| Organism | Ratio1 | Gene1 | Name1 | Description1 | Ratio2 | Gene2 | Name2 | Description2 | Cofit | Rank |
|---|
| Pseudomonas putida KT2440 | 1.0 | PP_4734 | | DNA-binding transcriptional dual regulator, LldR-L-lactate | 1.0 | PP_1655 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | 0.27 | 2 |
| Pseudomonas fluorescens SBW25 | 0.87 | PFLU_RS25940 | | FCD domain-containing protein | 0.73 | PFLU_RS22100 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 109 |
| Pseudomonas fluorescens SBW25-INTG | 0.87 | PFLU_RS25940 | | FCD domain-containing protein | 0.73 | PFLU_RS22100 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | 0.18 | 66 |
| Pseudomonas fluorescens FW300-N2C3 | 0.87 | AO356_07545 | | transcriptional regulator PdhR | 0.72 | AO356_19055 | | 23S rRNA methyltransferase | low | > 104 |
| Pseudomonas fluorescens FW300-N1B4 | 0.86 | Pf1N1B4_1185 | | Lactate-responsive regulator LldR in Enterobacteria, GntR family | 0.72 | Pf1N1B4_3507 | | 23S rRNA (Uracil-5-) -methyltransferase RumA (EC 2.1.1.-) ## LSU rRNA m(5)U1939 | low | > 87 |
| Pseudomonas fluorescens FW300-N2E2 | 0.86 | Pf6N2E2_3379 | | Lactate-responsive regulator LldR in Enterobacteria, GntR family | 0.72 | Pf6N2E2_5722 | | 23S rRNA (Uracil-5-) -methyltransferase RumA (EC 2.1.1.-) ## LSU rRNA m(5)U1939 | low | > 103 |
| Pseudomonas sp. RS175 | 0.86 | PFR28_00064 | | Pyruvate dehydrogenase complex repressor | 0.72 | PFR28_03224 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 88 |
| Pseudomonas fluorescens GW456-L13 | 0.85 | PfGW456L13_5113 | | Lactate-responsive regulator LldR in Enterobacteria, GntR family | 0.69 | PfGW456L13_2033 | | 23S rRNA (Uracil-5-) -methyltransferase RumA (EC 2.1.1.-) ## LSU rRNA m(5)U1939 | low | > 87 |
| Pseudomonas fluorescens FW300-N2E3 | 0.85 | AO353_05695 | | transcriptional regulator PdhR | 0.69 | AO353_02715 | | 23S rRNA methyltransferase | low | > 101 |
| Pseudomonas simiae WCS417 | 0.84 | PS417_24100 | | transcriptional regulator PdhR | 0.72 | PS417_20155 | | 23S rRNA methyltransferase | low | > 88 |
| Pseudomonas stutzeri RCH2 | 0.76 | Psest_0956 | | Transcriptional regulators | 0.69 | Psest_1639 | | 23S rRNA (uracil-5-)-methyltransferase RumA | low | > 67 |
| Pseudomonas sp. S08-1 | 0.75 | OH686_17020 | | Lactate-responsive regulator LldR in Enterobacteria, GntR family | 0.72 | OH686_18955 | | 23S rRNA (uracil-5-)-methyltransferase RumA | low | > 80 |
| Marinobacter adhaerens HP15 | 0.63 | HP15_4087 | | transcriptional regulator, GntR family | 0.40 | HP15_790 | | 23S rRNA 5-methyluridine methyltransferase | low | > 73 |
| Enterobacter asburiae PDN3 | 0.40 | EX28DRAFT_3708 | | Transcriptional regulators | 0.35 | EX28DRAFT_2865 | | 23S rRNA (uracil-5-)-methyltransferase RumA | low | > 76 |
| Enterobacter sp. TBS_079 | 0.40 | MPMX20_00806 | | Pyruvate dehydrogenase complex repressor | 0.35 | MPMX20_03654 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 85 |
| Escherichia coli ECRC101 | 0.40 | MCAODC_01025 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | MCAODC_10770 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia coli ECRC98 | 0.40 | JDDGAC_14105 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | JDDGAC_23910 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia coli ECOR27 | 0.40 | NOLOHH_02855 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | NOLOHH_12120 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 57 |
| Vibrio cholerae E7946 ATCC 55056 | 0.40 | CSW01_12225 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.40 | CSW01_12410 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 62 |
| Escherichia coli ECRC101 | 0.40 | OKFHMN_10510 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | OKFHMN_20245 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia fergusonii Becca | 0.40 | EFB2_03932 | | Pyruvate dehydrogenase complex repressor | 0.34 | EFB2_01132 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 86 |
| Escherichia coli HS(pFamp)R (ATCC 700891) | 0.40 | OHPLBJKB_03548 | | Pyruvate dehydrogenase complex repressor | 0.34 | OHPLBJKB_00946 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 73 |
| Escherichia coli ECRC62 | 0.40 | BNILDI_08755 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | BNILDI_10625 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia coli ECRC102 | 0.40 | NIAGMN_08360 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | NIAGMN_18015 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia coli Nissle 1917 | 0.40 | ECOLIN_RS00635 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | ECOLIN_RS15520 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 52 |
| Escherichia coli BL21 | 0.40 | ECD_00112 | | pyruvate dehydrogenase complex repressor; autorepressor | 0.34 | ECD_02630 | | 23S rRNA m(5)U1939 methyltransferase, SAM-dependent | low | > 60 |
| Escherichia coli BW25113 | 0.40 | b0113 | pdhR | transcriptional regulator of pyruvate dehydrogenase complex (NCBI) | 0.34 | b2785 | rumA | 23S rRNA (uracil-5-)-methyltransferase (NCBI) | low | > 76 |
| Escherichia coli ECRC99 | 0.40 | KEDOAH_17645 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | KEDOAH_07885 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | — | — |
| Escherichia coli ECOR38 | 0.40 | HEPCGN_08490 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.35 | HEPCGN_19495 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 85 |
| Dickeya dadantii 3937 | 0.39 | DDA3937_RS17930 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | DDA3937_RS17020 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 74 |
| Dickeya dianthicola 67-19 | 0.39 | HGI48_RS17855 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.32 | HGI48_RS17075 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 71 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868 | 0.39 | GFF123 | | Transcriptional repressor for pyruvate dehydrogenase complex | 0.34 | GFF4838 | | 23S rRNA (Uracil-5-) -methyltransferase RumA (EC 2.1.1.-) | low | > 78 |
| Shewanella loihica PV-4 | 0.39 | Shew_3432 | pdhR | transcriptional regulator PdhR (RefSeq) | 0.37 | Shew_1201 | rumA | 23S rRNA 5-methyluridine methyltransferase (RefSeq) | low | > 60 |
| Serratia liquefaciens MT49 | 0.39 | IAI46_21330 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.37 | IAI46_03595 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 86 |
| Dickeya dianthicola ME23 | 0.39 | DZA65_RS19005 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.33 | DZA65_RS18150 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 75 |
| Klebsiella michiganensis M5al | 0.39 | BWI76_RS04875 | | transcriptional regulator PdhR | 0.33 | BWI76_RS22810 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase | low | > 92 |
| Shewanella sp. ANA-3 | 0.39 | Shewana3_0425 | pdhR | transcriptional regulator PdhR (RefSeq) | 0.37 | Shewana3_1110 | rumA | 23S rRNA 5-methyluridine methyltransferase (RefSeq) | low | > 73 |
| Shewanella amazonensis SB2B | 0.39 | Sama_0374 | pdhR | transcriptional regulator PdhR (RefSeq) | 0.38 | Sama_1032 | rumA | 23S rRNA 5-methyluridine methyltransferase (RefSeq) | low | > 62 |
| Shewanella oneidensis MR-1 | 0.39 | SO0423 | pdhR | pyruvate dehydrogenase complex repressor (NCBI ptt file) | 0.37 | SO3456 | | RNA methyltransferase, TrmA family (NCBI ptt file) | low | > 76 |
| Pectobacterium carotovorum WPP14 | 0.38 | HER17_RS03285 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.35 | HER17_RS04110 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 75 |
| Pantoea sp. MT58 | 0.38 | IAI47_15815 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.36 | IAI47_04115 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | 0.55 | 59 |
| Rahnella sp. WP5 | 0.38 | EX31_RS03485 | | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.34 | EX31_RS07960 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 89 |
| Erwinia tracheiphila SCR3 | 0.37 | LU632_RS03075 | pdhR | pyruvate dehydrogenase complex transcriptional repressor PdhR | 0.35 | LU632_RS06345 | rlmD | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 74 |
| Magnetospirillum magneticum AMB-1 | 0.36 | AMB_RS01210 | | FCD domain-containing protein | 0.16 | AMB_RS01660 | | class I SAM-dependent RNA methyltransferase | — | — |
| Phaeobacter inhibens DSM 17395 | 0.34 | PGA1_c00760 | | putative pyruvate dehydrogenase complex repressor | 0.14 | PGA1_c34810 | | putative RNA methyltransferase | low | > 62 |
| Alteromonas macleodii MIT1002 | 0.34 | MIT1002_03004 | | Pyruvate dehydrogenase complex repressor | 0.31 | MIT1002_00793 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 70 |
| Dinoroseobacter shibae DFL-12 | 0.34 | Dshi_3026 | | GntR domain protein (RefSeq) | 0.13 | Dshi_3492 | | (Uracil-5)-methyltransferase (RefSeq) | low | > 64 |
| Castellaniella sp019104865 MT123 | 0.33 | ABCV34_RS10290 | | transcriptional regulator LldR | 0.33 | ABCV34_RS03050 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 48 |
| Agrobacterium fabrum C58 | 0.32 | Atu0662 | | transcriptional regulator, GntR family | 0.16 | Atu0735 | | RNA methyltransferase | low | > 89 |
| Sinorhizobium meliloti 1021 | 0.31 | SMc00829 | | transcriptional regulator | 0.16 | SMc00974 | | RNA methyltransferase | low | > 103 |
| Paraburkholderia bryophila 376MFSha3.1 | 0.30 | H281DRAFT_02906 | | transcriptional regulator, GntR family | 0.33 | H281DRAFT_00846 | | 23S rRNA m(5)U-1939 methyltransferase | low | > 103 |
| Cupriavidus basilensis FW507-4G11 | 0.29 | RR42_RS21300 | | GntR family transcriptional regulator | 0.32 | RR42_RS13170 | | 23S rRNA methyltransferase | low | > 128 |
| Burkholderia phytofirmans PsJN | 0.29 | BPHYT_RS26990 | | GntR family transcriptional regulator | 0.33 | BPHYT_RS09125 | | 23S rRNA methyltransferase | low | > 109 |
| Azospirillum sp. SherDot2 | 0.29 | MPMX19_06090 | | Pyruvate dehydrogenase complex repressor | 0.14 | MPMX19_02196 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | 0.25 | 108 |
| Paraburkholderia sabiae LMG 24235 | 0.28 | QEN71_RS10135 | | FadR/GntR family transcriptional regulator | 0.33 | QEN71_RS22225 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 153 |
| Acinetobacter radioresistens SK82 | 0.27 | MPMX26_02258 | | Putative L-lactate dehydrogenase operon regulatory protein | 0.38 | MPMX26_00538 | | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | low | > 36 |
| Rhodospirillum rubrum S1H | 0.24 | Rru_A1414 | | regulatory protein GntR (NCBI) | 0.14 | Rru_A2107 | | 23S rRNA (uracil-5-)-methyltransferase RumA (NCBI) | — | — |
| Azospirillum brasilense Sp245 | 0.23 | AZOBR_RS25130 | | GntR family transcriptional regulator | 0.14 | AZOBR_RS01195 | | RNA methyltransferase | low | > 97 |
| Desulfovibrio vulgaris Hildenborough JW710 | 0.20 | DVU2785 | pdhR | transcriptional regulator, GntR family (TIGR) | 0.15 | DVU0924 | rumA | 23S rRNA (uracil-5-)-methyltransferase RumA (TIGR) | low | > 55 |
| Caulobacter crescentus NA1000 | 0.19 | CCNA_01037 | | GntR-family transcriptional regulator | 0.16 | CCNA_01387 | | tRNA (uracil-5-)-methyltransferase related protein | low | > 66 |
| Caulobacter crescentus NA1000 Δfur | 0.19 | CCNA_01037 | | GntR-family transcriptional regulator | 0.16 | CCNA_01387 | | tRNA (uracil-5-)-methyltransferase related protein | low | > 67 |
| Rhizobium sp. OAE497 | 0.18 | ABIE40_RS25825 | | FadR/GntR family transcriptional regulator | 0.16 | ABIE40_RS03880 | | class I SAM-dependent RNA methyltransferase | low | > 107 |
| Bifidobacterium breve UCC2003 | 0.13 | BBR_RS11160 | | FadR family transcriptional regulator | 0.13 | BBR_RS16615 | | class I SAM-dependent RNA methyltransferase | low | > 34 |
| Kangiella aquimarina DSM 16071 | 0.11 | B158DRAFT_2208 | | transcriptional regulator, GntR family | 0.37 | B158DRAFT_2275 | | 23S rRNA (uracil-5-)-methyltransferase RumA | low | > 40 |
Not shown: 3 genomes with orthologs for PP_4734 only; 35 genomes with orthologs for PP_1655 only