|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
47-327 |
1.15e-170 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 475.41 E-value: 1.15e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 47 EGEKLQKVLARAGKGSRREIEAMIAANRVSVNGKMATLGDRVVVNANLKIRIDGHIVNLQQAQKEICRVLMYYKPEGELC 126
Cdd:PRK10700 1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 127 TRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKGV 206
Cdd:PRK10700 81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 207 QLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWEEMDLANVNYL 286
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 516416852 287 RELVGLEPETQSKLDVTKQRRRAKTGQIRRAIKRYVDVNKR 327
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGG 281
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
47-279 |
1.41e-108 |
|
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: 315.43 E-value: 1.41e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 47 EGEKLQKVLARAGKGSRREIEAMIAANRVSVNGKMAT-LGDRVvvNANLKIRIDGHIVNLQQAqkeiCRVLMYYKPEGEL 125
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKV--DPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 126 CTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKG 205
Cdd:COG1187 75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516416852 206 VQLEDGPASFKSIKPMGGQGiNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGWEEMD 279
Cdd:COG1187 155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
114-279 |
2.25e-93 |
|
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: 274.96 E-value: 2.25e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 114 RVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 193
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 194 VDETMLARLRKGVQLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRG 273
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*.
gi 516416852 274 GWEEMD 279
Cdd:cd02556 161 QWEELP 166
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
152-280 |
4.13e-62 |
|
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: 193.70 E-value: 4.13e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 152 VGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKGVQLEDGPASFKSIKPMGGQGINQWFD 231
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 516416852 232 VTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGWEEMDL 280
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
115-244 |
9.97e-17 |
|
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: 75.90 E-value: 9.97e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 115 VLMYYKPEGELCTRHDPEG---RATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMH--PSREVEREYSVR 189
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516416852 190 VFG----------QVDETMLARLRKGVQLEDGPAS---FKSIKPmGGQGINQWFDVTLMEGRNREVRR 244
Cdd:pfam00849 81 VDKpeeeegtiksPIKKEKNKSPFRKEEELGGKKAvthLKVLKS-GSKGDYSLLELELVTGRKHQIRA 147
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
51-98 |
3.84e-04 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 37.96 E-value: 3.84e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 516416852 51 LQKVLARAG-KGSRREIEAMIAANRVSVNGKMAT-------LGDRVVVNANLKIRI 98
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISVRGKELKRL 58
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
47-327 |
1.15e-170 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 475.41 E-value: 1.15e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 47 EGEKLQKVLARAGKGSRREIEAMIAANRVSVNGKMATLGDRVVVNANLKIRIDGHIVNLQQAQKEICRVLMYYKPEGELC 126
Cdd:PRK10700 1 MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 127 TRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKGV 206
Cdd:PRK10700 81 TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 207 QLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWEEMDLANVNYL 286
Cdd:PRK10700 161 QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL 240
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 516416852 287 RELVGLEPETQSKLDVTKQRRRAKTGQIRRAIKRYVDVNKR 327
Cdd:PRK10700 241 RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGG 281
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
47-279 |
1.41e-108 |
|
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: 315.43 E-value: 1.41e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 47 EGEKLQKVLARAGKGSRREIEAMIAANRVSVNGKMAT-LGDRVvvNANLKIRIDGHIVNLQQAqkeiCRVLMYYKPEGEL 125
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKV--DPGDEVTVDGKPLKLPEE----PVYLLLNKPAGVV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 126 CTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKG 205
Cdd:COG1187 75 STTKDPEGRPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREG 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516416852 206 VQLEDGPASFKSIKPMGGQGiNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGWEEMD 279
Cdd:COG1187 155 VELEDGPTKPAKVEILSGEA-NTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTL-GDLPPGEWRELT 226
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
114-279 |
2.25e-93 |
|
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: 274.96 E-value: 2.25e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 114 RVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 193
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 194 VDETMLARLRKGVQLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRG 273
Cdd:cd02556 81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160
|
....*.
gi 516416852 274 GWEEMD 279
Cdd:cd02556 161 QWEELP 166
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
152-280 |
4.13e-62 |
|
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: 193.70 E-value: 4.13e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 152 VGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKGVQLEDGPASFKSIKPMGGQGINQWFD 231
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTWLR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 516416852 232 VTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGWEEMDL 280
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
115-261 |
1.01e-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: 183.08 E-value: 1.01e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 115 VLMYYKPEGELCTRHDPEGRATVFDRLPRlTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQV 194
Cdd:cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKD-VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVP 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516416852 195 DETMLARLRKGVQLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRY 261
Cdd:cd02870 80 SEEELRRLRAGVELDDGKTAPAKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
115-261 |
6.10e-46 |
|
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: 153.30 E-value: 6.10e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 115 VLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQV 194
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516416852 195 DETMLARLRK-------GVQLEDGPASFKSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRY 261
Cdd:cd02550 81 DEEGIEDLATvrrgrlsGLVDEGVPLAVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
114-281 |
7.38e-37 |
|
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: 129.95 E-value: 7.38e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 114 RVLMYYKPEGELCTRHDPEGRaTVFDRLPRLTGSRWI-AVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFG 192
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHHP-TVIDLLPEPDRRRDLfPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 193 QVDETMLARLRKGVQLEDG----PASFKSIKPmggqginQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMK 268
Cdd:cd02553 80 PLTEDDIEAFAEGVLLHDGyptkPAKLEILSP-------TTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDD 152
|
170
....*....|...
gi 516416852 269 TLPRGGWEEMDLA 281
Cdd:cd02553 153 DLAPGEWRPLTEE 165
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
115-266 |
4.53e-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: 4.53e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 115 VLMYYKPEGELCT-RHDPEGRATVFDRLPrLTGSRwiAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQ 193
Cdd:cd02566 1 LILFNKPYGVLSQfTDESEKHKTLKDYID-DPGVY--AAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 194 VDETMLARLRKGVQLEDGPASFKSIKPMG---------------GQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIR 258
Cdd:cd02566 78 PTEDALEQLRNGVELGDGLTLPAKVEKVDeppwlwereppirfrKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIR 157
|
....*...
gi 516416852 259 IRYGNIKL 266
Cdd:cd02566 158 VSIGDIGL 165
|
|
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
50-319 |
1.21e-23 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 98.26 E-value: 1.21e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 50 KLQKVLARAGKGSRREIEAMIAANRVSVNGKMATLGDRVVvnANLKIRIDGHIVNLQQAQKEICRVLmyYKPEGELCTRH 129
Cdd:PRK10475 8 RLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVK--AGDVVKVNGQLIEPREAEDLVLIAL--NKPVGIVSTTE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 130 DPEgRATVFDRLPRltGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLRKGVqle 209
Cdd:PRK10475 84 DGE-RDNIVDFVNH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGV--- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 210 dgpasfksikPMGGQGINQW---------FDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGWEEMDL 280
Cdd:PRK10475 158 ----------PILGTVTKKCkvkkeapfvFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDLTD 226
|
250 260 270
....*....|....*....|....*....|....*....
gi 516416852 281 ANVNYLRELVglepETQSKLDVTKQRRRAKTGQIRRAIK 319
Cdd:PRK10475 227 DELIDLFKLI----ENSSSEAKPKAKAKPKTAGIKRPVV 261
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
116-275 |
6.81e-22 |
|
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: 90.45 E-value: 6.81e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 116 LMYYKPEGELCTRHDPEgRATVFDRLPRltGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVD 195
Cdd:cd02554 3 IAYNKPVGIDCTLERAD-EDNIIDFVNP--PPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 196 ETMLARLRKGVQLEDGPasfkSIKPMGGQGINQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLmKTLPRGGW 275
Cdd:cd02554 80 DEFIEGMSNGVVILGTV----TKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIEL-GDLAPGEW 154
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
50-273 |
7.53e-20 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 86.70 E-value: 7.53e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 50 KLQKVLARAGKGSRREIEAMIAANRVSVNGKmatlgdrVVVNANLK------IRIDGHIVNLQQAQkeicRVLMYYKPEG 123
Cdd:PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGE-------IVKNGAFKllpehdVAYDGNPLAQQHGP----RYFMLNKPQG 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 124 ELCTRHDPEgRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDETMLARLR 203
Cdd:PRK10839 71 YVCSTDDPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFA 149
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516416852 204 KGVQLED-----GPASFKSIKPmggqginQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRG 273
Cdd:PRK10839 150 KGVQLHNekdltKPAVLEVITP-------TQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPG 217
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
106-277 |
3.13e-18 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 82.10 E-value: 3.13e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 106 QQAQKEICRVLMYYKPEGELCTRHDPEGRATVFDRLPrLTGSrwIAVGRLDINTSGLLLFTTDGELANRLMHPSREVERE 185
Cdd:PRK11394 32 RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-VQGV--YAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKI 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 186 YSVRVFGQVDETMLARLRKGVQLEDGPAsfksiKPMGGQGINQ--------------------WFDVTLMEGRNREVRRL 245
Cdd:PRK11394 109 YYVQVEGIPTQDALEALRNGVTLNDGPT-----LPAGAELVDEpawlwprnppirerksiptsWLKITLYEGRNRQVRRM 183
|
170 180 190
....*....|....*....|....*....|..
gi 516416852 246 WESQGIQVSRLIRIRYGNIKLmKTLPRGGWEE 277
Cdd:PRK11394 184 TAHVGFPTLRLIRYAMGDYSL-DNLANGEWRE 214
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
116-275 |
3.21e-18 |
|
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: 80.91 E-value: 3.21e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 116 LMYYKPEGELCTRHDP---EGRATVFDRLPR--LTG--SRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSV 188
Cdd:cd02555 7 LLLHKPAGMVSEQALAllgPGQRSAADRSGRrpLKGhfARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 189 RVFGQVDETMLARLRKGVQLEDgpasfKSIKPMGGQGIN-QWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLM 267
Cdd:cd02555 87 EVRGELTAGGLERLNHGLTYDG-----RELPPAKVSWQNeQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLG 161
|
....*...
gi 516416852 268 KtLPRGGW 275
Cdd:cd02555 162 K-LPLGQW 168
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
115-244 |
9.97e-17 |
|
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: 75.90 E-value: 9.97e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516416852 115 VLMYYKPEGELCTRHDPEG---RATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMH--PSREVEREYSVR 189
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTkllSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516416852 190 VFG----------QVDETMLARLRKGVQLEDGPAS---FKSIKPmGGQGINQWFDVTLMEGRNREVRR 244
Cdd:pfam00849 81 VDKpeeeegtiksPIKKEKNKSPFRKEEELGGKKAvthLKVLKS-GSKGDYSLLELELVTGRKHQIRA 147
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
51-115 |
4.84e-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: 40.70 E-value: 4.84e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516416852 51 LQKVLARAGK-GSRREIEAMIAANRVSVNGKMAT-LGDRVVVNANLKIRIDGHIVNLQQAQKEICRV 115
Cdd:cd00165 3 LDKILARLGLaPSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKSIEEDIVYEDKKLLVV 69
|
|
| PseudoU_synth_ScRIB2 |
cd02557 |
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ... |
154-192 |
3.11e-04 |
|
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: 41.46 E-value: 3.11e-04
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 516416852 154 RLDINTSGLLLFTTDGELANRL--MHPSREVEREYSVRVFG 192
Cdd:cd02557 65 RLDRLTSGLLLFAKTSQTASRLqqQIRSREVKKEYLARVKG 105
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
51-98 |
3.84e-04 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 37.96 E-value: 3.84e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 516416852 51 LQKVLARAG-KGSRREIEAMIAANRVSVNGKMAT-------LGDRVVVNANLKIRI 98
Cdd:smart00363 3 LDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTkpsyivkPGDVISVRGKELKRL 58
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
49-83 |
5.09e-04 |
|
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: 37.47 E-value: 5.09e-04
10 20 30
....*....|....*....|....*....|....*.
gi 516416852 49 EKLQKVLARAGKG-SRREIEAMIAANRVSVNGKMAT 83
Cdd:pfam01479 1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVK 36
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