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Conserved domains on  [gi|504220544|ref|WP_014407646|]
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pseudouridine synthase [Streptococcus pyogenes]

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, ...
 1-228 7.49e-87

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: 256.88  E-value: 7.49e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTPL-VYESFVYYLLNKPSGYVSATQDRQ 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLkLPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  80 Q-ATVMELLDDtARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDH 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 159 QCLPAHLEVLAsdlQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLT 228
Cdd:COG1187  161 PTKPAKVEILS---GEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGEWRELT 226
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-228 7.49e-87

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: 256.88  E-value: 7.49e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTPL-VYESFVYYLLNKPSGYVSATQDRQ 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLkLPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  80 Q-ATVMELLDDtARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDH 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 159 QCLPAHLEVLAsdlQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLT 228
Cdd:COG1187  161 PTKPAKVEILS---GEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGEWRELT 226
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 61-232 3.57e-82

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: 242.81  E-value: 3.57e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  61 VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGI 140
Cdd:cd02553    1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 141 MTEADKDYFARGISLKD-HQCLPAHLEVLasdlqqQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSL 219
Cdd:cd02553   81 LTEDDIEAFAEGVLLHDgYPTKPAKLEIL------SPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDL 154

                        170
                 ....*....|...
gi 504220544 220 AEGEFRRLTPEEL 232
Cdd:cd02553  155 APGEWRPLTEEEL 167
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-235 3.09e-48

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 158.73  E-value: 3.09e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDlVTYQGTPLVYESFV-YYLLNKPSGYVSATQDRQ 79
Cdd:PRK10839   1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHD-VAYDGNPLAQQHGPrYFMLNKPQGYVCSTDDPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  80 QATVMELLDDTARQKaVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQ 159
Cdd:PRK10839  80 HPTVLYFLDEPVAYK-LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEK 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504220544 160 CL--PAHLEVLASdlqqqtSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 235
Cdd:PRK10839 159 DLtkPAVLEVITP------TQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASV 230
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 99-229 8.89e-43

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: 141.31  E-value: 8.89e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   99 VGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTsl 178
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTW-- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 504220544  179 VKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLTP 229
Cdd:TIGR00093  79 LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLN-GLPPGEWRPLTL 128
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-197 7.04e-26

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: 98.63  E-value: 7.04e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   62 YYLLNKPSGYVSATQD---RQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAK 136
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDsltKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504220544  137 VAGIMTEADK----------DYFARGISLKDHQCLPAHLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAA 197
Cdd:pfam00849  81 VDKPEEEEGTikspikkeknKSPFRKEEELGGKKAVTHLKVLKSGSKGDYSLLELELVTGRKHQIRAHLAA 151
S4 smart00363
S4 RNA-binding domain;
1-55 7.83e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 7.83e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 504220544     1 MRLDKFLV-ATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTPL 55
Cdd:smart00363   1 RRLDKFLArLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKP-GDVISVRGKEL 55
 
Name Accession Description Interval E-value
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 1-228 7.49e-87

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: 256.88  E-value: 7.49e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTPL-VYESFVYYLLNKPSGYVSATQDRQ 79
Cdd:COG1187    3 MRLQKFLANAGVGSRREAEELIEAGRVTVNGKVVTELGTKVDP-GDEVTVDGKPLkLPEEPVYLLLNKPAGVVSTTKDPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  80 Q-ATVMELLDDtARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDH 158
Cdd:COG1187   82 GrPTVFDLLPE-ARKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVTEEDLERLREGVELEDG 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 159 QCLPAHLEVLAsdlQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLT 228
Cdd:COG1187  161 PTKPAKVEILS---GEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRIGPLTLG-DLPPGEWRELT 226
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 61-232 3.57e-82

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: 242.81  E-value: 3.57e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  61 VYYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGI 140
Cdd:cd02553    1 VYLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 141 MTEADKDYFARGISLKD-HQCLPAHLEVLasdlqqQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSL 219
Cdd:cd02553   81 LTEDDIEAFAEGVLLHDgYPTKPAKLEIL------SPTTVRLTITEGKYHQVKRMFAAVGNKVVALHRIRIGGLELDDDL 154

                        170
                 ....*....|...
gi 504220544 220 AEGEFRRLTPEEL 232
Cdd:cd02553  155 APGEWRPLTEEEL 167
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 62-209 4.41e-49

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: 158.04  E-value: 4.41e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  62 YYLLNKPSGYVSATQD-RQQATVMELLDDtaRQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGI 140
Cdd:cd02870    1 YLLLNKPRGVVSTVRDpEGRPTVLDLLKD--VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGV 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504220544 141 MTEADKDYFARGISLKDHQCLPAHLEVLASDlqQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLS 209
Cdd:cd02870   79 PSEEELRRLRAGVELDDGKTAPAKVKVLSRD--PKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVR 145
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
1-235 3.09e-48

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 158.73  E-value: 3.09e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDlVTYQGTPLVYESFV-YYLLNKPSGYVSATQDRQ 79
Cdd:PRK10839   1 MRLDKFISQQLGVSRAIAGRELRANRVTVDGEIVKNGAFKLLPEHD-VAYDGNPLAQQHGPrYFMLNKPQGYVCSTDDPD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  80 QATVMELLDDTARQKaVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQ 159
Cdd:PRK10839  80 HPTVLYFLDEPVAYK-LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEK 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504220544 160 CL--PAHLEVLASdlqqqtSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 235
Cdd:PRK10839 159 DLtkPAVLEVITP------TQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAITLDADLAPGEYRPLTEEEIASV 230
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 99-229 8.89e-43

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: 141.31  E-value: 8.89e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   99 VGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTsl 178
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGFPTW-- 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 504220544  179 VKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLTP 229
Cdd:TIGR00093  79 LRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLN-GLPPGEWRPLTL 128
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 61-234 7.48e-36

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: 124.73  E-value: 7.48e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  61 VYYLLNKPSGYVSATQDRQQATVMELLDDTARqkaVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGI 140
Cdd:cd02554    1 VYIAYNKPVGIDCTLERADEDNIIDFVNPPPR---IFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 141 MTEADKDYFARGISLKDHQCLPAHLEVLASDlqqqtsLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLA 220
Cdd:cd02554   78 ITDEFIEGMSNGVVILGTVTKPCKVERLAKD------KFRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMNIELG-DLA 150

                        170
                 ....*....|....
gi 504220544 221 EGEFRRLTPEELQS 234
Cdd:cd02554  151 PGEWRPLTDAELFE 164
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 62-210 4.44e-32

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: 114.78  E-value: 4.44e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  62 YYLLNKPSGYVSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIM 141
Cdd:cd02550    1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504220544 142 TEADKDYFA-------RGISLKDHQCLPAHLEVLASdlQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSM 210
Cdd:cd02550   81 DEEGIEDLAtvrrgrlSGLVDEGVPLAVTKVRVIGE--HGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVRI 154
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 62-216 1.62e-30

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: 111.32  E-value: 1.62e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  62 YYLLNKPSGYVSATQD--RQQATVMELLDDtarqKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAG 139
Cdd:cd02566    1 LILFNKPYGVLSQFTDesEKHKTLKDYIDD----PGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 140 IMTEADKDYFARGISLKDHQCLPAHLEVLASDLQ-------------QQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQ 206
Cdd:cd02566   77 VPTEDALEQLRNGVELGDGLTLPAKVEKVDEPPWlwereppirfrknIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLI 156

                        170
                 ....*....|
gi 504220544 207 RLSMGPLKLD 216
Cdd:cd02566  157 RVSIGDIGLD 166
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 64-229 1.83e-27

Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.


Pssm-ID: 211330 [Multi-domain]  Cd Length: 167  Bit Score: 103.16  E-value: 1.83e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  64 LLNKPSGYVSATQD-RQQATVMELLDDtARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMT 142
Cdd:cd02556    4 IYHKPEGLICTRKDpKGRPTVFDLLPK-LGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQVT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 143 EADKDYFARGISLKDHqcLPAHLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEG 222
Cdd:cd02556   83 DEQLKSLKKGVELEDG--FAGFKSIQLEGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRIRYGPIFLPGNLKRG 160


                 ....*..
gi 504220544 223 EFRRLTP 229
Cdd:cd02556  161 QWEELPP 167
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 62-197 7.04e-26

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: 98.63  E-value: 7.04e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   62 YYLLNKPSGYVSATQD---RQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKHVTKEYLAK 136
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDsltKLLSLLALLLRRELGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLnkLFPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504220544  137 VAGIMTEADK----------DYFARGISLKDHQCLPAHLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAA 197
Cdd:pfam00849  81 VDKPEEEEGTikspikkeknKSPFRKEEELGGKKAVTHLKVLKSGSKGDYSLLELELVTGRKHQIRAHLAA 151
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
1-235 4.86e-24

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 97.11  E-value: 4.86e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   1 MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKvetsaKAHI-DEYK--DLVTYQGT---PLVYESFVYYLLNKPSGYVSA 74
Cdd:PRK10475   7 TRLNKYISESGICSRREADRYIEQGNVFINGK-----RATIgDQVKagDVVKVNGQliePREAEDLVLIALNKPVGIVST 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  75 TQDRQQATVMELLDDTARqkaVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTeadkDYFARGIS 154
Cdd:PRK10475  82 TEDGERDNIVDFVNHSKR---VFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPIT----DEFIRGMG 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 155 lkdhqclpAHLEVLAS-----DLQQQTSLV-KITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDpSLAEGEFRRLT 228
Cdd:PRK10475 155 --------AGVPILGTvtkkcKVKKEAPFVfRITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLS-GIPLGEWRDLT 225


                 ....*..
gi 504220544 229 PEELQSL 235
Cdd:PRK10475 226 DDELIDL 232
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
64-228 8.90e-23

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 92.50  E-value: 8.90e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  64 LLNKPSGYVSA-TQDRQQATVMELLDdtarQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMT 142
Cdd:PRK11394  43 LFNKPYDVLPQfTDEAGRKTLKEFIP----VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPT 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 143 EADKDYFARGISLKDHQCLPAHLEVLAS---------DLQQQ----TSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLS 209
Cdd:PRK11394 119 QDALEALRNGVTLNDGPTLPAGAELVDEpawlwprnpPIRERksipTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYA 198

                        170
                 ....*....|....*....
gi 504220544 210 MGPLKLDpSLAEGEFRRLT 228
Cdd:PRK11394 199 MGDYSLD-NLANGEWREAT 216
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 61-231 9.74e-19

Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.


Pssm-ID: 211329 [Multi-domain]  Cd Length: 177  Bit Score: 80.53  E-value: 9.74e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  61 VYYLLNKPSGYVS--ATQDRQQATVMELLDDTARQ-----KAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEY 133
Cdd:cd02555    5 VTLLLHKPAGMVSeqALALLGPGQRSAADRSGRRPlkghfARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEY 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 134 LAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVlasdlqQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPL 213
Cdd:cd02555   85 LVEVRGELTAGGLERLNHGLTYDGRELPPAKVSW------QNEQRLRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRV 158

                        170
                 ....*....|....*...
gi 504220544 214 KLDpSLAEGEFRRLTPEE 231
Cdd:cd02555  159 SLG-KLPLGQWRYLTTGE 175
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
2-235 1.30e-13

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 68.64  E-value: 1.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   2 RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVET---------SAKAHIDEYkdLVTYQGT-PLVYESFVYYllnKPSGY 71
Cdd:PRK10700   4 KLQKVLARAGHGSRREIESIIEAGRVSVDGKIATlgdrvevtpGLKIRIDGH--LISVKESaEQICRVLAYY---KPEGE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  72 VSATQDRQ-QATVMELLD--DTARQKAVfpvGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDY 148
Cdd:PRK10700  79 LCTRNDPEgRPTVFDRLPklRGARWIAV---GRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRQ 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 149 FARGISLKDHqclPAHLEVLA-SDLQQQTSLVKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRL 227
Cdd:PRK10700 156 LSRGVQLEDG---PAAFKTIKfSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTEL 232


                 ....*...
gi 504220544 228 TPEELQSL 235
Cdd:PRK10700 233 DLAQTNYL 240
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 62-190 7.94e-13

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: 64.67  E-value: 7.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  62 YYLLNKPSGYVS-ATQDRQQATVMELLDDTARQKA----VFPVGRLDKDTRGLLLLTNNgQLAHDLLS---PKKHVTKEY 133
Cdd:cd02869    1 LLVVNKPAGLPVhPGPGHLTGTLVNALLKLLLLLGeefrPGLVHRLDKDTSGLLLVAKN-KKAAAKLSkqfKERKVKKTY 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504220544 134 LAKVAGIMTEA---DKDYFARGISLK------DHQCLPA--HLEVLASDlqQQTSLVKITIQEGKFHQ 190
Cdd:cd02869   80 LALVDGKPPEDegtIDAPLGRKKRKKrarvvvSEDGKPAitHYKVLERF--GNVTLVELQLETGRTHQ 145
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 1-192 1.37e-11

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 62.73  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544    1 MRLDKFLVAT-GVGTRSQVKLLLKKKAIFVNQKVeTSAKAHIDEYKDLVTY------------QGTPL--VYESFVYYLL 65
Cdd:TIGR00005   6 QRLDDFLASLlPDLSRSRIQKLIENGQVKVNGKV-TANPKLKVKDGDRITVrvpeeeehevppQDIPLdiLFEDEDIIVI 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544   66 NKPSGYVS-ATQDRQQATVMELL----DDTARQKAVFPVGRLDKDTRGLLLLTNNgQLAHDLLS---PKKHVTKEYLAKV 137
Cdd:TIGR00005  85 NKPSGLVVhPGGGNPFGTVLNALlahcPPIAGVERVGIVHRLDRDTSGLMVVAKT-PLALRELQrqlKNRTVTKEYVALV 163

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504220544  138 AGIMTEADKDYFA-----------RGISlKDHQCLPA--HLEVLASDlqQQTSLVKITIQEGKFHQVK 192
Cdd:TIGR00005 164 HGQFDSGGGTVDAplgrvpnnrglMAVH-PSSEGKPAvtHFRVLERF--GNASLVECELETGRTHQIR 228
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 48-191 2.05e-11

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: 61.49  E-value: 2.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  48 VTYQGTPLVYESFVYYLLNKPSGY-VSATQDRQQATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSP- 125
Cdd:cd02557   11 VTNDPIKIVHEDDDLLVVDKPSGIpVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQi 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504220544 126 -KKHVTKEYLAKVAG------------IMTEADKDYFARGISLKDHQCLpAHLEVLASDLQQQTSLVKITIQEGKFHQV 191
Cdd:cd02557   91 rSREVKKEYLARVKGefpdgevvvdqpIGLVSPKGGLRNDVDEKGKDAR-TIFKRLSYNGDLNTSVVLCKPITGRTHQI 168
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 65-190 4.05e-08

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 52.06  E-value: 4.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  65 LNKPSGYVS-ATQDRQQATVMELL----DDTARQKAVFPVGRLDKDTRGLLLLTNNgQLAHDLLSP---KKHVTKEYLAK 136
Cdd:COG0564   11 VNKPAGLVVhPGSGGDDGTLVNALrahlGELSGVPRPGLVHRLDRDTSGLLLVAKT-RKAARRLSEqfrEREVEKRYLAL 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504220544 137 VAGIMTEA--------DKDYFARGI-SLKDHQCLPA--HLEVLASdlQQQTSLVKITIQEGKFHQ 190
Cdd:COG0564   90 VEGKPKEDegtidaplGRDPKDRKKmAVVDEDGKPAvtHYRVLER--FGGYSLVEVRLETGRTHQ 152
S4 cd00165
S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, ...
 1-66 5.36e-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: 48.78  E-value: 5.36e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504220544   1 MRLDKFLVATG-VGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTP----LVYESFVYYLLN 66
Cdd:cd00165    1 MRLDKILARLGlAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKP-GDVIEVDGKSieedIVYEDKKLLVVN 70
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
 66-196 1.23e-06

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 48.12  E-value: 1.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  66 NKPSGYV--SATQDRQQAT-VMELLDDTARQKaVFPVGRLDKDTRGLLLLTNNGQLAHdLLSPK---KHVTKEYLAKVAG 139
Cdd:PRK11112  15 NKPAGWLvhRSWLDRHETVfVMQTVRDQIGQH-VFTAHRLDRPTSGVLLMALSSEVAR-LLAQQfeqHQIQKTYHAIVRG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 140 IMTEA-----------DK--DYFARgislKDHQCLPA--HLEVLA------SDLQQQT---SLVKITIQEGKFHQVKRMV 195
Cdd:PRK11112  93 WLMEEavldyplkeelDKiaDKFAR----EDKAPQPAvtHYRGLAtvempvATGRYPTtrySLVELEPKTGRKHQLRRHM 168


                 .
gi 504220544 196 A 196
Cdd:PRK11112 169 A 169
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 54-193 1.48e-06

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 47.72  E-value: 1.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  54 PLVYESFVYYLLNKPSGY-VSATQDRQQATV--MELLDDTARQKaVFPVGRLDKDTRGLLLLTNNGQLAHDL--LSPKKH 128
Cdd:cd02563    2 EILYQDEHLVAINKPSGLlVHRSELDRHETRfaLQTLRDQLGQH-VYPVHRLDRPTSGVLLFALSSEVARKLgeQFTEHR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544 129 VTKEYLAKVAGIMTEAD-------------KDYFARGISLKD----HQCLPAHLEVLASDLQQQT---SLVKITIQEGKF 188
Cdd:cd02563   81 VHKTYLAVVRGYVPESGtidyplseeldklADKFASDDKAPQaattHYRLLAVEELPVVVGKYPTsrySLVELTPHTGRK 160


                 ....*
gi 504220544 189 HQVKR 193
Cdd:cd02563  161 HQLRR 165
S4 smart00363
S4 RNA-binding domain;
1-55 7.83e-06

S4 RNA-binding domain;


Pssm-ID: 214638 [Multi-domain]  Cd Length: 60  Bit Score: 42.19  E-value: 7.83e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 504220544     1 MRLDKFLV-ATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEyKDLVTYQGTPL 55
Cdd:smart00363   1 RRLDKFLArLGLAPSRSQARRLIEQGRVKVNGKKVTKPSYIVKP-GDVISVRGKEL 55
rluD PRK11180
23S rRNA pseudouridine(1911/1915/1917) synthase RluD;
14-142 3.14e-05

23S rRNA pseudouridine(1911/1915/1917) synthase RluD;


Pssm-ID: 183020 [Multi-domain]  Cd Length: 325  Bit Score: 44.28  E-value: 3.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504220544  14 TRSQVKLLLKKKAIFVNQKVETSAK------------AHIDEYKDLVTyQGTPL--VYESFVYYLLNKPSGYV----SAT 75
Cdd:PRK11180  32 SRSRIKEWILDQRVLVNGKVINKPKekvlggeqvaidAEIEEEARFEP-QDIPLdiVYEDDDILVINKPRDLVvhpgAGN 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504220544  76 QDRqqaTVMELLDDTARQKAVFP----VGRLDKDTRGLLLLTNN----GQLAHDLlsPKKHVTKEYLAKVAGIMT 142
Cdd:PRK11180 111 PDG---TVLNALLHYYPPIADVPragiVHRLDKDTTGLMVVAKTvpaqTRLVEAL--QKREITREYEAVAIGHMT 180
S4 pfam01479
S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was ...
 1-43 2.89e-04

S4 domain; The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.


Pssm-ID: 396182 [Multi-domain]  Cd Length: 48  Bit Score: 37.47  E-value: 2.89e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 504220544    1 MRLDKFLVATGVG-TRSQVKLLLKKKAIFVNQKVETSAKAHIDE 43
Cdd:pfam01479   1 RRLDKVLARLGLAsSRSQARQLIEHGRVLVNGKVVKDPSYRVKP 44
 
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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