| Organism | Ratio1 | Gene1 | Name1 | Description1 | Ratio2 | Gene2 | Name2 | Description2 | Cofit | Rank |
|---|
| Serratia liquefaciens MT49 | 1.0 | IAI46_03985 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 1.0 | IAI46_24960 | | nitrogen regulation protein NR(I) | 0.63 | 13 |
| Rahnella sp. WP5 | 0.92 | EX31_RS07570 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.97 | EX31_RS15880 | | nitrogen regulation protein NR(I) | low | > 89 |
| Pectobacterium carotovorum WPP14 | 0.91 | HER17_RS05400 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.94 | HER17_RS21440 | | nitrogen regulation protein NR(I) | low | > 75 |
| Dickeya dadantii 3937 | 0.91 | DDA3937_RS16110 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.94 | DDA3937_RS00125 | | nitrogen regulation protein NR(I) | low | > 74 |
| Dickeya dianthicola ME23 | 0.90 | DZA65_RS17330 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.94 | DZA65_RS22210 | | nitrogen regulation protein NR(I) | low | > 75 |
| Dickeya dianthicola 67-19 | 0.90 | HGI48_RS16235 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.94 | HGI48_RS21235 | | nitrogen regulation protein NR(I) | low | > 71 |
| Pantoea sp. MT58 | 0.89 | IAI47_04425 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.94 | IAI47_00450 | | nitrogen regulation protein NR(I) | low | > 76 |
| Escherichia coli BW25113 | 0.88 | b2594 | rluD | 23S rRNA pseudouridine synthase (NCBI) | 0.92 | b3868 | glnG | fused DNA-binding response regulator in two-component regulatory system with GlnL: response regulator/sigma54 interaction protein (NCBI) | — | — |
| Escherichia fergusonii Becca | 0.88 | EFB2_01296 | | Ribosomal large subunit pseudouridine synthase D | 0.92 | EFB2_04748 | | DNA-binding transcriptional regulator NtrC | low | > 86 |
| Escherichia coli ECRC99 | 0.88 | KEDOAH_06970 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | KEDOAH_14040 | glnG | nitrogen regulation protein NR(I) | — | — |
| Escherichia coli ECRC98 | 0.88 | JDDGAC_24915 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | JDDGAC_17735 | glnG | nitrogen regulation protein NR(I) | — | — |
| Escherichia coli ECOR38 | 0.88 | HEPCGN_20375 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | HEPCGN_12740 | glnG | nitrogen regulation protein NR(I) | low | > 85 |
| Escherichia coli BL21 | 0.88 | ECD_02484 | | 23S rRNA pseudouridine(1911,1915,1917) synthase | 0.92 | ECD_03753 | | fused DNA-binding response regulator in two-component regulatory system with GlnL: response regulator/sigma54 interaction protein | low | > 60 |
| Escherichia coli Nissle 1917 | 0.88 | ECOLIN_RS14675 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | ECOLIN_RS22295 | | nitrogen regulation protein NR(I) | low | > 52 |
| Escherichia coli ECRC102 | 0.88 | NIAGMN_19020 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | NIAGMN_11865 | glnG | nitrogen regulation protein NR(I) | — | — |
| Escherichia coli HS(pFamp)R (ATCC 700891) | 0.88 | OHPLBJKB_01112 | | Ribosomal large subunit pseudouridine synthase D | 0.92 | OHPLBJKB_04184 | | DNA-binding transcriptional regulator NtrC | low | > 73 |
| Escherichia coli ECRC101 | 0.88 | OKFHMN_21250 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | OKFHMN_14110 | glnG | nitrogen regulation protein NR(I) | — | — |
| Escherichia coli ECRC101 | 0.88 | MCAODC_11780 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | MCAODC_04610 | glnG | nitrogen regulation protein NR(I) | — | — |
| Enterobacter sp. TBS_079 | 0.88 | MPMX20_03463 | | Ribosomal large subunit pseudouridine synthase D | 0.93 | MPMX20_04597 | | DNA-binding transcriptional regulator NtrC | low | > 85 |
| Enterobacter asburiae PDN3 | 0.87 | EX28DRAFT_2695 | | pseudouridine synthase, RluA family | 0.93 | EX28DRAFT_4350 | | nitrogen regulation protein NR(I) | low | > 76 |
| Escherichia coli ECOR27 | 0.87 | NOLOHH_12925 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | NOLOHH_06240 | glnG | nitrogen regulation protein NR(I) | low | > 57 |
| Escherichia coli ECRC62 | 0.87 | BNILDI_11730 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.92 | BNILDI_05290 | glnG | nitrogen regulation protein NR(I) | — | — |
| Klebsiella michiganensis M5al | 0.87 | BWI76_RS21450 | | 23S rRNA pseudouridine(1911/1915/1917) synthase | 0.93 | BWI76_RS00385 | | nitrogen assimilation regulatory protein | low | > 92 |
| Salmonella enterica subsp. enterica serovar Typhimurium str. MS1868 | 0.87 | GFF4182 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.92 | GFF2220 | | Nitrogen regulation protein NR(I) | 0.91 | 2 |
| Erwinia tracheiphila SCR3 | 0.86 | LU632_RS16945 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.93 | LU632_RS22135 | glnG | nitrogen regulation protein NR(I) | low | > 74 |
| Vibrio cholerae E7946 ATCC 55056 | 0.70 | CSW01_03695 | | ribosomal large subunit pseudouridine synthase D | 0.72 | CSW01_13865 | | nitrogen regulation protein NR(I) | low | > 62 |
| Alteromonas macleodii MIT1002 | 0.66 | MIT1002_02679 | | Ribosomal large subunit pseudouridine synthase D | 0.70 | MIT1002_03186 | | Nitrogen regulation protein NR(I) | low | > 70 |
| Shewanella sp. ANA-3 | 0.65 | Shewana3_3171 | | ribosomal large subunit pseudouridine synthase D (RefSeq) | 0.70 | Shewana3_0258 | | nitrogen metabolism transcriptional regulator, NtrC, Fis family (RefSeq) | low | > 73 |
| Shewanella loihica PV-4 | 0.64 | Shew_2950 | | RluA family pseudouridine synthase (RefSeq) | 0.69 | Shew_3561 | | nitrogen metabolism transcriptional regulator, NtrC, Fis family (RefSeq) | 0.48 | 59 |
| Shewanella amazonensis SB2B | 0.62 | Sama_2605 | | pseudouridylate synthase (RefSeq) | 0.70 | Sama_3427 | | response regulator receiver protein (RefSeq) | — | — |
| Pseudomonas fluorescens FW300-N2C3 | 0.56 | AO356_15925 | | ribosomal large subunit pseudouridine synthase D | 0.68 | AO356_09730 | | nitrogen regulation protein NR(I) | low | > 104 |
| Pseudomonas sp. S08-1 | 0.55 | OH686_16410 | | LSU rRNA pseudouridine(1911/1915/1917) synthase | 0.67 | OH686_10640 | | nitrogen regulation protein NR(I) | low | > 80 |
| Pseudomonas putida KT2440 | 0.55 | PP_0623 | | 23S rRNA pseudouridine(1911,1915,1917) synthase | 0.68 | PP_5048 | | two-component system DNA-binding transcriptional dual regulator GlnL/GlnG | — | — |
| Pseudomonas fluorescens SBW25 | 0.55 | PFLU_RS03870 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.69 | PFLU_RS01685 | | nitrogen regulation protein NR(I) | low | > 109 |
| Pseudomonas sp. RS175 | 0.55 | PFR28_03748 | | Ribosomal large subunit pseudouridine synthase D | 0.68 | PFR28_04944 | | DNA-binding transcriptional regulator NtrC | low | > 88 |
| Pseudomonas fluorescens SBW25-INTG | 0.55 | PFLU_RS03870 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.69 | PFLU_RS01685 | | nitrogen regulation protein NR(I) | low | > 109 |
| Pseudomonas simiae WCS417 | 0.55 | PS417_03820 | | ribosomal large subunit pseudouridine synthase D | 0.69 | PS417_01635 | | nitrogen regulation protein NR(I) | — | — |
| Pseudomonas fluorescens FW300-N2E3 | 0.55 | AO353_14220 | | ribosomal large subunit pseudouridine synthase D | 0.68 | AO353_12145 | | nitrogen regulation protein NR(I) | low | > 101 |
| Pseudomonas fluorescens FW300-N2E2 | 0.55 | Pf6N2E2_5127 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.68 | Pf6N2E2_3826 | | Nitrogen regulation protein NR(I) | — | — |
| Pseudomonas fluorescens GW456-L13 | 0.55 | PfGW456L13_1493 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.68 | PfGW456L13_347 | | Nitrogen regulation protein NR(I) | — | — |
| Pseudomonas syringae pv. syringae B728a | 0.54 | Psyr_0726 | | ribosomal large subunit pseudouridine synthase D | 0.68 | Psyr_4822 | | Helix-turn-helix, Fis-type:Nitrogen regulation protein NR(I) | low | > 86 |
| Pseudomonas syringae pv. syringae B728a ΔmexB | 0.54 | Psyr_0726 | | ribosomal large subunit pseudouridine synthase D | 0.68 | Psyr_4822 | | Helix-turn-helix, Fis-type:Nitrogen regulation protein NR(I) | — | — |
| Pseudomonas fluorescens FW300-N1B4 | 0.54 | Pf1N1B4_2822 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.68 | Pf1N1B4_1611 | | Nitrogen regulation protein NR(I) | — | — |
| Pseudomonas stutzeri RCH2 | 0.54 | Psest_0709 | | pseudouridine synthase, RluA family | 0.67 | Psest_3932 | | nitrogen regulation protein NR(I) | low | > 67 |
| Lysobacter sp. OAE881 | 0.53 | ABIE51_RS04885 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.49 | ABIE51_RS01360 | | nitrogen regulation protein NR(I) | low | > 62 |
| Marinobacter adhaerens HP15 | 0.52 | HP15_527 | | pseudouridine synthase, RluA family | 0.66 | HP15_425 | | two-component response regulator NtrC | low | > 73 |
| Xanthomonas campestris pv. campestris strain 8004 | 0.52 | Xcc-8004.1362.1 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.49 | Xcc-8004.252.1 | | Nitrogen regulation protein NtrC | low | > 74 |
| Rhodanobacter denitrificans FW104-10B01 | 0.51 | LRK54_RS04965 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.47 | LRK54_RS07980 | | nitrogen regulation protein NR(I) | low | > 59 |
| Rhodanobacter denitrificans MT42 | 0.51 | LRK55_RS04745 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.47 | LRK55_RS07730 | | nitrogen regulation protein NR(I) | low | > 63 |
| Dyella japonica UNC79MFTsu3.2 | 0.50 | ABZR86_RS10965 | | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.44 | ABZR86_RS15515 | | nitrogen regulation protein NR(I) | low | > 74 |
| Rhodanobacter sp. FW510-T8 | 0.48 | OKGIIK_01790 | rluD | 23S rRNA pseudouridine(1911/1915/1917) synthase RluD | 0.45 | OKGIIK_14465 | ntrC | nitrogen regulation protein NR(I) | — | — |
| Acinetobacter radioresistens SK82 | 0.42 | MPMX26_00735 | | Ribosomal large subunit pseudouridine synthase D | 0.63 | MPMX26_01292 | | DNA-binding transcriptional regulator NtrC | low | > 36 |
| Ralstonia solanacearum PSI07 | 0.41 | RPSI07_RS15970 | | RluA family pseudouridine synthase | 0.57 | RPSI07_RS17815 | | nitrogen regulation protein NR(I) | low | > 81 |
| Ralstonia solanacearum GMI1000 | 0.41 | RS_RS08205 | | RluA family pseudouridine synthase | 0.56 | RS_RS06320 | | nitrogen regulation protein NR(I) | — | — |
| Ralstonia solanacearum UW163 | 0.41 | UW163_RS14830 | | RluA family pseudouridine synthase | 0.56 | UW163_RS13000 | | nitrogen regulation protein NR(I) | — | — |
| Ralstonia solanacearum IBSBF1503 | 0.41 | RALBFv3_RS01520 | | RluA family pseudouridine synthase | 0.56 | RALBFv3_RS15540 | | nitrogen regulation protein NR(I) | — | — |
| Ralstonia sp. UNC404CL21Col | 0.39 | ABZR87_RS13315 | | RluA family pseudouridine synthase | 0.56 | ABZR87_RS11070 | | nitrogen regulation protein NR(I) | low | > 80 |
| Herbaspirillum seropedicae SmR1 | 0.37 | HSERO_RS15070 | | ribosomal large subunit pseudouridine synthase D | 0.57 | HSERO_RS15680 | | chemotaxis protein CheY | low | > 78 |
| Hydrogenophaga sp. GW460-11-11-14-LB1 | 0.35 | GFF4870 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.53 | GFF5269 | | Nitrogen regulation protein NR(I) | low | > 90 |
| Sphingomonas koreensis DSMZ 15582 | 0.35 | Ga0059261_0664 | | pseudouridine synthase, RluA family | 0.38 | Ga0059261_0137 | | nitrogen regulation protein NR(I) | low | > 68 |
| Rhodopseudomonas palustris CGA009 | 0.35 | TX73_001905 | | RluA family pseudouridine synthase | 0.40 | TX73_013420 | | nitrogen regulation protein NR(I) | low | > 86 |
| Azospirillum sp. SherDot2 | 0.35 | MPMX19_05442 | | Ribosomal large subunit pseudouridine synthase D | 0.41 | MPMX19_01112 | | DNA-binding transcriptional regulator NtrC | — | — |
| Castellaniella sp019104865 MT123 | 0.34 | ABCV34_RS01885 | | RluA family pseudouridine synthase | 0.51 | ABCV34_RS03540 | | nitrogen regulation protein NR(I) | low | > 48 |
| Rhodospirillum rubrum S1H | 0.34 | Rru_A1111 | | Pseudouridine synthase, RluD (NCBI) | 0.40 | Rru_A1678 | | Nitrogen Metabolism Transcriptional Regulator, NtrC, Fis Family (NCBI) | low | > 58 |
| Rhizobium sp. OAE497 | 0.33 | ABIE40_RS14790 | | RluA family pseudouridine synthase | 0.41 | ABIE40_RS09090 | | nitrogen regulation protein NR(I) | 0.64 | 13 |
| Magnetospirillum magneticum AMB-1 | 0.33 | AMB_RS16095 | | RluA family pseudouridine synthase | 0.40 | AMB_RS11950 | | nitrogen regulation protein NR(I) | — | — |
| Acidovorax sp. GW101-3H11 | 0.32 | Ac3H11_1787 | | Ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) | 0.54 | Ac3H11_4432 | | Nitrogen regulation protein NR(I) | low | > 79 |
| Phaeobacter inhibens DSM 17395 | 0.32 | PGA1_c09000 | | ribosomal large subunit pseudouridine synthase D | 0.29 | PGA1_c14810 | | nitrogen assimilation regulatory protein NtrX | — | — |
| Fusobacterium nucleatum SB010 | 0.31 | HUW76_08575 | | RluA family pseudouridine synthase | 0.25 | HUW76_02090 | | sigma-54-dependent Fis family transcriptional regulator | low | > 35 |
| Variovorax sp. SCN45 | 0.31 | GFF988 | | LSU rRNA pseudouridine(1911/1915/1917) synthase (EC 5.4.99.23) | 0.54 | GFF3066 | | Nitrogen regulation protein NR(I), GlnG (=NtrC) | — | — |
| Sinorhizobium meliloti 1021 | 0.30 | SMc00647 | | ribosomal large subunit pseudouridine synthase | 0.42 | SMc01043 | | nitrogen assimilation regulatory protein | low | > 103 |
| Agrobacterium fabrum C58 | 0.30 | Atu2443 | | ribosomal large subunit pseudouridine synthase, RluD subfamily | 0.41 | Atu1446 | | two component response regulator | — | — |
| Bacteroides thetaiotaomicron VPI-5482 | 0.29 | BT3712 | | ribosomal large subunit pseudouridine synthase D (NCBI ptt file) | 0.32 | BT2433 | | two-component system response regulator (NCBI ptt file) | low | > 81 |
| Phocaeicola vulgatus CL09T03C04 | 0.29 | HMPREF1058_RS08615 | | RluA family pseudouridine synthase | 0.35 | HMPREF1058_RS04160 | | sigma-54-dependent Fis family transcriptional regulator | low | > 67 |
| Phocaeicola dorei CL03T12C01 | 0.29 | ABI39_RS02845 | | RluA family pseudouridine synthase | 0.35 | ABI39_RS17060 | | sigma-54-dependent Fis family transcriptional regulator | low | > 72 |
| Variovorax sp. OAS795 | 0.29 | ABID97_RS14190 | | RluA family pseudouridine synthase | 0.54 | ABID97_RS09945 | | nitrogen regulation protein NR(I) | low | > 91 |
| Caulobacter crescentus NA1000 | 0.29 | CCNA_00485 | | ribosomal large subunit pseudouridine synthase D | 0.34 | CCNA_03424 | | AAA-family response regulator tacA | low | > 66 |
| Caulobacter crescentus NA1000 Δfur | 0.29 | CCNA_00485 | | ribosomal large subunit pseudouridine synthase D | 0.34 | CCNA_03424 | | AAA-family response regulator tacA | low | > 67 |
| Bosea sp. OAE506 | 0.29 | ABIE41_RS05635 | | RluA family pseudouridine synthase | 0.41 | ABIE41_RS16785 | | nitrogen regulation protein NR(I) | low | > 77 |
| Bacteroides ovatus ATCC 8483 | 0.29 | BACOVA_03528 | | pseudouridine synthase, RluA family | 0.33 | BACOVA_01571 | | Sigma-54 interaction domain protein | low | > 94 |
| Echinicola vietnamensis KMM 6221, DSM 17526 | 0.29 | Echvi_0642 | | pseudouridine synthase, RluA family | 0.33 | Echvi_0196 | | Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains | low | > 79 |
| Bacteroides stercoris CC31F | 0.28 | HMPREF1181_RS03250 | | RluA family pseudouridine synthase | 0.33 | HMPREF1181_RS03655 | | sigma-54-dependent Fis family transcriptional regulator | low | > 56 |
| Pontibacter actiniarum KMM 6156, DSM 19842 | 0.28 | CA264_15205 | | RNA pseudouridine synthase | 0.34 | CA264_16520 | | DNA-binding response regulator | low | > 74 |
| Pedobacter sp. GW460-11-11-14-LB5 | 0.27 | CA265_RS14415 | | pseudouridine synthase | 0.32 | CA265_RS01040 | | sigma-54-dependent Fis family transcriptional regulator | low | > 88 |
| Dinoroseobacter shibae DFL-12 | 0.27 | Dshi_2610 | | pseudouridine synthase, RluA family (RefSeq) | 0.31 | Dshi_1572 | | two component, sigma54 specific, transcriptional regulator, Fis family (RefSeq) | — | — |
| Brevundimonas sp. GW460-12-10-14-LB2 | 0.27 | A4249_RS10060 | | RluA family pseudouridine synthase | 0.32 | A4249_RS09115 | | sigma-54 dependent transcriptional regulator | low | > 48 |
| Parabacteroides merdae CL09T00C40 | 0.27 | HMPREF1078_RS12640 | | RluA family pseudouridine synthase | 0.33 | HMPREF1078_RS14380 | | sigma-54 dependent transcriptional regulator | low | > 61 |
Not shown: 7 genomes with orthologs for IAI46_03985 only; 10 genomes with orthologs for IAI46_24960 only