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Conserved domains on  [gi|488148299|ref|WP_002219507|]
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MULTISPECIES: pseudouridine synthase [Neisseria]

Protein Classification

pseudouridine synthase( domain architecture ID 11439600)

pseudouridine synthase may catalyze the formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit, or at position 2605 in 23S rRNA

CATH:  3.30.2350.10
EC:  5.4.99.-
Gene Ontology:  GO:0140098|GO:0001522|GO:0009451|GO:0003723|GO:0009982

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 12-246 4.94e-99

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: 4.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  12 DAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRIELNKKAHEQQAARITILLNKPVGYVSAQA-E 89
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKdP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  90 KGYKSAAELItPENRWEGdtgrirfdpkhkigLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDE 169
Cdd:COG1187   81 EGRPTVFDLL-PEARKER--------------LFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 170 KGLALLNHGLSLDGEKLRPAQVEWQN---EDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYL 246
Cdd:COG1187  146 EDLERLREGVELEDGPTKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWREL 225
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 12-246 4.94e-99

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: 4.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  12 DAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRIELNKKAHEQQAARITILLNKPVGYVSAQA-E 89
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKdP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  90 KGYKSAAELItPENRWEGdtgrirfdpkhkigLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDE 169
Cdd:COG1187   81 EGRPTVFDLL-PEARKER--------------LFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 170 KGLALLNHGLSLDGEKLRPAQVEWQN---EDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYL 246
Cdd:COG1187  146 EDLERLREGVELEDGPTKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWREL 225
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 69-252 2.96e-76

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: 228.83  E-value: 2.96e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  69 QAARITILLNKPVGYVSAQAEkgyksaaELITPENRWEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQL 148
Cdd:cd02555    1 QLEPVTLLLHKPAGMVSEQAL-------ALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKL 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 149 IGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRI 228
Cdd:cd02555   74 IGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRI 153

                        170       180
                 ....*....|....*....|....
gi 488148299 229 RMGKVKLGRLPPGKWRYLAPGESF 252
Cdd:cd02555  154 RIGRVSLGKLPLGQWRYLTTGERF 177
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
10-250 1.54e-45

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 154.12  E-value: 1.54e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  10 TEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTAVLGQKVSPADRIELNKKAHEQQAAR--ITILLNKPVGYVSaq 87
Cdd:PRK10475   3 TDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEdlVLIALNKPVGIVS-- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  88 aekgyksaaeliTPEnrwEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKL 167
Cdd:PRK10475  81 ------------TTE---DGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPI 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 168 DEKGLALLNHGLSLDGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYLA 247
Cdd:PRK10475 146 TDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


                 ...
gi 488148299 248 PGE 250
Cdd:PRK10475 226 DDE 228
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 125-248 3.88e-33

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: 117.04  E-value: 3.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  125 AGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNED----QLR 200
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPgfptWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 488148299  201 FVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYLAP 248
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 75-216 1.65e-12

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: 63.19  E-value: 1.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299   75 ILLNKPVGYVSAqaekgyksaaeLITPENRWEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQL--IGEN 152
Cdd:pfam00849   2 IVVNKPAGVPVH-----------PTDSLTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPE 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  153 SGSEKEYLVRVRGKLDEKGLA----------LLNHGLSLDGEKLRPAQVE------WQNEDQLRFVLKQGKKRQIRRMCE 216
Cdd:pfam00849  71 RKIEKEYLALVDKPEEEEGTIkspikkeknkSPFRKEEELGGKKAVTHLKvlksgsKGDYSLLELELVTGRKHQIRAHLA 150
S4 smart00363
S4 RNA-binding domain;
14-67 9.11e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 9.11e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488148299    14 VRLSKRMAQLGL-CSRREADGYIEQGWVTVNGKTAV-LGQKVSPADRIELNKKAHE 67
Cdd:smart00363   1 RRLDKFLARLGLaPSRSQARRLIEQGRVKVNGKKVTkPSYIVKPGDVISVRGKELK 56
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 12-246 4.94e-99

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: 4.94e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  12 DAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTA-VLGQKVSPADRIELNKKAHEQQAARITILLNKPVGYVSAQA-E 89
Cdd:COG1187    1 EGMRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVtELGTKVDPGDEVTVDGKPLKLPEEPVYLLLNKPAGVVSTTKdP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  90 KGYKSAAELItPENRWEGdtgrirfdpkhkigLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDE 169
Cdd:COG1187   81 EGRPTVFDLL-PEARKER--------------LFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 170 KGLALLNHGLSLDGEKLRPAQVEWQN---EDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYL 246
Cdd:COG1187  146 EDLERLREGVELEDGPTKPAKVEILSgeaNTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLGDLPPGEWREL 225
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 69-252 2.96e-76

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: 228.83  E-value: 2.96e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  69 QAARITILLNKPVGYVSAQAEkgyksaaELITPENRWEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQL 148
Cdd:cd02555    1 QLEPVTLLLHKPAGMVSEQAL-------ALLGPGQRSAADRSGRRPLKGHFARLAPIGPLDKDASGLLVFSQDGRVLRKL 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 149 IGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRI 228
Cdd:cd02555   74 IGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRELPPAKVSWQNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRI 153

                        170       180
                 ....*....|....*....|....
gi 488148299 229 RMGKVKLGRLPPGKWRYLAPGESF 252
Cdd:cd02555  154 RIGRVSLGKLPLGQWRYLTTGERF 177
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
10-250 1.54e-45

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 154.12  E-value: 1.54e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  10 TEDAVRLSKRMAQLGLCSRREADGYIEQGWVTVNGKTAVLGQKVSPADRIELNKKAHEQQAAR--ITILLNKPVGYVSaq 87
Cdd:PRK10475   3 TDSSTRLNKYISESGICSRREADRYIEQGNVFINGKRATIGDQVKAGDVVKVNGQLIEPREAEdlVLIALNKPVGIVS-- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  88 aekgyksaaeliTPEnrwEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKL 167
Cdd:PRK10475  81 ------------TTE---DGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPI 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 168 DEKGLALLNHGLSLDGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYLA 247
Cdd:PRK10475 146 TDEFIRGMGAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


                 ...
gi 488148299 248 PGE 250
Cdd:PRK10475 226 DDE 228
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 75-250 2.16e-45

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: 149.59  E-value: 2.16e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  75 ILLNKPVGYVSAQAEKGYKSAAELITPENRwegdtgrirfdpkhKIGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSG 154
Cdd:cd02553    3 LMLNKPAGVVCATKDPHHPTVIDLLPEPDR--------------RRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKH 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 155 SEKEYLVRVRGKLDEKGLALLNHGLSL-DGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKV 233
Cdd:cd02553   69 VPKTYEVTLAGPLTEDDIEAFAEGVLLhDGYPTKPAKLEILSPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGL 148

                        170
                 ....*....|....*...
gi 488148299 234 KLG-RLPPGKWRYLAPGE 250
Cdd:cd02553  149 ELDdDLAPGEWRPLTEEE 166
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 74-229 8.37e-42

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: 139.55  E-value: 8.37e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  74 TILLNKPVGYVSAQAEkgyksaaelitPENRwegDTgRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENS 153
Cdd:cd02870    1 YLLLNKPRGVVSTVRD-----------PEGR---PT-VLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRY 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 154 GSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIR 229
Cdd:cd02870   66 GVEKTYLVKVRGVPSEEELRRLRAGVELDDGKTAPAKVKVLSRDpkntLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVR 145
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 75-250 6.33e-39

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: 132.82  E-value: 6.33e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  75 ILLNKPVGYVSAQAEKGYKSAAELITPENRwegdtgrirfdpkhkigLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSG 154
Cdd:cd02554    3 IAYNKPVGIDCTLERADEDNIIDFVNPPPR-----------------IFPIGRLDKDSEGLILLTNDGDLVNKILHADNN 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 155 SEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVK 234
Cdd:cd02554   66 HEKEYLVTVNKPITDEFIEGMSNGVVILGTVTKPCKVERLAKDKFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIE 145

                        170
                 ....*....|....*.
gi 488148299 235 LGRLPPGKWRYLAPGE 250
Cdd:cd02554  146 LGDLAPGEWRPLTDAE 161
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 125-248 3.88e-33

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: 117.04  E-value: 3.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  125 AGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNED----QLR 200
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPgfptWLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 488148299  201 FVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYLAP 248
Cdd:TIGR00093  81 VTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLTL 128
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 74-230 6.26e-27

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: 101.68  E-value: 6.26e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  74 TILLNKPVGYVSaqaekgyksaaeliTPENRWEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENS 153
Cdd:cd02550    1 ILVLNKPSGLVC--------------HPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRR 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 154 GSEKEYLVRVRGKLDEKGLALL-------NHGLSLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRV 222
Cdd:cd02550   67 EIEKEYLVTVRGELDEEGIEDLatvrrgrLSGLVDEGVPLAVTKVRVIGEHggtgRLRLTLKTGRTHQIRRHCAAVGFPV 146


                 ....*...
gi 488148299 223 VGLKRIRM 230
Cdd:cd02550  147 LRLHRVRI 154
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
15-250 1.70e-26

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 102.88  E-value: 1.70e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  15 RLSKRMA-QLGLcSRREADGYIEQGWVTVNGKTAVLGQ-KVSPADRIELNKKAHEQQAARITILLNKPVGYVSAQAEKGY 92
Cdd:PRK10839   2 RLDKFISqQLGV-SRAIAGRELRANRVTVDGEIVKNGAfKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  93 KSAAELITpenrwegdtgrirfDP-KHKigLAPAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKG 171
Cdd:PRK10839  81 PTVLYFLD--------------EPvAYK--LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDT 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 172 LALLNHGLSLDGEKL--RPAQVEWQNEDQLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL-GRLPPGKWRYLAP 248
Cdd:PRK10839 145 AEQFAKGVQLHNEKDltKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLdADLAPGEYRPLTE 224


                 ..
gi 488148299 249 GE 250
Cdd:PRK10839 225 EE 226
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 75-248 3.55e-25

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: 97.38  E-value: 3.55e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  75 ILLNKPVGYVSAQAEkgyksaaelitPENRwegdtgRIRFD--PKHKIG-LAPAGRLDIDSVGLLVLTQDGRIAKQLIGE 151
Cdd:cd02556    3 LIYHKPEGLICTRKD-----------PKGR------PTVFDllPKLGIPrWISVGRLDLNTEGLLLFTNDGELANRLMHP 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 152 NSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVewQNEDQ------LRFVLKQGKKRQIRRMCELVGLRVVGL 225
Cdd:cd02556   66 SNEIEREYAVRVFGQVTDEQLKSLKKGVELEDGFAGFKSI--QLEGGegknswYRVTLREGRNREVRRLWEAFGLQVSRL 143

                        170       180
                 ....*....|....*....|....
gi 488148299 226 KRIRMGK-VKLGRLPPGKWRYLAP 248
Cdd:cd02556  144 IRIRYGPiFLPGNLKRGQWEELPP 167
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 75-238 3.33e-24

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: 95.14  E-value: 3.33e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  75 ILLNKPVGYVS--AQAEKGYKSAAELItpenrwegdtgrirFDPkhkiGLAPAGRLDIDSVGLLVLTQDGRIAKQLIGEN 152
Cdd:cd02566    2 ILFNKPYGVLSqfTDESEKHKTLKDYI--------------DDP----GVYAAGRLDRDSEGLLLLTDDGRLQHRITDPS 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 153 SGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVE--------WQNEDQLRF-----------VLKQGKKRQIRR 213
Cdd:cd02566   64 FKHPKTYYVQVEGVPTEDALEQLRNGVELGDGLTLPAKVEkvdeppwlWEREPPIRFrkniptswieiTICEGKNRQVRR 143

                        170       180
                 ....*....|....*....|....*
gi 488148299 214 MCELVGLRVVGLKRIRMGKVKLGRL 238
Cdd:cd02566  144 MTAAVGFPTLRLIRVSIGDIGLDNL 168
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
15-243 5.23e-24

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 97.53  E-value: 5.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  15 RLSKRMAQLGLCSRREADGYIEQGWVTVNGKTAVLGQKV--SPADRIELNK-----KAHEQQAARItillnkpVGYvsaq 87
Cdd:PRK10700   4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVevTPGLKIRIDGhlisvKESAEQICRV-------LAY---- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  88 aekgYKSAAELIT---PENRwegdtgRIRFDPKHKIGLA---PAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLV 161
Cdd:PRK10700  73 ----YKPEGELCTrndPEGR------PTVFDRLPKLRGArwiAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAV 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 162 RVRGKLDEKGLALLNHGLSLD-------------GEKLRpaqvEWQNedqlrFVLKQGKKRQIRRMCELVGLRVVGLKRI 228
Cdd:PRK10700 143 RVFGQVDDAKLRQLSRGVQLEdgpaafktikfsgGEGIN----QWYN-----VTLTEGRNREVRRLWEAVGVQVSRLIRV 213

                        250
                 ....*....|....*.
gi 488148299 229 RMGKVKLGR-LPPGKW 243
Cdd:PRK10700 214 RYGDIPLPKgLPRGGW 229
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
45-244 5.59e-16

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 74.39  E-value: 5.59e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  45 KTAVLGQKVSPADRIELNKKAHEQQAARItILLNKPVGYVSA-QAEKGYKSAAELITPEnrwegdtgrirfdpkhkiGLA 123
Cdd:PRK11394  13 KTSFRNHQVKRFSSQRSTRRKPENQPTRV-ILFNKPYDVLPQfTDEAGRKTLKEFIPVQ------------------GVY 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 124 PAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQVEWQNEDQ----- 198
Cdd:PRK11394  74 AAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAwlwpr 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299 199 --------------LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244
Cdd:PRK11394 154 nppirerksiptswLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWR 213
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 75-216 1.65e-12

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: 63.19  E-value: 1.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299   75 ILLNKPVGYVSAqaekgyksaaeLITPENRWEGDTGRIRFDPKHKIGLAPAGRLDIDSVGLLVLTQDGRIAKQL--IGEN 152
Cdd:pfam00849   2 IVVNKPAGVPVH-----------PTDSLTKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPE 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488148299  153 SGSEKEYLVRVRGKLDEKGLA----------LLNHGLSLDGEKLRPAQVE------WQNEDQLRFVLKQGKKRQIRRMCE 216
Cdd:pfam00849  71 RKIEKEYLALVDKPEEEEGTIkspikkeknkSPFRKEEELGGKKAVTHLKvlksgsKGDYSLLELELVTGRKHQIRAHLA 150
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 14-68 1.33e-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: 50.33  E-value: 1.33e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488148299  14 VRLSKRMAQLGLC-SRREADGYIEQGWVTVNGKTAV-LGQKVSPADRIELNKKAHEQ 68
Cdd:cd00165    1 MRLDKILARLGLApSRSEARQLIKHGHVLVNGKVVTkPSYKVKPGDVIEVDGKSIEE 57
S4 smart00363
S4 RNA-binding domain;
14-67 9.11e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 9.11e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488148299    14 VRLSKRMAQLGL-CSRREADGYIEQGWVTVNGKTAV-LGQKVSPADRIELNKKAHE 67
Cdd:smart00363   1 RRLDKFLARLGLaPSRSQARRLIEQGRVKVNGKKVTkPSYIVKPGDVISVRGKELK 56
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 14-59 8.59e-05

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: 39.01  E-value: 8.59e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 488148299   14 VRLSKRMAQLGLC-SRREADGYIEQGWVTVNGKTA-VLGQKVSPADRI 59
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVkDPSYRVKPGDEI 48
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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