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Conserved domains on  [gi|1243242315|ref|WP_095965705|]
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MULTISPECIES: pseudouridine synthase [Pseudomonas]

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 ...
 35-200 2.81e-93

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: 270.02  E-value: 2.81e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSD-GEGRATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSA 113
Cdd:cd02566     1 LILFNKPYGVLSQFTDeSEKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 114 EQLQRLRDGVELNDGMTLPAEARQLDEPE-LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRI 192
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 1243242315 193 GDWTIEGL 200
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 ...
 35-200 2.81e-93

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: 270.02  E-value: 2.81e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSD-GEGRATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSA 113
Cdd:cd02566     1 LILFNKPYGVLSQFTDeSEKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 114 EQLQRLRDGVELNDGMTLPAEARQLDEPE-LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRI 192
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 1243242315 193 GDWTIEGL 200
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
20-208 3.83e-75

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 225.78  E-value: 3.83e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  20 AAPRRVAKAPPAEP-KLILFNKPFDVLTQFSDGEGRATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHK 98
Cdd:PRK11394   25 SSQRSTRRKPENQPtRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  99 LAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDEPE-LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMT 177
Cdd:PRK11394  105 TGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMT 184

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1243242315 178 AAVGLPTLRLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:PRK11394  185 AHVGFPTLRLIRYAMGDYSLDNLANGEWREA 215
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 29-208 8.75e-67

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: 204.50  E-value: 8.75e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  29 PPAEPKLILFNKPFDVLTQFSDGEGRATLKDYID---VPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWV 105
Cdd:COG1187    58 LPEEPVYLLLNKPAGVVSTTKDPEGRPTVFDLLPearKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLV 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 106 QVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDepelwprnppvrfrkSVPTSWLELVIREGRNRQVRRMTAAVGLPTL 185
Cdd:COG1187   138 RVDGPVTEEDLERLREGVELEDGPTKPAKVEILS---------------GEANTWLRITLTEGRNRQVRRMFEAVGLPVV 202

                         170       180
                  ....*....|....*....|...
gi 1243242315 186 RLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:COG1187   203 RLKRVRIGPLTLGDLPPGEWREL 225
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 69-208 1.02e-53

pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272902  Cd Length: 128  Bit Score: 168.28  E-value: 1.02e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  69 AGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDEPELwprnp 148
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGF----- 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 149 pvrfrksvPTsWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:TIGR00093  76 --------PT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPL 126
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 35-179 3.26e-22

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: 88.23  E-value: 3.26e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSDGE-GRATLKDYIDVPG-----IYPAGRLDRDSEGLLLLTNDGQLQARIAD--PKHKLAKTYWVQ 106
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLtKLLSLLALLLRRElgvkrLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1243242315 107 VEGEPSAEQLQRLRDGVElndgmtlPAEARQLDEPELWPRNPPVRFRK-----SVPTSWLELVIREGRNRQVRRMTAA 179
Cdd:pfam00849  81 VDKPEEEEGTIKSPIKKE-------KNKSPFRKEEELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAHLAA 151
 
Name Accession Description Interval E-value
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 35-200 2.81e-93

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: 270.02  E-value: 2.81e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSD-GEGRATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSA 113
Cdd:cd02566     1 LILFNKPYGVLSQFTDeSEKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 114 EQLQRLRDGVELNDGMTLPAEARQLDEPE-LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRI 192
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 1243242315 193 GDWTIEGL 200
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
20-208 3.83e-75

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 225.78  E-value: 3.83e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  20 AAPRRVAKAPPAEP-KLILFNKPFDVLTQFSDGEGRATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHK 98
Cdd:PRK11394   25 SSQRSTRRKPENQPtRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  99 LAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDEPE-LWPRNPPVRFRKSVPTSWLELVIREGRNRQVRRMT 177
Cdd:PRK11394  105 TGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMT 184

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1243242315 178 AAVGLPTLRLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:PRK11394  185 AHVGFPTLRLIRYAMGDYSLDNLANGEWREA 215
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 29-208 8.75e-67

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: 204.50  E-value: 8.75e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  29 PPAEPKLILFNKPFDVLTQFSDGEGRATLKDYID---VPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWV 105
Cdd:COG1187    58 LPEEPVYLLLNKPAGVVSTTKDPEGRPTVFDLLPearKERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEKEYLV 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 106 QVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDepelwprnppvrfrkSVPTSWLELVIREGRNRQVRRMTAAVGLPTL 185
Cdd:COG1187   138 RVDGPVTEEDLERLREGVELEDGPTKPAKVEILS---------------GEANTWLRITLTEGRNRQVRRMFEAVGLPVV 202

                         170       180
                  ....*....|....*....|...
gi 1243242315 186 RLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:COG1187   203 RLKRVRIGPLTLGDLPPGEWREL 225
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 36-192 8.76e-62

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: 189.24  E-value: 8.76e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  36 ILFNKPFDVLTQFSDGEGRATLKDYI--DVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSA 113
Cdd:cd02870     2 LLLNKPRGVVSTVRDPEGRPTVLDLLkdVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1243242315 114 EQLQRLRDGVELNDGMTLPAEARQLDEPElwprnppvrfrksvPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRI 192
Cdd:cd02870    82 EELRRLRAGVELDDGKTAPAKVKVLSRDP--------------KNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 69-208 1.02e-53

pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272902  Cd Length: 128  Bit Score: 168.28  E-value: 1.02e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  69 AGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARQLDEPELwprnp 148
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEPGF----- 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 149 pvrfrksvPTsWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:TIGR00093  76 --------PT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPL 126
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 36-208 2.02e-42

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: 140.73  E-value: 2.02e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  36 ILFNKPFDVLTQFSDGEGR---ATLKDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPS 112
Cdd:cd02553     3 LMLNKPAGVVCATKDPHHPtviDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGPLT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 113 AEQLQRLRDGVELNDG-MTLPAEARQLDEpelwprnppvrfrksvptSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVR 191
Cdd:cd02553    83 EDDIEAFAEGVLLHDGyPTKPAKLEILSP------------------TTVRLTITEGKYHQVKRMFAAVGNKVVALHRIR 144

                         170
                  ....*....|....*...
gi 1243242315 192 IGDWTI-EGLDQGQWKEV 208
Cdd:cd02553   145 IGGLELdDDLAPGEWRPL 162
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 34-209 1.34e-37

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: 128.20  E-value: 1.34e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  34 KLILFNKPFDVLTQFSDGEGRATLKDYIDVPGI---YPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGE 110
Cdd:cd02556     1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIprwISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 111 PSAEQLQRLRDGVELNDGMTLPAEARQLDEPElwpRNppvrfrksvptSWLELVIREGRNRQVRRMTAAVGLPTLRLVRV 190
Cdd:cd02556    81 VTDEQLKSLKKGVELEDGFAGFKSIQLEGGEG---KN-----------SWYRVTLREGRNREVRRLWEAFGLQVSRLIRI 146

                         170       180
                  ....*....|....*....|
gi 1243242315 191 RIGDWT-IEGLDQGQWKEVP 209
Cdd:cd02556   147 RYGPIFlPGNLKRGQWEELP 166
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 35-192 4.69e-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: 124.02  E-value: 4.69e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSDGEGRATL---KDYIDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEP 111
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVvvrLDKLHGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 112 SAEQLQRLRDgVELNDGMTLPAEARQLdEPELWPRNPPVRfrksvPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVR 191
Cdd:cd02550    81 DEEGIEDLAT-VRRGRLSGLVDEGVPL-AVTKVRVIGEHG-----GTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVR 153


                  .
gi 1243242315 192 I 192
Cdd:cd02550   154 I 154
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 36-207 1.29e-32

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: 115.48  E-value: 1.29e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  36 ILFNKPFDVLTQFSDGEgRATLKDYIDVPG-IYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSAE 114
Cdd:cd02554     3 IAYNKPVGIDCTLERAD-EDNIIDFVNPPPrIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITDE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 115 QLQRLRDGVELNDGMTLPAEARQLDEPelwprnppvRFRksvptswleLVIREGRNRQVRRMTAAVGLPTLRLVRVRIGD 194
Cdd:cd02554    82 FIEGMSNGVVILGTVTKPCKVERLAKD---------KFR---------IVLTQGLNRQIRRMCEALGYRVTDLKRVRIMN 143

                         170
                  ....*....|...
gi 1243242315 195 WTIEGLDQGQWKE 207
Cdd:cd02554   144 IELGDLAPGEWRP 156
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
33-206 7.05e-23

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 92.09  E-value: 7.05e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  33 PKLILFNKPFDVLTQfSDGEGRATLKDYIDVPGIY---PAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEG 109
Cdd:PRK10839   60 PRYFMLNKPQGYVCS-TDDPDHPTVLYFLDEPVAYklhAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLES 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 110 EPSAEQLQRLRDGVELNDGMTL--PAEARQLDEPElwprnppVRfrksvptswleLVIREGRNRQVRRMTAAVGLPTLRL 187
Cdd:PRK10839  139 PVADDTAEQFAKGVQLHNEKDLtkPAVLEVITPTQ-------VR-----------LTISEGRYHQVKRMFAAVGNHVVEL 200

                         170       180
                  ....*....|....*....|
gi 1243242315 188 VRVRIGDWTI-EGLDQGQWK 206
Cdd:PRK10839  201 HRERIGAITLdADLAPGEYR 220
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
34-209 2.41e-22

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 91.75  E-value: 2.41e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  34 KLILFNKPFDVLTQFSDGEGRATLKDYIdvPGIYPA-----GRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVE 108
Cdd:PRK10700   68 RVLAYYKPEGELCTRNDPEGRPTVFDRL--PKLRGArwiavGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 109 GEPSAEQLQRLRDGVELNDGmtlPAEARQldepelwprnppVRFRKSVP-TSWLELVIREGRNRQVRRMTAAVGLPTLRL 187
Cdd:PRK10700  146 GQVDDAKLRQLSRGVQLEDG---PAAFKT------------IKFSGGEGiNQWYNVTLTEGRNREVRRLWEAVGVQVSRL 210

                         170       180
                  ....*....|....*....|...
gi 1243242315 188 VRVRIGDWTI-EGLDQGQWKEVP 209
Cdd:PRK10700  211 IRVRYGDIPLpKGLPRGGWTELD 233
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 35-179 3.26e-22

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: 88.23  E-value: 3.26e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSDGE-GRATLKDYIDVPG-----IYPAGRLDRDSEGLLLLTNDGQLQARIAD--PKHKLAKTYWVQ 106
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLtKLLSLLALLLRRElgvkrLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1243242315 107 VEGEPSAEQLQRLRDGVElndgmtlPAEARQLDEPELWPRNPPVRFRK-----SVPTSWLELVIREGRNRQVRRMTAA 179
Cdd:pfam00849  81 VDKPEEEEGTIKSPIKKE-------KNKSPFRKEEELGGKKAVTHLKVlksgsKGDYSLLELELVTGRKHQIRAHLAA 151
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 49-211 1.42e-20

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: 84.76  E-value: 1.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  49 SDGEGRATLKDyiDVPGIYPAGRLDRDSEGLLLLTNDGQLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDG 128
Cdd:cd02555    32 ADRSGRRPLKG--HFARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTYDGR 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 129 MTLPAEARQLDEPELwprnppvRFrksvptswlelVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWKEV 208
Cdd:cd02555   110 ELPPAKVSWQNEQRL-------RF-----------ALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLPLGQWRYL 171


                  ...
gi 1243242315 209 PAR 211
Cdd:cd02555   172 TTG 174
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
32-207 2.56e-17

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 78.23  E-value: 2.56e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  32 EPK------LILFNKPFDVLTQFSDGEgRATLKDYID-VPGIYPAGRLDRDSEGLLLLTNDGQLQARI--ADPKHKlaKT 102
Cdd:PRK10475   60 EPReaedlvLIALNKPVGIVSTTEDGE-RDNIVDFVNhSKRVFPIGRLDKDSQGLIFLTNHGDLVNKIlrAGNDHE--KE 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 103 YWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARQldepelwprNPPVRFRksvptswLELVirEGRNRQVRRMTAAVGL 182
Cdd:PRK10475  137 YLVTVDKPITDEFIRGMGAGVPILGTVTKKCKVKK---------EAPFVFR-------ITLV--QGLNRQIRRMCEHFGY 198

                         170       180
                  ....*....|....*....|....*
gi 1243242315 183 PTLRLVRVRIGDWTIEGLDQGQWKE 207
Cdd:PRK10475  199 EVTKLERTRIMNVSLSGIPLGEWRD 223
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 35-183 9.78e-06

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: 44.25  E-value: 9.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSDGEGRATLKDYI--------DVPGIYPAGRLDRDSEGLLLLTNDGQLQARIAD--PKHKLAKTYW 104
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALlklllllgEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKqfKERKVKKTYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315 105 VQVEGEPSAEQLQRLRDGVELNDGMtlpaEARQLDEPElwpRNPPV-RFRK---SVPTSWLELVIREGRNRQVRRMTAAV 180
Cdd:cd02869    81 ALVDGKPPEDEGTIDAPLGRKKRKK----RARVVVSED---GKPAItHYKVlerFGNVTLVELQLETGRTHQIRVHLASI 153


                  ...
gi 1243242315 181 GLP 183
Cdd:cd02869   154 GHP 156
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 35-115 4.20e-04

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: 39.73  E-value: 4.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  35 LILFNKPFDVLTQFSDGEGRATL--------KDYIDVPGIYPAGRLDRDSEGLLLL--TNDGQ--LQARIADpkHKLAKT 102
Cdd:COG0564     8 LLVVNKPAGLVVHPGSGGDDGTLvnalrahlGELSGVPRPGLVHRLDRDTSGLLLVakTRKAArrLSEQFRE--REVEKR 85

                          90
                  ....*....|...
gi 1243242315 103 YWVQVEGEPSAEQ 115
Cdd:COG0564    86 YLALVEGKPKEDE 98
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 66-185 7.44e-04

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: 39.24  E-value: 7.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1243242315  66 IYPAGRLDRDSEGLLLLTNDGQLQARIAD--PKHKLAKTYWVQVEGEPSA---------EQLQRLRDGVELNDGMTLPAE 134
Cdd:cd02563    46 VYPVHRLDRPTSGVLLFALSSEVARKLGEqfTEHRVHKTYLAVVRGYVPEsgtidyplsEELDKLADKFASDDKAPQAAT 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1243242315 135 A--RQLDEPElwprnPPVRFRK--SVPTSWLELVIREGRNRQVRRMTAAVGLPTL 185
Cdd:cd02563   126 ThyRLLAVEE-----LPVVVGKypTSRYSLVELTPHTGRKHQLRRHLAHIRHPII 175
 
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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