|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
9-295 |
2.92e-142 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 401.84 E-value: 2.92e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 9 EKLQKVLARAGKGSRREMEKVIDAGRVSIDGKVSRLGDRV--GPHQQIRLDGHVVKIEAEENRICRVLMYNKPEGELCTR 86
Cdd:PRK10700 3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVevTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCTR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 87 KDPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVEL 166
Cdd:PRK10700 83 NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 167 EDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNPKLPQGGWEELALANVNYFRS 246
Cdd:PRK10700 163 EDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRE 242
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 1238723754 247 SVQLPNETETKLSVMPEKRsekRAKNQRIRKAVKKH-QIRAKQVQKKRKK 295
Cdd:PRK10700 243 LVELPPETSSKVAVEKDRR---RMKANQIRRAVKRHsQVSGGRRSGGRNN 289
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
9-236 |
4.34e-105 |
|
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]; Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification
Pssm-ID: 440800 [Multi-domain] Cd Length: 226 Bit Score: 305.42 E-value: 4.34e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 9 EKLQKVLARAGKGSRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQIRLDGHVVKIEAEenriCRVLMYNKPEGELCTRK 87
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKvVTELGTKVDPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVVSTTK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 88 DPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELE 167
Cdd:COG1187 79 DPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE 158
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238723754 168 DGMAKFLKITPRpGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLnPKLPQGGWEEL 236
Cdd:COG1187 159 DGPTKPAKVEIL-SGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
72-236 |
2.23e-88 |
|
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Pssm-ID: 211330 [Multi-domain] Cd Length: 167 Bit Score: 260.70 E-value: 2.23e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 72 RVLMYNKPEGELCTRKDPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGE 151
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 152 VEATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNPKLPQG 231
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*
gi 1238723754 232 GWEEL 236
Cdd:cd02556 161 QWEEL 165
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
110-238 |
7.89e-50 |
|
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272902 Cd Length: 128 Bit Score: 161.34 E-value: 7.89e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 110 VGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYN 189
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1238723754 190 VLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNpKLPQGGWEELAL 238
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLN-GLPPGEWRPLTL 128
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
73-202 |
1.20e-18 |
|
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Pssm-ID: 459961 [Multi-domain] Cd Length: 151 Bit Score: 80.53 E-value: 1.20e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 VLMYNKPEGELCTRKDPEG---RPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMR--PSYEIEREYAVR 147
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238723754 148 VFGEVEatTLKTLTTGVELEDGMAKF--------------LKITPRPGEGINRWYNVLLTEGRNREVRR 202
Cdd:pfam00849 81 VDKPEE--EEGTIKSPIKKEKNKSPFrkeeelggkkavthLKVLKSGSKGDYSLLELELVTGRKHQIRA 147
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
11-63 |
4.18e-04 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 37.96 E-value: 4.18e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1238723754 11 LQKVLARAG-KGSRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQIRLDGHVVKI 63
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKkVTKPSYIVKPGDVISVRGKELKR 57
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
9-295 |
2.92e-142 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 401.84 E-value: 2.92e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 9 EKLQKVLARAGKGSRREMEKVIDAGRVSIDGKVSRLGDRV--GPHQQIRLDGHVVKIEAEENRICRVLMYNKPEGELCTR 86
Cdd:PRK10700 3 EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVevTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCTR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 87 KDPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVEL 166
Cdd:PRK10700 83 NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 167 EDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNPKLPQGGWEELALANVNYFRS 246
Cdd:PRK10700 163 EDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRE 242
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 1238723754 247 SVQLPNETETKLSVMPEKRsekRAKNQRIRKAVKKH-QIRAKQVQKKRKK 295
Cdd:PRK10700 243 LVELPPETSSKVAVEKDRR---RMKANQIRRAVKRHsQVSGGRRSGGRNN 289
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
9-236 |
4.34e-105 |
|
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]; Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification
Pssm-ID: 440800 [Multi-domain] Cd Length: 226 Bit Score: 305.42 E-value: 4.34e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 9 EKLQKVLARAGKGSRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQIRLDGHVVKIEAEenriCRVLMYNKPEGELCTRK 87
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKvVTELGTKVDPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVVSTTK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 88 DPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELE 167
Cdd:COG1187 79 DPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE 158
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238723754 168 DGMAKFLKITPRpGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLnPKLPQGGWEEL 236
Cdd:COG1187 159 DGPTKPAKVEIL-SGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
72-236 |
2.23e-88 |
|
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Pssm-ID: 211330 [Multi-domain] Cd Length: 167 Bit Score: 260.70 E-value: 2.23e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 72 RVLMYNKPEGELCTRKDPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGE 151
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 152 VEATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNPKLPQG 231
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*
gi 1238723754 232 GWEEL 236
Cdd:cd02556 161 QWEEL 165
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
73-219 |
4.08e-57 |
|
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Pssm-ID: 211347 [Multi-domain] Cd Length: 146 Bit Score: 180.38 E-value: 4.08e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 VLMYNKPEGELCTRKDPEGRPTVFDRLPRlDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEV 152
Cdd:cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVP 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1238723754 153 EATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRY 219
Cdd:cd02870 80 SEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
110-238 |
7.89e-50 |
|
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272902 Cd Length: 128 Bit Score: 161.34 E-value: 7.89e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 110 VGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYN 189
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1238723754 190 VLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNpKLPQGGWEELAL 238
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLN-GLPPGEWRPLTL 128
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
73-219 |
5.91e-45 |
|
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Pssm-ID: 211325 [Multi-domain] Cd Length: 154 Bit Score: 149.45 E-value: 5.91e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 VLMYNKPEGELCTRKDPEGRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEV 152
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1238723754 153 -------EATTLKTLTTGVELEDGMAKFLKITPRPGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRY 219
Cdd:cd02550 81 deegiedLATVRRGRLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
72-236 |
4.18e-35 |
|
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Pssm-ID: 211327 [Multi-domain] Cd Length: 167 Bit Score: 124.55 E-value: 4.18e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 72 RVLMYNKPEGELCTRKDPEGrPTVFDRLPRLDGERWI-AVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFG 150
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLfPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 151 EVEATTLKTLTTGVELEDGM----AKFLKITPrpgeginRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNP 226
Cdd:cd02553 80 PLTEDDIEAFAEGVLLHDGYptkpAKLEILSP-------TTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDD 152
|
170
....*....|
gi 1238723754 227 KLPQGGWEEL 236
Cdd:cd02553 153 DLAPGEWRPL 162
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
74-236 |
4.25e-26 |
|
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Pssm-ID: 211328 [Multi-domain] Cd Length: 164 Bit Score: 100.85 E-value: 4.25e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 74 LMYNKPEGELCTRKDPEgRPTVFDRLPRldGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVE 153
Cdd:cd02554 3 IAYNKPVGIDCTLERAD-EDNIIDFVNP--PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 154 ATTLKTLTTGVELEDGMAKFLKITprpgEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNpKLPQGGW 233
Cdd:cd02554 80 DEFIEGMSNGVVILGTVTKPCKVE----RLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELG-DLAPGEW 154
|
...
gi 1238723754 234 EEL 236
Cdd:cd02554 155 RPL 157
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
10-236 |
7.92e-26 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 102.11 E-value: 7.92e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 10 KLQKVLARAGKGSRREMEKVIDAGRVSIDGKVSRLGD-RVGPHQQIRLDGHVVkieaEENRICRVLMYNKPEGELCTRKD 88
Cdd:PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAfKLLPEHDVAYDGNPL----AQQHGPRYFMLNKPQGYVCSTDD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 89 PEgRPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELED 168
Cdd:PRK10839 78 PD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1238723754 169 GM-----AKFLKITPrpgeginrwYNVLLT--EGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNPKLPQGGWEEL 236
Cdd:PRK10839 157 EKdltkpAVLEVITP---------TQVRLTisEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPL 222
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
73-224 |
2.73e-25 |
|
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Pssm-ID: 211334 [Multi-domain] Cd Length: 168 Bit Score: 98.99 E-value: 2.73e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 VLMYNKPEGELCT-RKDPEGRPTVFDRLPrLDGERwiAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGE 151
Cdd:cd02566 1 LILFNKPYGVLSQfTDESEKHKTLKDYID-DPGVY--AAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 152 VEATTLKTLTTGVELEDGMAKFLKIT---------PR------PGEGINRWYNVLLTEGRNREVRRLWQSQGVDVSRLIR 216
Cdd:cd02566 78 PTEDALEQLRNGVELGDGLTLPAKVEkvdeppwlwEReppirfRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIR 157
|
....*...
gi 1238723754 217 VRYGDLKL 224
Cdd:cd02566 158 VSIGDIGL 165
|
|
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
10-295 |
4.83e-25 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 101.35 E-value: 4.83e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 10 KLQKVLARAGKGSRREMEKVIDAGRVSIDGKVSRLGDRVGPHQQIRLDGHVVKIEAEENRICRVLmyNKPEGELCTRKDP 89
Cdd:PRK10475 8 RLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDLVLIAL--NKPVGIVSTTEDG 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 90 EgRPTVFDRLPRldGERWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELEDG 169
Cdd:PRK10475 86 E-RDNIVDFVNH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGT 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 170 MAKFLKITPrpgEGINRwYNVLLTEGRNREVRRLWQSQGVDVSRLIRVRYGDLKLNpKLPQGGWEELALAN-VNYFR--- 245
Cdd:PRK10475 163 VTKKCKVKK---EAPFV-FRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLS-GIPLGEWRDLTDDElIDLFKlie 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|..
gi 1238723754 246 -SSVQLPNETETKLSVMPEKR-SEKRAKNQriRKAVKKHQIRAKQVQKKRKK 295
Cdd:PRK10475 238 nSSSEAKPKAKAKPKTAGIKRpVVKMEKTA--EKGGRPASNGKRFTSPGRKK 287
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
51-235 |
3.40e-19 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 84.02 E-value: 3.40e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 51 HQQIRLDGHVVKIEAEENRICRVLMYNKPEGELCTRKDPEGRPTVFDRLPRldgERWIAVGRLDVNTSGLLLFTNDGELA 130
Cdd:PRK11394 19 HQVKRFSSQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPV---QGVYAAGRLDRDSEGLLVLTNNGALQ 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 131 NRLMRPSYEIEREYAVRVFGEVEATTLKTLTTGVELEDG--MAKFLKITPRPGEGINR-------------WYNVLLTEG 195
Cdd:PRK11394 96 ARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGptLPAGAELVDEPAWLWPRnppirerksiptsWLKITLYEG 175
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1238723754 196 RNREVRRLWQSQGVDVSRLIRVRYGDLKLNpKLPQGGWEE 235
Cdd:PRK11394 176 RNRQVRRMTAHVGFPTLRLIRYAMGDYSLD-NLANGEWRE 214
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
73-202 |
1.20e-18 |
|
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Pssm-ID: 459961 [Multi-domain] Cd Length: 151 Bit Score: 80.53 E-value: 1.20e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 VLMYNKPEGELCTRKDPEG---RPTVFDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMR--PSYEIEREYAVR 147
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238723754 148 VFGEVEatTLKTLTTGVELEDGMAKF--------------LKITPRPGEGINRWYNVLLTEGRNREVRR 202
Cdd:pfam00849 81 VDKPEE--EEGTIKSPIKKEKNKSPFrkeeelggkkavthLKVLKSGSKGDYSLLELELVTGRKHQIRA 147
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
74-239 |
1.69e-15 |
|
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Pssm-ID: 211329 [Multi-domain] Cd Length: 177 Bit Score: 72.82 E-value: 1.69e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 74 LMYNKPEGELCTRKDP---EGRPTVFDRLPR--LDGE--RWIAVGRLDVNTSGLLLFTNDGELANRLMRPSYEIEREYAV 146
Cdd:cd02555 7 LLLHKPAGMVSEQALAllgPGQRSAADRSGRrpLKGHfaRLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 147 RVFGEVEATTLKTLTTGVELEDGMAKFLKITprpgeginrWYN-----VLLTEGRNREVRRLWQSQGVDVSRLIRVRYGD 221
Cdd:cd02555 87 EVRGELTAGGLERLNHGLTYDGRELPPAKVS---------WQNeqrlrFALKEPQPGQIRRMCESVGLEVVALRRIRIGR 157
|
170
....*....|....*...
gi 1238723754 222 LKLNpKLPQGGWEELALA 239
Cdd:cd02555 158 VSLG-KLPLGQWRYLTTG 174
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
11-73 |
2.69e-05 |
|
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Pssm-ID: 238095 [Multi-domain] Cd Length: 70 Bit Score: 41.47 E-value: 2.69e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1238723754 11 LQKVLARAGK-GSRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQIRLDGH--VVKIEAEENRICRV 73
Cdd:cd00165 3 LDKILARLGLaPSRSEARQLIKHGHVLVNGKvVTKPSYKVKPGDVIEVDGKsiEEDIVYEDKKLLVV 69
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
9-54 |
4.98e-05 |
|
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.
Pssm-ID: 396182 [Multi-domain] Cd Length: 48 Bit Score: 40.17 E-value: 4.98e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1238723754 9 EKLQKVLARAGKG-SRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQI 54
Cdd:pfam01479 1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKvVKDPSYRVKPGDEI 48
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
11-63 |
4.18e-04 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 37.96 E-value: 4.18e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1238723754 11 LQKVLARAG-KGSRREMEKVIDAGRVSIDGK-VSRLGDRVGPHQQIRLDGHVVKI 63
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKkVTKPSYIVKPGDVISVRGKELKR 57
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
77-187 |
9.34e-04 |
|
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Pssm-ID: 211346 [Multi-domain] Cd Length: 185 Bit Score: 39.24 E-value: 9.34e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 77 NKPEGELCTRKDPEGRPTV-----FDRLPRLDGERWIAVGRLDVNTSGLLLFTNDGELANRLMR--PSYEIEREYAVRVF 149
Cdd:cd02869 5 NKPAGLPVHPGPGHLTGTLvnallKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKqfKERKVKKTYLALVD 84
|
90 100 110
....*....|....*....|....*....|....*...
gi 1238723754 150 GEVEATTLKTLTTGVELEDGMAKFLKITPRPGEGINRW 187
Cdd:cd02869 85 GKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAITHY 122
|
|
| PseudoU_synth_ScRIB2 |
cd02557 |
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ... |
112-151 |
1.54e-03 |
|
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Pssm-ID: 211331 [Multi-domain] Cd Length: 213 Bit Score: 39.15 E-value: 1.54e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1238723754 112 RLDVNTSGLLLFTNDGELANRL---MRpSYEIEREYAVRVFGE 151
Cdd:cd02557 65 RLDRLTSGLLLFAKTSQTASRLqqqIR-SREVKKEYLARVKGE 106
|
|
| rluA_subfam |
TIGR00005 |
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ... |
8-151 |
2.87e-03 |
|
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 161659 [Multi-domain] Cd Length: 299 Bit Score: 38.46 E-value: 2.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 8 DEKLQKVLARAGKGSRREM-EKVIDAGRVSIDGKVS-------RLGDRVG-------PHQQIRLDGhVVKIEAEENRIcr 72
Cdd:TIGR00005 5 GQRLDDFLASLLPDLSRSRiQKLIENGQVKVNGKVTanpklkvKDGDRITvrvpeeeEHEVPPQDI-PLDILFEDEDI-- 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238723754 73 vLMYNKPEGELCtrkDPEGR---PTVFDRL-----PRLDGERWIAVGRLDVNTSGLLLF--TNDG--ELANRLMRpsYEI 140
Cdd:TIGR00005 82 -IVINKPSGLVV---HPGGGnpfGTVLNALlahcpPIAGVERVGIVHRLDRDTSGLMVVakTPLAlrELQRQLKN--RTV 155
|
170
....*....|.
gi 1238723754 141 EREYAVRVFGE 151
Cdd:TIGR00005 156 TKEYVALVHGQ 166
|
|
| |
