH2 (RL4614). eAlso known as PfrI in P. putida, and PbrA in P. fluorescens.