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Conserved domains on  [gi|2771595271|ref|WP_367122689|]
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pseudouridine synthase [Methylophaga sp.]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 1007)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PseudoU_synth super family cl00130
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
 12-177 5.81e-84

Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


The actual alignment was detected with superfamily member cd02566:

Pssm-ID: 469624 [Multi-domain]  Cd Length: 168  Bit Score: 247.30  E-value: 5.81e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKD-GRTTLKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA 90
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  91 *A**QLQ*GV**KDG*TKPA*A*LI**P**-WER*PPVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPWlWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2771595271 170 G*WQLNDL 177
Cdd:cd02566   161 GDIGLDNL 168
 
Name Accession Description Interval E-value
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 12-177 5.81e-84

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: 247.30  E-value: 5.81e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKD-GRTTLKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA 90
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  91 *A**QLQ*GV**KDG*TKPA*A*LI**P**-WER*PPVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPWlWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2771595271 170 G*WQLNDL 177
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
10-185 1.39e-59

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 187.26  E-value: 1.39e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  10 TKLIAFNKPYDVLTQFNDKDGRTTLKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PD 89
Cdd:PRK11394   39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPT 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  90 A*A**QLQ*GV**KDG*TKPA*A*LI**P*-*WER*PPVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVA 168
Cdd:PRK11394  119 QDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYA 198

                         170
                  ....*....|....*..
gi 2771595271 169 IG*WQLNDLQPGQWCEV 185
Cdd:PRK11394  199 MGDYSLDNLANGEWREA 215
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 13-186 3.82e-52

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: 168.29  E-value: 3.82e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  13 IAFNKPYDVLTQFNDKDGRTTLKDYIDIA---DVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PD 89
Cdd:COG1187    65 LLLNKPAGVVSTTKDPEGRPTVFDLLPEArkeRLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVT 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  90 A*A**QLQ*GV**KDG*TKPA*a*li**p**wer*ppVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:COG1187   145 EEDLERLREGVELEDGPTKPAK---------------VEILSGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRI 209

                         170
                  ....*....|....*..
gi 2771595271 170 G*WQLNDLQPGQWCEVN 186
Cdd:COG1187   210 GPLTLGDLPPGEWRELT 226
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 46-186 2.44e-45

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: 147.86  E-value: 2.44e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  46 AGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA*A**QLQ*GV**KDG*TKPA*A*LI**P**wer*p 125
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPG------ 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2771595271 126 pvrfrqsIPTqW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAIG*WQLNDLQPGQWCEVN 186
Cdd:TIGR00093  75 -------FPT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLT 127
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 12-156 3.19e-15

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: 70.51  E-value: 3.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFND-KDGRTTLKDYIDIAD-----VYPAGRLDRDSEGLLLLTDDG----RLQHHIsdPRHKLSKTYW 81
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDsLTKLLSLLALLLRRElgvkrLYPVHRLDKNTSGLLLLAKDGeaanKLNKLF--PERKIEKEYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  82 **VEN*PDA*A**QLQ*GV**KDG*TKPA*a*li**P**WER*PPVRFRQ-----SIPTQW*E*QISEGKNRQVRRMTAA 156
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSPFRKE-------EELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAHLAA 151
 
Name Accession Description Interval E-value
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 12-177 5.81e-84

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: 247.30  E-value: 5.81e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKD-GRTTLKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA 90
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  91 *A**QLQ*GV**KDG*TKPA*A*LI**P**-WER*PPVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPWlWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2771595271 170 G*WQLNDL 177
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
10-185 1.39e-59

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 187.26  E-value: 1.39e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  10 TKLIAFNKPYDVLTQFNDKDGRTTLKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PD 89
Cdd:PRK11394   39 TRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPT 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  90 A*A**QLQ*GV**KDG*TKPA*A*LI**P*-*WER*PPVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVA 168
Cdd:PRK11394  119 QDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYA 198

                         170
                  ....*....|....*..
gi 2771595271 169 IG*WQLNDLQPGQWCEV 185
Cdd:PRK11394  199 MGDYSLDNLANGEWREA 215
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 13-186 3.82e-52

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: 168.29  E-value: 3.82e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  13 IAFNKPYDVLTQFNDKDGRTTLKDYIDIA---DVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PD 89
Cdd:COG1187    65 LLLNKPAGVVSTTKDPEGRPTVFDLLPEArkeRLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLVRVDGPVT 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  90 A*A**QLQ*GV**KDG*TKPA*a*li**p**wer*ppVRFRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:COG1187   145 EEDLERLREGVELEDGPTKPAK---------------VEILSGEANTWLRITLTEGRNRQVRRMFEAVGLPVVRLKRVRI 209

                         170
                  ....*....|....*..
gi 2771595271 170 G*WQLNDLQPGQWCEVN 186
Cdd:COG1187   210 GPLTLGDLPPGEWRELT 226
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 13-169 1.35e-48

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: 156.50  E-value: 1.35e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  13 IAFNKPYDVLTQFNDKDGRTTLKDYI--DIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA 90
Cdd:cd02870     2 LLLNKPRGVVSTVRDPEGRPTVLDLLkdVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2771595271  91 *A**QLQ*GV**KDG*TKPA*A*LI**p**wer*ppvrfRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:cd02870    82 EELRRLRAGVELDDGKTAPAKVKVL--------------SRDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 46-186 2.44e-45

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: 147.86  E-value: 2.44e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  46 AGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA*A**QLQ*GV**KDG*TKPA*A*LI**P**wer*p 125
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPG------ 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2771595271 126 pvrfrqsIPTqW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVAIG*WQLNDLQPGQWCEVN 186
Cdd:TIGR00093  75 -------FPT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPLT 127
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 13-182 2.86e-37

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: 128.41  E-value: 2.86e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  13 IAFNKPYDVLTQFNDKDGRTT---LKDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PD 89
Cdd:cd02553     3 LMLNKPAGVVCATKDPHHPTVidlLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGPLT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  90 A*A**QLQ*GV**KDG*-TKPA*A*li**p**wER*PPVRFRQSiptqw*e*qISEGKNRQVRRMTAAVGHPTLRLIRVA 168
Cdd:cd02553    83 EDDIEAFAEGVLLHDGYpTKPAKL---------EILSPTTVRLT---------ITEGKYHQVKRMFAAVGNKVVALHRIR 144

                         170
                  ....*....|....*
gi 2771595271 169 IG*WQL-NDLQPGQW 182
Cdd:cd02553   145 IGGLELdDDLAPGEW 159
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 12-169 1.55e-36

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: 126.33  E-value: 1.55e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKDGRTTL---KDYIDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*P 88
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVvvrLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  89 DA*A**QLQ*GV**KDG*TKPA*A*Li**P**WER*PPVRfrqsiPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRVA 168
Cdd:cd02550    81 DEEGIEDLATVRRGRLSGLVDEGVPL--AVTKVRVIGEHG-----GTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVR 153


                  .
gi 2771595271 169 I 169
Cdd:cd02550   154 I 154
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 11-186 1.17e-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: 103.54  E-value: 1.17e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  11 KLIAFNKPYDVLTQFNDKDGRTTLKDYI---DIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN* 87
Cdd:cd02556     1 RVLIYHKPEGLICTRKDPKGRPTVFDLLpklGIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  88 PDA*A**QLQ*GV**KDG*TKPA*A*LI**p**wer*ppvrfRQSIPTQW*E*QISEGKNRQVRRMTAAVGHPTLRLIRV 167
Cdd:cd02556    81 VTDEQLKSLKKGVELEDGFAGFKSIQLE--------------GGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRI 146

                         170       180
                  ....*....|....*....|
gi 2771595271 168 AIG*-WQLNDLQPGQWCEVN 186
Cdd:cd02556   147 RYGPiFLPGNLKRGQWEELP 166
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 13-182 3.79e-27

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: 102.00  E-value: 3.79e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  13 IAFNKPYDVLTQFNDKDgRTTLKDYIDIAD-VYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA* 91
Cdd:cd02554     3 IAYNKPVGIDCTLERAD-EDNIIDFVNPPPrIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITDE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  92 A**QLQ*GV**KDG*TKPA*A*li**p**wER*PPVRFRQsIPTQw*e*qiseGKNRQVRRMTAAVGHPTLRLIRVAIG* 171
Cdd:cd02554    82 FIEGMSNGVVILGTVTKPCKV---------ERLAKDKFRI-VLTQ--------GLNRQIRRMCEALGYRVTDLKRVRIMN 143

                         170
                  ....*....|.
gi 2771595271 172 WQLNDLQPGQW 182
Cdd:cd02554   144 IELGDLAPGEW 154
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
16-182 2.97e-20

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 85.93  E-value: 2.97e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  16 NKPYDVLTQFNDKDGRTTLKdYID--IAD-VYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA*A 92
Cdd:PRK10839   66 NKPQGYVCSTDDPDHPTVLY-FLDepVAYkLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDT 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  93 **QLQ*GV*---*KDg*TKPA*A*LI**p**wer*pPVRFRQSiptqw*e*qISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:PRK10839  145 AEQFAKGVQlhnEKD-LTKPAVLEVIT---------PTQVRLT---------ISEGRYHQVKRMFAAVGNHVVELHRERI 205

                         170
                  ....*....|....
gi 2771595271 170 G*WQLN-DLQPGQW 182
Cdd:PRK10839  206 GAITLDaDLAPGEY 219
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 12-156 3.19e-15

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: 70.51  E-value: 3.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFND-KDGRTTLKDYIDIAD-----VYPAGRLDRDSEGLLLLTDDG----RLQHHIsdPRHKLSKTYW 81
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDsLTKLLSLLALLLRRElgvkrLYPVHRLDKNTSGLLLLAKDGeaanKLNKLF--PERKIEKEYL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  82 **VEN*PDA*A**QLQ*GV**KDG*TKPA*a*li**P**WER*PPVRFRQ-----SIPTQW*E*QISEGKNRQVRRMTAA 156
Cdd:pfam00849  79 ALVDKPEEEEGTIKSPIKKEKNKSPFRKE-------EELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAHLAA 151
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
2-190 5.88e-15

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 72.49  E-value: 5.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271   2 ISGTDITMTKLIAFNKPYDVLTQFNDKDGRTTLKDY---IDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSK 78
Cdd:PRK10700   59 VKESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRlpkLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVER 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  79 TYW**VEN*PDA*A**QLQ*GV**KDG*tkPA*A*LI**p**wer*ppvRFR--QSIpTQW*E*QISEGKNRQVRRMTAA 156
Cdd:PRK10700  139 EYAVRVFGQVDDAKLRQLSRGVQLEDG---PAAFKTI------------KFSggEGI-NQWYNVTLTEGRNREVRRLWEA 202

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2771595271 157 VGHPTLRLIRVAIG*WQL-NDLQPGQWCEVNFQTV 190
Cdd:PRK10700  203 VGVQVSRLIRVRYGDIPLpKGLPRGGWTELDLAQT 237
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 27-182 7.87e-14

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: 67.43  E-value: 7.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  27 DKDGRTTLKDyiDIADVYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VEN*PDA*A**QLQ*GV**KDG* 106
Cdd:cd02555    33 DRSGRRPLKG--HFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGRE 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2771595271 107 TKPA*A*li**p**WER*PPVRFrqsiptqw*e*QISEGKNRQVRRMTAAVGHPTLRLIRVAIG*WQLNDLQPGQW 182
Cdd:cd02555   111 LPPAKV-------SWQNEQRLRF-----------ALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLPLGQW 168
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
12-182 5.83e-10

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 58.20  E-value: 5.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKDgRTTLKDYIDIAD-VYPAGRLDRDSEGLLLLTDDGRLQHHISDPRHKLSKTYW**VeN*PDA 90
Cdd:PRK10475   69 LIALNKPVGIVSTTEDGE-RDNIVDFVNHSKrVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTV-DKPIT 146

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  91 *A**Q-LQ*GV**KDG*TKPA*A*li**p**wER*PPVRFRQSiptqw*e*qISEGKNRQVRRMTAAVGHPTLRLIRVAI 169
Cdd:PRK10475  147 DEFIRgMGAGVPILGTVTKKCKV---------KKEAPFVFRIT---------LVQGLNRQIRRMCEHFGYEVTKLERTRI 208

                         170
                  ....*....|...
gi 2771595271 170 G*WQLNDLQPGQW 182
Cdd:PRK10475  209 MNVSLSGIPLGEW 221
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 12-90 5.09e-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: 39.63  E-value: 5.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKDGRTTLKDYIDIAD--------VYPAGRLDRDSEGLLLLTDD----GRLQHHISDprHKLSKT 79
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLlllgeefrPGLVHRLDKDTSGLLLVAKNkkaaAKLSKQFKE--RKVKKT 78

                          90
                  ....*....|.
gi 2771595271  80 YW**VEN*PDA 90
Cdd:cd02869    79 YLALVDGKPPE 89
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 12-162 5.96e-03

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: 36.93  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQ--FNDKDGR----TTLKDYIDiADVYPAGRLDRDSEGLLLLTDDGRLQHHISD--PRHKLSKTYW** 83
Cdd:cd02563    10 LVAINKPSGLLVHrsELDRHETrfalQTLRDQLG-QHVYPVHRLDRPTSGVLLFALSSEVARKLGEqfTEHRVHKTYLAV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  84 VEN*PDA*A------**QLQ*GV**KDG*TKPA*A*L--------I**P**WER*PPVRFrqsiptQW*E*QISEGKNRQ 149
Cdd:cd02563    89 VRGYVPESGtidyplSEELDKLADKFASDDKAPQAATthyrllavEELPVVVGKYPTSRY------SLVELTPHTGRKHQ 162

                         170
                  ....*....|...
gi 2771595271 150 VRRMTAAVGHPTL 162
Cdd:cd02563   163 LRRHLAHIRHPII 175
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 12-89 9.57e-03

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: 36.27  E-value: 9.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2771595271  12 LIAFNKPYDVLTQFNDKDGRTT----LKDYIDIAD----VYPAGRLDRDSEGLLLL--TDD--GRLQHHISDprHKLSKT 79
Cdd:COG0564     8 LLVVNKPAGLVVHPGSGGDDGTlvnaLRAHLGELSgvprPGLVHRLDRDTSGLLLVakTRKaaRRLSEQFRE--REVEKR 85

                          90
                  ....*....|
gi 2771595271  80 YW**VEN*PD 89
Cdd:COG0564    86 YLALVEGKPK 95
 
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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