|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
1-290 |
0e+00 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 655.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 1 MLPDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80
Cdd:PRK10475 1 MLTDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 81 TTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160
Cdd:PRK10475 81 TTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPIL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 161 GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
Cdd:PRK10475 161 GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 446859121 241 SEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290
Cdd:PRK10475 241 SEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
5-225 |
2.11e-98 |
|
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: 288.09 E-value: 2.11e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 5 SSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPREaeDLVLIALNKPVGIVSTTE 83
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKVDPGDEVTVDGKPLKLPE--EPVYLLLNKPAGVVSTTK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 84 DGE-RDNIVDFV--NHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160
Cdd:COG1187 79 DPEgRPTVFDLLpeARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE 158
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446859121 161 GTV---TKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225
Cdd:COG1187 159 DGPtkpAKVEILSGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
68-231 |
2.48e-96 |
|
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: 280.74 E-value: 2.48e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 68 VLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITE 147
Cdd:cd02554 1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 148 EFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDD 227
Cdd:cd02554 81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160
|
....
gi 446859121 228 ELID 231
Cdd:cd02554 161 ELFE 164
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
103-226 |
2.83e-55 |
|
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: 174.82 E-value: 2.83e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 103 IGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVF----R 178
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 446859121 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTD 226
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
69-195 |
3.27e-25 |
|
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: 98.25 E-value: 3.27e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVSTTEDGERD------NIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKI--LRAGNDHEKEYLVT 140
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTKllsllaLLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446859121 141 VDKPITEEFI--RGMSAGVPILGTVTKKCKVKKEAPFVFR--------------ITLVQGLNRQIRRMCEH 195
Cdd:pfam00849 81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKvlksgskgdyslleLELVTGRKHQIRAHLAA 151
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
7-56 |
1.03e-09 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 53.37 E-value: 1.03e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 446859121 7 VRLNKYISESG-ICSRREADRYIEQGNVFLNGKRATI-GDQVKPGDVVKVNG 56
Cdd:smart00363 1 RRLDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTKpSYIVKPGDVISVRG 52
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
1-290 |
0e+00 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 655.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 1 MLPDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80
Cdd:PRK10475 1 MLTDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEDLVLIALNKPVGIVS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 81 TTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160
Cdd:PRK10475 81 TTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPIL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 161 GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
Cdd:PRK10475 161 GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 446859121 241 SEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290
Cdd:PRK10475 241 SEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKGR 290
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
5-225 |
2.11e-98 |
|
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: 288.09 E-value: 2.11e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 5 SSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEPREaeDLVLIALNKPVGIVSTTE 83
Cdd:COG1187 1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTeLGTKVDPGDEVTVDGKPLKLPE--EPVYLLLNKPAGVVSTTK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 84 DGE-RDNIVDFV--NHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160
Cdd:COG1187 79 DPEgRPTVFDLLpeARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELE 158
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446859121 161 GTV---TKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225
Cdd:COG1187 159 DGPtkpAKVEILSGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
68-231 |
2.48e-96 |
|
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: 280.74 E-value: 2.48e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 68 VLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITE 147
Cdd:cd02554 1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 148 EFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDD 227
Cdd:cd02554 81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160
|
....
gi 446859121 228 ELID 231
Cdd:cd02554 161 ELFE 164
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
103-226 |
2.83e-55 |
|
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: 174.82 E-value: 2.83e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 103 IGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVF----R 178
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 446859121 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTD 226
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
70-208 |
8.03e-50 |
|
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: 161.51 E-value: 8.03e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 70 IALNKPVGIVSTTEDGERDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITE 147
Cdd:cd02870 2 LLLNKPRGVVSTVRDPEGRPTVldLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSE 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446859121 148 EFIRGMSAGVPILGTV----TKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRI 208
Cdd:cd02870 82 EELRRLRAGVELDDGKtapaKVKVLSRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
69-208 |
1.47e-47 |
|
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: 155.99 E-value: 1.47e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVSTTEDGERDNIV---DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPI 145
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVvvrLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446859121 146 TEEFIRGMS-------AGVPILGTVTKKCKVKKEAPF----VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRI 208
Cdd:cd02550 81 DEEGIEDLAtvrrgrlSGLVDEGVPLAVTKVRVIGEHggtgRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
68-229 |
9.84e-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: 123.40 E-value: 9.84e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 68 VLIALNKPVGIVSTTEDGERDNIVDFVN---HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKP 144
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHHPTVIDLLPepdRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 145 ITEEFIRGMSAGVPIL-GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWR 222
Cdd:cd02553 81 LTEDDIEAFAEGVLLHdGYPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELdDDLAPGEWR 160
|
....*..
gi 446859121 223 DLTDDEL 229
Cdd:cd02553 161 PLTEEEL 167
|
|
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
6-279 |
4.89e-28 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 109.08 E-value: 4.89e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 6 SVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGD--QVKPGDVVKVNGQLIEPREAEDLV--LIALNKPVGIVST 81
Cdd:PRK10700 2 SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDrvEVTPGLKIRIDGHLISVKESAEQIcrVLAYYKPEGELCT 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 82 TEDGE-RDNIVDFVN--HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVP 158
Cdd:PRK10700 82 RNDPEgRPTVFDRLPklRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGVQ 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 159 IlgtvtkkckvkKEAPFVFR---------------ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWR 222
Cdd:PRK10700 162 L-----------EDGPAAFKtikfsggeginqwynVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLpKGLPRGGWT 230
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 223 DL---TDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKmeKTAEKGGRPASNGKR 279
Cdd:PRK10700 231 ELdlaQTNYLRELVELPPETSSKVAVEKDRRRMKANQIRRAVK--RHSQVSGGRRSGGRN 288
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
69-195 |
3.27e-25 |
|
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: 98.25 E-value: 3.27e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVSTTEDGERD------NIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKI--LRAGNDHEKEYLVT 140
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSLTKllsllaLLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446859121 141 VDKPITEEFI--RGMSAGVPILGTVTKKCKVKKEAPFVFR--------------ITLVQGLNRQIRRMCEH 195
Cdd:pfam00849 81 VDKPEEEEGTikSPIKKEKNKSPFRKEEELGGKKAVTHLKvlksgskgdyslleLELVTGRKHQIRAHLAA 151
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
69-216 |
2.16e-23 |
|
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: 93.60 E-value: 2.16e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVS--TTEDGERDNIVDFVNhSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPIT 146
Cdd:cd02566 1 LILFNKPYGVLSqfTDESEKHKTLKDYID-DPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 147 EEFIRGMSAGVPILGTVTKKCKVKK----------EAPFVFR---------ITLVQGLNRQIRRMCEHFGYEVKKLERTR 207
Cdd:cd02566 80 EDALEQLRNGVELGDGLTLPAKVEKvdeppwlwerEPPIRFRkniptswieITICEGKNRQVRRMTAAVGFPTLRLIRVS 159
|
....*....
gi 446859121 208 IMNVSLSGI 216
Cdd:cd02566 160 IGDIGLDNL 168
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
69-225 |
3.55e-23 |
|
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: 93.14 E-value: 3.55e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVSTTEDGE-RDNIVDFVNH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPI 145
Cdd:cd02556 2 VLIYHKPEGLICTRKDPKgRPTVFDLLPKlgIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 146 TEEFIRGMSAGVPIL----GTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSG-IPLGE 220
Cdd:cd02556 82 TDEQLKSLKKGVELEdgfaGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGnLKRGQ 161
|
....*
gi 446859121 221 WRDLT 225
Cdd:cd02556 162 WEELP 166
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
8-229 |
3.80e-22 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 92.09 E-value: 3.80e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 8 RLNKYISESGICSRREADRYIEQGNVFLNGKRATIGD-QVKPGDVVKVNGQLIE----PReaedlvLIALNKPVGIVSTT 82
Cdd:PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAfKLLPEHDVAYDGNPLAqqhgPR------YFMLNKPQGYVCST 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 83 EDGERDNIVDFVNH--SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL 160
Cdd:PRK10839 76 DDPDHPTVLYFLDEpvAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLH 155
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446859121 161 GTVTKKCKVKKE--APFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSL-SGIPLGEWRDLTDDEL 229
Cdd:PRK10839 156 NEKDLTKPAVLEviTPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLdADLAPGEYRPLTEEEI 227
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
68-228 |
6.42e-21 |
|
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: 87.46 E-value: 6.42e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 68 VLIALNKPVGIVS----------TTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEY 137
Cdd:cd02555 5 VTLLLHKPAGMVSeqalallgpgQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEY 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 138 LVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIP 217
Cdd:cd02555 85 LVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLP 164
|
170
....*....|.
gi 446859121 218 LGEWRDLTDDE 228
Cdd:cd02555 165 LGQWRYLTTGE 175
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
51-226 |
8.41e-17 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 77.47 E-value: 8.41e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 51 VVKVNGQLIEPREAED--LVLIALNKPVGIVST-TEDGERDNIVDFVNhSKRVFPIGRLDKDSQGLIFLTNHGDLVNKIL 127
Cdd:PRK11394 21 VKRFSSQRSTRRKPENqpTRVILFNKPYDVLPQfTDEAGRKTLKEFIP-VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 128 RAGNDHEKEYLVTVDKPITEEFIRGMSAGVPIL-GTVTKKCKVKKEAP------------------FVFRITLVQGLNRQ 188
Cdd:PRK11394 100 QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNdGPTLPAGAELVDEPawlwprnppirerksiptSWLKITLYEGRNRQ 179
|
170 180 190
....*....|....*....|....*....|....*...
gi 446859121 189 IRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTD 226
Cdd:PRK11394 180 VRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATD 217
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
7-73 |
7.07e-11 |
|
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: 56.87 E-value: 7.07e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 7 VRLNKYISESGIC-SRREADRYIEQGNVFLNGKRATI-GDQVKPGDVVKVNGQLIEPREA-EDLVLIALN 73
Cdd:cd00165 1 MRLDKILARLGLApSRSEARQLIKHGHVLVNGKVVTKpSYKVKPGDVIEVDGKSIEEDIVyEDKKLLVVN 70
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
7-56 |
1.03e-09 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 53.37 E-value: 1.03e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 446859121 7 VRLNKYISESG-ICSRREADRYIEQGNVFLNGKRATI-GDQVKPGDVVKVNG 56
Cdd:smart00363 1 RRLDKFLARLGlAPSRSQARRLIEQGRVKVNGKKVTKpSYIVKPGDVISVRG 52
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
7-52 |
3.09e-09 |
|
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: 51.72 E-value: 3.09e-09
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 446859121 7 VRLNKYISESGIC-SRREADRYIEQGNVFLNGKRATI-GDQVKPGDVV 52
Cdd:pfam01479 1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVKDpSYRVKPGDEI 48
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
69-150 |
3.05e-05 |
|
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: 43.87 E-value: 3.05e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446859121 69 LIALNKPVGIVSTTEDGERDN-IVDFVNH-------SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDH--EKEYL 138
Cdd:cd02869 1 LLVVNKPAGLPVHPGPGHLTGtLVNALLKlllllgeEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERkvKKTYL 80
|
90
....*....|...
gi 446859121 139 -VTVDKPITEEFI 150
Cdd:cd02869 81 aLVDGKPPEDEGT 93
|
|
| |
