|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
1-231 |
0e+00 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 514.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80
Cdd:PRK10839 1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDL 160
Cdd:PRK10839 81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDL 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 900135202 161 TKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEIASVG 231
Cdd:PRK10839 161 TKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASVG 231
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
1-223 |
3.92e-106 |
|
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: 3.92e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDP-D 79
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPeG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 80 HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKd 159
Cdd:COG1187 83 RPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGP- 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 900135202 160 lTKPATLEVIT---PVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDeNLAPGEYRPLT 223
Cdd:COG1187 162 -TKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGEWRELT 226
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
61-227 |
1.57e-100 |
|
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: 289.03 E-value: 1.57e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 61 RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYK-LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP 139
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRdLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 140 VADDTAAQFAKGVQLHNEkDLTKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEY 219
Cdd:cd02553 81 LTEDDIEAFAEGVLLHDG-YPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLAPGEW 159
|
....*...
gi 900135202 220 RPLTEEEI 227
Cdd:cd02553 160 RPLTEEEL 167
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
98-224 |
1.36e-63 |
|
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: 194.08 E-value: 1.36e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 98 AGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKdlTKPATLEVIT----PVQ 173
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGK--TKPAKLKVITepgfPTW 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 900135202 174 VRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLdENLAPGEYRPLTE 224
Cdd:TIGR00093 79 LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
62-192 |
3.01e-20 |
|
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: 83.61 E-value: 3.01e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVCSTDDP----DHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRIT--SPRHHCEKTYLVT 135
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSltklLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNklFPERKIEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 900135202 136 LESPVADDTAAQFA-----KGVQLHNEKDLTKPATLEVITPVQ---------VRLTISEGRYHQVKRMFAA 192
Cdd:pfam00849 81 VDKPEEEEGTIKSPikkekNKSPFRKEEELGGKKAVTHLKVLKsgskgdyslLELELVTGRKHQIRAHLAA 151
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
1-54 |
2.86e-08 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 49.13 E-value: 2.86e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 900135202 1 MRLDKFIAQQLGV-SRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPL 54
Cdd:smart00363 1 RRLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
1-231 |
0e+00 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 514.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80
Cdd:PRK10839 1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDL 160
Cdd:PRK10839 81 PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDL 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 900135202 161 TKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEIASVG 231
Cdd:PRK10839 161 TKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASVG 231
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
1-223 |
3.92e-106 |
|
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: 3.92e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDP-D 79
Cdd:COG1187 3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPeG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 80 HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKd 159
Cdd:COG1187 83 RPTVFDLLPEARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGP- 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 900135202 160 lTKPATLEVIT---PVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDeNLAPGEYRPLT 223
Cdd:COG1187 162 -TKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGEWRELT 226
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
61-227 |
1.57e-100 |
|
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: 289.03 E-value: 1.57e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 61 RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYK-LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP 139
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRdLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 140 VADDTAAQFAKGVQLHNEkDLTKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEY 219
Cdd:cd02553 81 LTEDDIEAFAEGVLLHDG-YPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDLAPGEW 159
|
....*...
gi 900135202 220 RPLTEEEI 227
Cdd:cd02553 160 RPLTEEEL 167
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
98-224 |
1.36e-63 |
|
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: 194.08 E-value: 1.36e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 98 AGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKdlTKPATLEVIT----PVQ 173
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGK--TKPAKLKVITepgfPTW 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 900135202 174 VRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLdENLAPGEYRPLTE 224
Cdd:TIGR00093 79 LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSL-NGLPPGEWRPLTL 128
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
62-205 |
8.44e-60 |
|
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: 185.01 E-value: 8.44e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVA 141
Cdd:cd02870 1 YLLLNKPRGVVSTVRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPS 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 900135202 142 DDTAAQFAKGVQLhnEKDLTKPATLEVITP----VQVRLTISEGRYHQVKRMFAAVGNRVVELHRERI 205
Cdd:cd02870 81 EEELRRLRAGVEL--DDGKTAPAKVKVLSRdpknTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
62-205 |
3.89e-54 |
|
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: 170.63 E-value: 3.89e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVCSTDDPDH-PTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPV 140
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRdPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 900135202 141 ADDTAAQFAKGV-----QLHNEKDLTKPATLEVITPV----QVRLTISEGRYHQVKRMFAAVGNRVVELHRERI 205
Cdd:cd02550 81 DEEGIEDLATVRrgrlsGLVDEGVPLAVTKVRVIGEHggtgRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
62-229 |
2.65e-41 |
|
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: 138.21 E-value: 2.65e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVayKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVA 141
Cdd:cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVNPPP--RIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPIT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 142 DDTAAQFAKGVQLHNEKdlTKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDEnLAPGEYRP 221
Cdd:cd02554 80 DEFIEGMSNGVVILGTV--TKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGD-LAPGEWRP 156
|
....*...
gi 900135202 222 LTEEEIAS 229
Cdd:cd02554 157 LTDAELFE 164
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
62-212 |
8.61e-32 |
|
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: 114.02 E-value: 8.61e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVC--STDDPDHPTVLYFLDEPvayKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP 139
Cdd:cd02566 1 LILFNKPYGVLSqfTDESEKHKTLKDYIDDP---GVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 140 VADDTAAQFAKGVQLhneKD-LTKPATLEVI----------TPVQVR---------LTISEGRYHQVKRMFAAVGNRVVE 199
Cdd:cd02566 78 PTEDALEQLRNGVEL---GDgLTLPAKVEKVdeppwlwerePPIRFRkniptswieITICEGKNRQVRRMTAAVGFPTLR 154
|
170
....*....|...
gi 900135202 200 LHRERIGAITLDE 212
Cdd:cd02566 155 LIRVSIGDIGLDN 167
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
61-224 |
1.19e-27 |
|
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: 103.16 E-value: 1.19e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 61 RYFMLNKPQGYVCSTDDPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP 139
Cdd:cd02556 1 RVLIYHKPEGLICTRKDPKgRPTVFDLLPKLGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 140 VADDTAAQFAKGVQLhnEKDLTKPATLEVI----TPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLA 215
Cdd:cd02556 81 VTDEQLKSLKKGVEL--EDGFAGFKSIQLEggegKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLK 158
|
....*....
gi 900135202 216 PGEYRPLTE 224
Cdd:cd02556 159 RGQWEELPP 167
|
|
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
2-227 |
5.85e-24 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 96.76 E-value: 5.85e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 2 RLDKFIAQQLGVSRaiagREIRG----NRVTVDGDIIK-NAAFKLLPEHAVAYDGNPLA----QQHGPRYFMLNKPQGYV 72
Cdd:PRK10700 4 KLQKVLARAGHGSR----REIESiieaGRVSVDGKIATlGDRVEVTPGLKIRIDGHLISvkesAEQICRVLAYYKPEGEL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 73 CSTDDPD-HPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKG 151
Cdd:PRK10700 80 CTRNDPEgRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 152 VQLHNekdltKPATLEVIT-------PVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTE 224
Cdd:PRK10700 160 VQLED-----GPAAFKTIKfsggegiNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDL 234
|
...
gi 900135202 225 EEI 227
Cdd:PRK10700 235 AQT 237
|
|
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
1-228 |
3.72e-23 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 94.41 E-value: 3.72e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGdiiKNAAF--KLLPEHAVAYDGnplaQQHGPR------YFMLNKPQGYV 72
Cdd:PRK10475 7 TRLNKYISESGICSRREADRYIEQGNVFING---KRATIgdQVKAGDVVKVNG----QLIEPReaedlvLIALNKPVGIV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 73 CSTDDPDHPTVLYFLDEPVayKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGV 152
Cdd:PRK10475 80 STTEDGERDNIVDFVNHSK--RVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGV 157
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 900135202 153 QLHNEkdLTKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLdENLAPGEYRPLTEEEIA 228
Cdd:PRK10475 158 PILGT--VTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSL-SGIPLGEWRDLTDDELI 230
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
62-192 |
3.01e-20 |
|
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: 83.61 E-value: 3.01e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 62 YFMLNKPQGYVCSTDDP----DHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRIT--SPRHHCEKTYLVT 135
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSltklLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNklFPERKIEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 900135202 136 LESPVADDTAAQFA-----KGVQLHNEKDLTKPATLEVITPVQ---------VRLTISEGRYHQVKRMFAA 192
Cdd:pfam00849 81 VDKPEEEEGTIKSPikkekNKSPFRKEEELGGKKAVTHLKVLKsgskgdyslLELELVTGRKHQIRAHLAA 151
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
60-226 |
2.86e-19 |
|
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: 81.68 E-value: 2.86e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 60 PRYFMLNKPQGYVCSTDDP---------DHPTVLYFLDEPVAyKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEK 130
Cdd:cd02555 4 PVTLLLHKPAGMVSEQALAllgpgqrsaADRSGRRPLKGHFA-RLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQ 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 131 TYLVTLESPVADDTAAQFAKGVQLhNEKDLtKPATLEVITPVQVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITL 210
Cdd:cd02555 83 EYLVEVRGELTAGGLERLNHGLTY-DGREL-PPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSL 160
|
170
....*....|....*.
gi 900135202 211 DeNLAPGEYRPLTEEE 226
Cdd:cd02555 161 G-KLPLGQWRYLTTGE 175
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
61-224 |
5.16e-17 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 76.70 E-value: 5.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 61 RYFMLNKPQGYVCS-TDDPDHPTVLYFLdePVAyKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESP 139
Cdd:PRK11394 40 RVILFNKPYDVLPQfTDEAGRKTLKEFI--PVQ-GVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGI 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 140 VADDTAAQFAKGVQLHNEKDLtkPATLEVIT----------PVQVR---------LTISEGRYHQVKRMFAAVGNRVVEL 200
Cdd:PRK11394 117 PTQDALEALRNGVTLNDGPTL--PAGAELVDepawlwprnpPIRERksiptswlkITLYEGRNRQVRRMTAHVGFPTLRL 194
|
170 180
....*....|....*....|....
gi 900135202 201 HRERIGAITLDeNLAPGEYRPLTE 224
Cdd:PRK11394 195 IRYAMGDYSLD-NLANGEWREATD 217
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
1-54 |
2.86e-08 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 49.13 E-value: 2.86e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 900135202 1 MRLDKFIAQQLGV-SRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPL 54
Cdd:smart00363 1 RRLDKFLARLGLApSRSQARRLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
1-66 |
3.15e-08 |
|
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: 49.17 E-value: 3.15e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 1 MRLDKFIAQQLGV-SRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQ---HGPRYFMLN 66
Cdd:cd00165 1 MRLDKILARLGLApSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDivyEDKKLLVVN 70
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
1-47 |
7.91e-07 |
|
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: 44.79 E-value: 7.91e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 900135202 1 MRLDKFIAQQ-LGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAV 47
Cdd:pfam01479 1 RRLDKVLARLgLASSRSQARQLIEHGRVLVNGKVVKDPSYRVKPGDEI 48
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
65-198 |
1.44e-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: 41.17 E-value: 1.44e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 900135202 65 LNKPQGYVC-STDDPDHPTVLYFL-----DEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITS--PRHHCEKTYL--- 133
Cdd:cd02869 4 VNKPAGLPVhPGPGHLTGTLVNALlklllLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKqfKERKVKKTYLalv 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 900135202 134 --------VTLESPVADDTAAQFAKGVQLHNEKD-LTKPATLEVITPV-QVRLTISEGRYHQVKRMFAAVGNRVV 198
Cdd:cd02869 84 dgkppedeGTIDAPLGRKKRKKRARVVVSEDGKPaITHYKVLERFGNVtLVELQLETGRTHQIRVHLASIGHPIV 158
|
|
| |
