|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
7-295 |
0e+00 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 552.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 7 KTEKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEVTPATKIRLDGRLLAIKEPEKEICRVMAYYKPEGELC 86
Cdd:PRK10700 1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 87 TRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGV 166
Cdd:PRK10700 81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 167 QLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGLEQTNYL 246
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 739087031 247 RELVELPVETESKVAVERDQRRIKANQIRRAVKRHTQVASRPASKRQSS 295
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
7-238 |
2.45e-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: 306.19 E-value: 2.45e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 7 KTEKLQKILARSGHGSRREIETFLQAGRISVDGKIAT-LGDRVevTPATKIRLDGRLLAIKEPekeiCRVMAYYKPEGEL 85
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKV--DPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 86 CTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQG 165
Cdd:COG1187 75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087031 166 VQLEDGPASFKTVSYRGGEGmNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTEL 238
Cdd:COG1187 155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
74-239 |
2.32e-96 |
|
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: 281.50 E-value: 2.32e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 74 RVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGE 153
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 154 INDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRG 233
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*.
gi 739087031 234 GWTELG 239
Cdd:cd02556 161 QWEELP 166
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
112-238 |
6.32e-57 |
|
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: 179.83 E-value: 6.32e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 112 VGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQWFN 191
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 739087031 192 VTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTEL 238
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPL 126
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
75-204 |
5.45e-19 |
|
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: 81.68 E-value: 5.45e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 75 VMAYYKPEGELCTRHDPEG---RPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMH--PSREVEREYAVR 149
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739087031 150 VFGEINDAKIRQL----------TQGVQLEDGPAS---FKTVSYrGGEGMNQWFNVTLTEGRNREVRR 204
Cdd:pfam00849 81 VDKPEEEEGTIKSpikkeknkspFRKEEELGGKKAvthLKVLKS-GSKGDYSLLELELVTGRKHQIRA 147
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
11-50 |
5.03e-03 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 34.88 E-value: 5.03e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 739087031 11 LQKILARSG-HGSRREIETFLQAGRISVDGKIAT-------LGDRVEV 50
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISV 50
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
7-295 |
0e+00 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 552.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 7 KTEKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEVTPATKIRLDGRLLAIKEPEKEICRVMAYYKPEGELC 86
Cdd:PRK10700 1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 87 TRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGV 166
Cdd:PRK10700 81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 167 QLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGLEQTNYL 246
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 739087031 247 RELVELPVETESKVAVERDQRRIKANQIRRAVKRHTQVASRPASKRQSS 295
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNN 289
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
7-238 |
2.45e-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: 306.19 E-value: 2.45e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 7 KTEKLQKILARSGHGSRREIETFLQAGRISVDGKIAT-LGDRVevTPATKIRLDGRLLAIKEPekeiCRVMAYYKPEGEL 85
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKV--DPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 86 CTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQG 165
Cdd:COG1187 75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739087031 166 VQLEDGPASFKTVSYRGGEGmNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTEL 238
Cdd:COG1187 155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWREL 225
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
74-239 |
2.32e-96 |
|
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: 281.50 E-value: 2.32e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 74 RVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGE 153
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 154 INDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRG 233
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*.
gi 739087031 234 GWTELG 239
Cdd:cd02556 161 QWEELP 166
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
77-221 |
3.22e-59 |
|
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: 186.16 E-value: 3.22e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 77 AYYKPEGELCTRHDPEGRPTVFNRLPRlTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEIND 156
Cdd:cd02870 3 LLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSE 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739087031 157 AKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRY 221
Cdd:cd02870 82 EELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
112-238 |
6.32e-57 |
|
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: 179.83 E-value: 6.32e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 112 VGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQWFN 191
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 739087031 192 VTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTEL 238
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPL 126
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
75-221 |
2.67e-49 |
|
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: 161.00 E-value: 2.67e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 75 VMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEI 154
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 739087031 155 NDAKIRQL-------TQGVQLEDGPASFKTVSYRGGEGMNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRY 221
Cdd:cd02550 81 DEEGIEDLatvrrgrLSGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
77-242 |
1.90e-39 |
|
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: 136.11 E-value: 1.90e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 77 AYY---KPEGELCTRHDPEGrPTVFNRLPRLTGARWI-AVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFG 152
Cdd:cd02553 1 VYLmlnKPAGVVCATKDPHH-PTVIDLLPEPDRRRDLfPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 153 EINDAKIRQLTQGVQLEDG----PASFKTVSyrggegmNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPK 228
Cdd:cd02553 80 PLTEDDIEAFAEGVLLHDGyptkPAKLEILS-------PTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDD 152
|
170
....*....|....
gi 739087031 229 GLPRGGWTELGLEQ 242
Cdd:cd02553 153 DLAPGEWRPLTEEE 166
|
|
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
5-303 |
1.53e-28 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 110.98 E-value: 1.53e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 5 PQKTEKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEvtPATKIRLDGRLLAIKEPEKEIcrVMAYYKPEGE 84
Cdd:PRK10475 3 TDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVK--AGDVVKVNGQLIEPREAEDLV--LIALNKPVGI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 85 LCTRHDPEGRPTV-FNRlprlTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLT 163
Cdd:PRK10475 79 VSTTEDGERDNIVdFVN----HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMG 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 164 QGVQLedgpasFKTVSYR---GGEGMNQwFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTELgl 240
Cdd:PRK10475 155 AGVPI------LGTVTKKckvKKEAPFV-FRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDL-- 224
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 739087031 241 eqTNylRELVEL--PVETESkvavERDQRRIKANQIRRAVKRHTQVASRPASKRQSSRPTAKRRT 303
Cdd:PRK10475 225 --TD--DELIDLfkLIENSS----SEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFT 281
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
77-238 |
6.77e-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: 100.46 E-value: 6.77e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 77 AYYKPEGELCT--RHDPEGRPTVFNRLPRLtgarwIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEI 154
Cdd:cd02554 4 AYNKPVGIDCTleRADEDNIIDFVNPPPRI-----FPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 155 NDAKIRQLTQGVQLEDG---PASFKTVSYRGgegmnqwFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLpKGLP 231
Cdd:cd02554 79 TDEFIEGMSNGVVILGTvtkPCKVERLAKDK-------FRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLA 150
|
....*..
gi 739087031 232 RGGWTEL 238
Cdd:cd02554 151 PGEWRPL 157
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
75-226 |
9.18e-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: 97.84 E-value: 9.18e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 75 VMAYYKPEGELCT-RHDPEGRPTV--FNRLPRLtgarwIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVF 151
Cdd:cd02566 1 LILFNKPYGVLSQfTDESEKHKTLkdYIDDPGV-----YAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 152 GEINDAKIRQLTQGVQLEDG---PASFKTVSYRGGEGMNQ------------WFNVTLTEGRNREVRRLWESVGVQVSRL 216
Cdd:cd02566 76 GVPTEDALEQLRNGVELGDGltlPAKVEKVDEPPWLWEREppirfrkniptsWIEITICEGKNRQVRRMTAAVGFPTLRL 155
|
170
....*....|
gi 739087031 217 IRVRYGDIDL 226
Cdd:cd02566 156 IRVSIGDIGL 165
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
10-244 |
3.20e-23 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 95.17 E-value: 3.20e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 10 KLQKILARSGHGSRREIETFLQAGRISVDGKIATLGdRVEVTPATKIRLDGRLLA-IKEPekeicRVMAYYKPEGELCTR 88
Cdd:PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNG-AFKLLPEHDVAYDGNPLAqQHGP-----RYFMLNKPQGYVCST 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 89 HDPEgRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQL 168
Cdd:PRK10839 76 DDPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 169 ED-----GPASFKTVSyrggegmNQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGLEQT 243
Cdd:PRK10839 155 HNekdltKPAVLEVIT-------PTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEI 227
|
.
gi 739087031 244 N 244
Cdd:PRK10839 228 A 228
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
75-204 |
5.45e-19 |
|
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: 81.68 E-value: 5.45e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 75 VMAYYKPEGELCTRHDPEG---RPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTDGELANRLMH--PSREVEREYAVR 149
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739087031 150 VFGEINDAKIRQL----------TQGVQLEDGPAS---FKTVSYrGGEGMNQWFNVTLTEGRNREVRR 204
Cdd:pfam00849 81 VDKPEEEEGTIKSpikkeknkspFRKEEELGGKKAvthLKVLKS-GSKGDYSLLELELVTGRKHQIRA 147
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
57-237 |
3.65e-18 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 81.33 E-value: 3.65e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 57 RLDGRLLAIKEPEKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPrLTGArwIAVGRLDVNTSGLLLFTTDGELANRLM 136
Cdd:PRK11394 23 RFSSQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-VQGV--YAAGRLDRDSEGLLVLTNNGALQARLT 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 137 HPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSY--------------RGGEGM-NQWFNVTLTEGRNRE 201
Cdd:PRK11394 100 QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELvdepawlwprnppiRERKSIpTSWLKITLYEGRNRQ 179
|
170 180 190
....*....|....*....|....*....|....*.
gi 739087031 202 VRRLWESVGVQVSRLIRVRYGDIDLpKGLPRGGWTE 237
Cdd:PRK11394 180 VRRMTAHVGFPTLRLIRYAMGDYSL-DNLANGEWRE 214
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
107-239 |
4.96e-16 |
|
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: 74.36 E-value: 4.96e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 107 ARWIAVGRLDVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGgegm 186
Cdd:cd02555 45 ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQN---- 120
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 739087031 187 NQWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKgLPRGGWTELG 239
Cdd:cd02555 121 EQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGK-LPLGQWRYLT 172
|
|
| PseudoU_synth_ScRIB2 |
cd02557 |
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ... |
114-160 |
6.22e-05 |
|
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: 43.39 E-value: 6.22e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 739087031 114 RLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFGEINDAKIR 160
Cdd:cd02557 65 RLDRLTSGLLLFAKTSQTASRLqqQIRSREVKKEYLARVKGEFPDGEVV 113
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
11-58 |
1.70e-04 |
|
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: 39.15 E-value: 1.70e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 739087031 11 LQKILARSG-HGSRREIETFLQAGRISVDGKIAT-------LGDRVEVTPATKIRL 58
Cdd:cd00165 3 LDKILARLGlAPSRSEARQLIKHGHVLVNGKVVTkpsykvkPGDVIEVDGKSIEED 58
|
|
| rluA_subfam |
TIGR00005 |
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ... |
6-155 |
8.80e-04 |
|
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: 40.38 E-value: 8.80e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 6 QKTEKLQKILARS-GHGSRREIETFLQAGRISVDGKiatlgdrVEVTPATKIRlDGRLLAIKEPEKEICRV--------- 75
Cdd:TIGR00005 3 QAGQRLDDFLASLlPDLSRSRIQKLIENGQVKVNGK-------VTANPKLKVK-DGDRITVRVPEEEEHEVppqdipldi 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 76 -------MAYYKPEGELCtrHdPEGR---PTVFNRL----PRLTGARWIA-VGRLDVNTSGLLLF--TTDG--ELANRLM 136
Cdd:TIGR00005 75 lfedediIVINKPSGLVV--H-PGGGnpfGTVLNALlahcPPIAGVERVGiVHRLDRDTSGLMVVakTPLAlrELQRQLK 151
|
170
....*....|....*....
gi 739087031 137 hpSREVEREYAVRVFGEIN 155
Cdd:TIGR00005 152 --NRTVTKEYVALVHGQFD 168
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
9-50 |
1.30e-03 |
|
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: 35.93 E-value: 1.30e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 739087031 9 EKLQKILARSGHG-SRREIETFLQAGRISVDGKIAT-LGDRVEV 50
Cdd:pfam01479 1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVKdPSYRVKP 44
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
11-50 |
5.03e-03 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 34.88 E-value: 5.03e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 739087031 11 LQKILARSG-HGSRREIETFLQAGRISVDGKIAT-------LGDRVEV 50
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISV 50
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
80-159 |
6.09e-03 |
|
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: 36.93 E-value: 6.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739087031 80 KPEGELCTRHDPEGRPTVFNRLP-----RLTGARWIAVGRLDVNTSGLLLFTTDGELANRL--MHPSREVEREYAVRVFG 152
Cdd:cd02869 6 KPAGLPVHPGPGHLTGTLVNALLkllllLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLskQFKERKVKKTYLALVDG 85
|
....*..
gi 739087031 153 EINDAKI 159
Cdd:cd02869 86 KPPEDEG 92
|
|
| |
