|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
6-261 |
2.94e-124 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 359.82 E-value: 2.94e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 6 QAKRLNKYISETGFCSRREADKLIDAGRVTINGKIPEMGTKVLPGDDVEIDNKPV--RSKEKPIYIALNKPTGITCTTER 83
Cdd:PRK10475 5 SSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIepREAEDLVLIALNKPVGIVSTTED 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 84 DIPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVT 163
Cdd:PRK10475 85 GERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVT 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 164 LPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILAMCEGSvSTED 243
Cdd:PRK10475 165 KKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENS-SSEA 243
|
250
....*....|....*...
gi 1589265902 244 ASKMNAKGqrirKATDAK 261
Cdd:PRK10475 244 KPKAKAKP----KTAGIK 257
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
9-224 |
6.92e-107 |
|
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: 313.12 E-value: 6.92e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 9 RLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVLPGDDVEIDNKPVRSKEKPIYIALNKPTGITCTTERDI-P 86
Cdd:COG1187 4 RLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPEgR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 87 GNIVDFIG--HHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTL 164
Cdd:COG1187 84 PTVFDLLPeaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGPTK 163
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1589265902 165 PCKVEK---ETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLS 224
Cdd:COG1187 164 PAKVEIlsgEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
67-230 |
5.47e-99 |
|
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: 290.75 E-value: 5.47e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 67 IYIALNKPTGITCTTERDIPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITT 146
Cdd:cd02554 1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 147 EFLKQMGAGVHILDTVTLPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDE 226
Cdd:cd02554 81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160
|
....
gi 1589265902 227 EITE 230
Cdd:cd02554 161 ELFE 164
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
102-225 |
5.59e-53 |
|
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: 171.74 E-value: 5.59e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 102 IGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKVEKETKFSF----R 177
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1589265902 178 ITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSD 225
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
68-194 |
2.96e-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: 86.31 E-value: 2.96e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTERD------IPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNH--EKEYVVR 139
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSltkllsLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERkiEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589265902 140 VDKPITTEFLKQ--MGAGVHILDTVTLPCKVEKETKFSFR--------------ITLTQGLNRQIRRMCEA 194
Cdd:pfam00849 81 VDKPEEEEGTIKspIKKEKNKSPFRKEEELGGKKAVTHLKvlksgskgdyslleLELVTGRKHQIRAHLAA 151
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
8-61 |
3.85e-08 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 49.51 E-value: 3.85e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1589265902 8 KRLNKYISETGF-CSRREADKLIDAGRVTINGKI---PemGTKVLPGDDVEIDNKPVR 61
Cdd:smart00363 1 RRLDKFLARLGLaPSRSQARRLIEQGRVKVNGKKvtkP--SYIVKPGDVISVRGKELK 56
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
236-360 |
2.66e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 39.89 E-value: 2.66e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 236 EGSVSTEDASKMNAKGQRIRKATDAKLFDSREENQTSTARRNQKENRTRTYRGNNADEFRHAPNSKRGRNSSNGESGGNT 315
Cdd:PRK12678 136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR 215
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1589265902 316 ENWKSNSRSERSNSDRNRSDRNRTDRDNtdRRSGKPANRSQDSNR 360
Cdd:PRK12678 216 EERGRRDGGDRRGRRRRRDRRDARGDDN--REDRGDRDGDDGEGR 258
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10475 |
PRK10475 |
23S rRNA pseudouridine(2604) synthase RluF; |
6-261 |
2.94e-124 |
|
23S rRNA pseudouridine(2604) synthase RluF;
Pssm-ID: 236698 [Multi-domain] Cd Length: 290 Bit Score: 359.82 E-value: 2.94e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 6 QAKRLNKYISETGFCSRREADKLIDAGRVTINGKIPEMGTKVLPGDDVEIDNKPV--RSKEKPIYIALNKPTGITCTTER 83
Cdd:PRK10475 5 SSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIepREAEDLVLIALNKPVGIVSTTED 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 84 DIPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVT 163
Cdd:PRK10475 85 GERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVT 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 164 LPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILAMCEGSvSTED 243
Cdd:PRK10475 165 KKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENS-SSEA 243
|
250
....*....|....*...
gi 1589265902 244 ASKMNAKGqrirKATDAK 261
Cdd:PRK10475 244 KPKAKAKP----KTAGIK 257
|
|
| RsuA |
COG1187 |
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ... |
9-224 |
6.92e-107 |
|
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: 313.12 E-value: 6.92e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 9 RLNKYISETGFCSRREADKLIDAGRVTINGKIP-EMGTKVLPGDDVEIDNKPVRSKEKPIYIALNKPTGITCTTERDI-P 86
Cdd:COG1187 4 RLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKDPEgR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 87 GNIVDFIG--HHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTL 164
Cdd:COG1187 84 PTVFDLLPeaRKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDGPTK 163
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1589265902 165 PCKVEK---ETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLS 224
Cdd:COG1187 164 PAKVEIlsgEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWRELT 226
|
|
| PseudoU_synth_RluF |
cd02554 |
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ... |
67-230 |
5.47e-99 |
|
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: 290.75 E-value: 5.47e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 67 IYIALNKPTGITCTTERDIPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITT 146
Cdd:cd02554 1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 147 EFLKQMGAGVHILDTVTLPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDE 226
Cdd:cd02554 81 EFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELGDLAPGEWRPLTDA 160
|
....
gi 1589265902 227 EITE 230
Cdd:cd02554 161 ELFE 164
|
|
| TIGR00093 |
TIGR00093 |
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ... |
102-225 |
5.59e-53 |
|
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: 171.74 E-value: 5.59e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 102 IGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKVEKETKFSF----R 177
Cdd:TIGR00093 1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFptwlR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1589265902 178 ITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSD 225
Cdd:TIGR00093 81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
|
|
| PseudoU_synth_RsuA_like |
cd02870 |
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ... |
68-207 |
4.85e-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: 164.97 E-value: 4.85e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTeRDIPG--NIVDFIGHH-KRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPI 144
Cdd:cd02870 1 YLLLNKPRGVVSTV-RDPEGrpTVLDLLKDVgERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVP 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1589265902 145 TTEFLKQMGAGVHILDTVTLPCKVEK----ETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRI 207
Cdd:cd02870 80 SEEELRRLRAGVELDDGKTAPAKVKVlsrdPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
|
|
| PseudoU_synth_Rsu_Rlu_like |
cd02550 |
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ... |
68-207 |
2.86e-41 |
|
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: 142.51 E-value: 2.86e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTERDIPGNIV---DFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPI 144
Cdd:cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVvvrLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1589265902 145 TTEFLKQM-------GAGVHILDTVTLPCKVEKETKFS----FRITLTQGLNRQIRRMCEALGYEVFKLRRVRI 207
Cdd:cd02550 81 DEEGIEDLatvrrgrLSGLVDEGVPLAVTKVRVIGEHGgtgrLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
|
|
| PseudoU_synth_RsuA |
cd02553 |
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ... |
67-228 |
1.19e-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: 138.42 E-value: 1.19e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 67 IYIALNKPTGITCTTERDIPGNIVDFIGHHKR---IFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKP 143
Cdd:cd02553 1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRrrdLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 144 ITTEFLKQMGAGVHILD-TVTLPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLD-GIPNGKWR 221
Cdd:cd02553 81 LTEDDIEAFAEGVLLHDgYPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDdDLAPGEWR 160
|
....*..
gi 1589265902 222 YLSDEEI 228
Cdd:cd02553 161 PLTEEEL 167
|
|
| PRK10839 |
PRK10839 |
16S rRNA pseudouridine(516) synthase RsuA; |
9-231 |
9.08e-35 |
|
16S rRNA pseudouridine(516) synthase RsuA;
Pssm-ID: 236774 [Multi-domain] Cd Length: 232 Bit Score: 127.92 E-value: 9.08e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 9 RLNKYISETGFCSRREADKLIDAGRVTINGKIPEMGT-KVLPGDDVEIDNKPVRSKEKPIYIALNKPTGITCTTERDIPG 87
Cdd:PRK10839 2 RLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAfKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 88 NIVDFIGH---HKrIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGV--HILDTV 162
Cdd:PRK10839 82 TVLYFLDEpvaYK-LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVqlHNEKDL 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 163 TLPCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLD-GIPNGKWRYLSDEEITEI 231
Cdd:PRK10839 161 TKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDaDLAPGEYRPLTEEEIASV 230
|
|
| PSSA_1 |
cd02555 |
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ... |
66-227 |
7.75e-30 |
|
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: 112.88 E-value: 7.75e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 66 PIYIALNKPTGITCTTERDI--PGNIVD--------FIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKE 135
Cdd:cd02555 4 PVTLLLHKPAGMVSEQALALlgPGQRSAadrsgrrpLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 136 YVVRVDKPITTEFLKQMGAGVhILDTVTL-PCKVEKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDG 214
Cdd:cd02555 84 YLVEVRGELTAGGLERLNHGL-TYDGRELpPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGK 162
|
170
....*....|...
gi 1589265902 215 IPNGKWRYLSDEE 227
Cdd:cd02555 163 LPLGQWRYLTTGE 175
|
|
| PseudoU_synth_RluE |
cd02566 |
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ... |
68-215 |
1.70e-29 |
|
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: 111.70 E-value: 1.70e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTERDIPGNIV--DFIgHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPIT 145
Cdd:cd02566 1 LILFNKPYGVLSQFTDESEKHKTlkDYI-DDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 146 TEFLKQMGAGVHILDTVTLPCKVEK----------ETKFSFR---------ITLTQGLNRQIRRMCEALGYEVFKLRRVR 206
Cdd:cd02566 80 EDALEQLRNGVELGDGLTLPAKVEKvdeppwlwerEPPIRFRkniptswieITICEGKNRQVRRMTAAVGFPTLRLIRVS 159
|
....*....
gi 1589265902 207 IMNISLDGI 215
Cdd:cd02566 160 IGDIGLDNL 168
|
|
| PRK10700 |
PRK10700 |
23S rRNA pseudouridine(2605) synthase RluB; |
7-281 |
5.81e-27 |
|
23S rRNA pseudouridine(2605) synthase RluB;
Pssm-ID: 182659 [Multi-domain] Cd Length: 289 Bit Score: 108.31 E-value: 5.81e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 7 AKRLNKYISETGFCSRREADKLIDAGRVTINGKIPEMGTKV--LPGDDVEIDNK--PVRSKEKPI--YIALNKPTGITCT 80
Cdd:PRK10700 2 SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVevTPGLKIRIDGHliSVKESAEQIcrVLAYYKPEGELCT 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 81 tERDIPGNIVDFIGHHK----RIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGV 156
Cdd:PRK10700 82 -RNDPEGRPTVFDRLPKlrgaRWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQLSRGV 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 157 HILDTvtlPCKVeKETKFS--------FRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISL-DGIPNGKWRYLSDEE 227
Cdd:PRK10700 161 QLEDG---PAAF-KTIKFSggeginqwYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLpKGLPRGGWTELDLAQ 236
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589265902 228 ITEILAMCEgsVSTEDASKM-------NAKGQRIRKATdaklfdsREENQTSTARRNQKEN 281
Cdd:PRK10700 237 TNYLRELVE--LPPETSSKVavekdrrRMKANQIRRAV-------KRHSQVSGGRRSGGRN 288
|
|
| PseudoU_synth_RluB |
cd02556 |
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ... |
69-224 |
1.55e-24 |
|
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: 98.53 E-value: 1.55e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 69 IALNKPTGITCTTE----RDIpgnIVDFIGHHK--RIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDK 142
Cdd:cd02556 3 LIYHKPEGLICTRKdpkgRPT---VFDLLPKLGipRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 143 PITTEFLKQMGAGVHILDTVTLPCKV----EKETKFSFRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNI-SLDGIPN 217
Cdd:cd02556 80 QVTDEQLKSLKKGVELEDGFAGFKSIqlegGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIfLPGNLKR 159
|
....*..
gi 1589265902 218 GKWRYLS 224
Cdd:cd02556 160 GQWEELP 166
|
|
| PseudoU_synth_2 |
pfam00849 |
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ... |
68-194 |
2.96e-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: 86.31 E-value: 2.96e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTERD------IPGNIVDFIGHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNH--EKEYVVR 139
Cdd:pfam00849 1 YIVVNKPAGVPVHPTDSltkllsLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKLFPERkiEKEYLAL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589265902 140 VDKPITTEFLKQ--MGAGVHILDTVTLPCKVEKETKFSFR--------------ITLTQGLNRQIRRMCEA 194
Cdd:pfam00849 81 VDKPEEEEGTIKspIKKEKNKSPFRKEEELGGKKAVTHLKvlksgskgdyslleLELVTGRKHQIRAHLAA 151
|
|
| PRK11394 |
PRK11394 |
23S rRNA pseudouridine(2457) synthase RluE; |
99-225 |
6.69e-16 |
|
23S rRNA pseudouridine(2457) synthase RluE;
Pssm-ID: 183115 Cd Length: 217 Bit Score: 75.93 E-value: 6.69e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 99 IFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHILDTVTLPCKVE--------- 169
Cdd:PRK11394 72 VYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAElvdepawlw 151
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1589265902 170 ------KETKFS----FRITLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSD 225
Cdd:PRK11394 152 prnppiRERKSIptswLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATD 217
|
|
| S4 |
cd00165 |
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ... |
8-72 |
4.61e-10 |
|
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: 55.33 E-value: 4.61e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1589265902 8 KRLNKYISETGFC-SRREADKLIDAGRVTINGK---IPemGTKVLPGDDVEIDNKPVRS---KEKPIYIALN 72
Cdd:cd00165 1 MRLDKILARLGLApSRSEARQLIKHGHVLVNGKvvtKP--SYKVKPGDVIEVDGKSIEEdivYEDKKLLVVN 70
|
|
| S4 |
smart00363 |
S4 RNA-binding domain; |
8-61 |
3.85e-08 |
|
S4 RNA-binding domain;
Pssm-ID: 214638 [Multi-domain] Cd Length: 60 Bit Score: 49.51 E-value: 3.85e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1589265902 8 KRLNKYISETGF-CSRREADKLIDAGRVTINGKI---PemGTKVLPGDDVEIDNKPVR 61
Cdd:smart00363 1 RRLDKFLARLGLaPSRSQARRLIEQGRVKVNGKKvtkP--SYIVKPGDVISVRGKELK 56
|
|
| S4 |
pfam01479 |
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ... |
9-53 |
3.26e-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: 46.33 E-value: 3.26e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1589265902 9 RLNKYISETGFC-SRREADKLIDAGRVTINGKI---PemGTKVLPGDDV 53
Cdd:pfam01479 2 RLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVvkdP--SYRVKPGDEI 48
|
|
| PseudoU_synth_RluA_like |
cd02869 |
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ... |
68-197 |
1.50e-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: 42.32 E-value: 1.50e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 68 YIALNKPTGITCTTERDIP-GNIVDFIGHH-------KRIFPIGRLDKPSDGLIFLTNDGDIVNKILRAGNNH--EKEYV 137
Cdd:cd02869 1 LLVVNKPAGLPVHPGPGHLtGTLVNALLKLllllgeeFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERkvKKTYL 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1589265902 138 VRVDKPITTEFLKQMGAGVHILDTVTLPCKVEKETKFS---FRiTLTQGLN-----------R--QIRRMCEALGY 197
Cdd:cd02869 81 ALVDGKPPEDEGTIDAPLGRKKRKKRARVVVSEDGKPAithYK-VLERFGNvtlvelqletgRthQIRVHLASIGH 155
|
|
| PseudoU_synth_ScRIB2 |
cd02557 |
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ... |
55-141 |
1.58e-03 |
|
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Pssm-ID: 211331 [Multi-domain] Cd Length: 213 Bit Score: 39.54 E-value: 1.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 55 IDNKPVRS-KEKPIYIALNKPTGITC-TTERDIPGNIVDFIGHH---KRIFPIGRLDKPSDGLIFL---TNDGDIVNKIL 126
Cdd:cd02557 11 VTNDPIKIvHEDDDLLVVDKPSGIPVhPTGRYRYNTVTEILKSEyglTELRPCHRLDRLTSGLLLFaktSQTASRLQQQI 90
|
90
....*....|....*
gi 1589265902 127 RAGNNHeKEYVVRVD 141
Cdd:cd02557 91 RSREVK-KEYLARVK 104
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
236-360 |
2.66e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 39.89 E-value: 2.66e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 236 EGSVSTEDASKMNAKGQRIRKATDAKLFDSREENQTSTARRNQKENRTRTYRGNNADEFRHAPNSKRGRNSSNGESGGNT 315
Cdd:PRK12678 136 AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR 215
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1589265902 316 ENWKSNSRSERSNSDRNRSDRNRTDRDNtdRRSGKPANRSQDSNR 360
Cdd:PRK12678 216 EERGRRDGGDRRGRRRRRDRRDARGDDN--REDRGDRDGDDGEGR 258
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
249-365 |
7.95e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 38.35 E-value: 7.95e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589265902 249 AKGQRIRKATDAKLFDSREENQTSTARRNQKENRTRTYRGNNADEFRHAPNSKRGRNSSNGESGGNTENWKSNSRSERSN 328
Cdd:PRK12678 134 GEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD 213
|
90 100 110
....*....|....*....|....*....|....*..
gi 1589265902 329 SDRNRSDRNRTDRDNTDRRSGKPANRSQDSNRPNKPA 365
Cdd:PRK12678 214 RREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250
|
|
| |
