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Conserved domains on  [gi|2067215155|dbj|GJC01101|]
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pseudouridine synthase [Aeromonas caviae]

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 ...
 54-219 2.57e-89

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: 263.47  E-value: 2.57e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEG-GRETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 133 EKLAALRAGVALNDGMTLPAGARIMDDPA-VWPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAI 211
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2067215155 212 GEWTLDGL 219
Cdd:cd02566   161 GDIGLDNL 168
PHA03378 super family cl33729
EBNA-3B; Provisional
 164-300 8.58e-03

EBNA-3B; Provisional


The actual alignment was detected with superfamily member PHA03378:

Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 37.74  E-value: 8.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 164 PRNPPIRERREIPTCWLEITIVEGRNRQVrrmtahiGHPTLRLIRYAIGEWTLDGLAPGEsraLPAPELAPAP--RPAAT 241
Cdd:PHA03378  651 PHQPPQVEITPYKPTWTQIGHIPYQPSPT-------GANTMLPIQWAPGTMQPPPRAPTP---MRPPAAPPGRaqRPAAA 720

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2067215155 242 QGKARASAAAggTGRSAPRTARPTDQDPPQGRERRgADPRQANRSGGRTTARRPARTKP 300
Cdd:PHA03378  721 TGRARPPAAA--PGRARPPAAAPGRARPPAAAPGR-ARPPAAAPGRARPPAAAPGAPTP 776
 
Name Accession Description Interval E-value
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 54-219 2.57e-89

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: 263.47  E-value: 2.57e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEG-GRETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 133 EKLAALRAGVALNDGMTLPAGARIMDDPA-VWPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAI 211
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2067215155 212 GEWTLDGL 219
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
42-225 3.59e-82

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 247.35  E-value: 3.59e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  42 ERKPATAPVdrKLLLLNKPYMVLCQFTDEGGRETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKT 121
Cdd:PRK11394   31 RRKPENQPT--RVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKI 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 122 YWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPA-VWPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIG 200
Cdd:PRK11394  109 YYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVG 188

                         170       180
                  ....*....|....*....|....*
gi 2067215155 201 HPTLRLIRYAIGEWTLDGLAPGESR 225
Cdd:PRK11394  189 FPTLRLIRYAMGDYSLDNLANGEWR 213
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 44-227 1.24e-59

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: 189.86  E-value: 1.24e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  44 KPATAPVDRKLLLLNKPYMVLCQFTDEGGRETLKDYITE---PGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPK 120
Cdd:COG1187    54 KPLKLPEEPVYLLLNKPAGVVSTTKDPEGRPTVFDLLPEarkERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEK 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 121 TYWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPAvwprnppirerreipTCWLEITIVEGRNRQVRRMTAHIG 200
Cdd:COG1187   134 EYLVRVDGPVTEEDLERLREGVELEDGPTKPAKVEILSGEA---------------NTWLRITLTEGRNRQVRRMFEAVG 198

                         170       180
                  ....*....|....*....|....*..
gi 2067215155 201 HPTLRLIRYAIGEWTLDGLAPGESRAL 227
Cdd:COG1187   199 LPVVRLKRVRIGPLTLGDLPPGEWREL 225
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 88-227 2.47e-56

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: 177.91  E-value: 2.47e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  88 AGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPavwprnp 167
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEP------- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 168 pirerrEIPTcWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAIGEWTLDGLAPGESRAL 227
Cdd:TIGR00093  74 ------GFPT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPL 126
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 54-198 4.30e-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: 90.16  E-value: 4.30e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEGGRETLKDYI------TEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQ--PGEKTPKTYWVQ 125
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALllrrelGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2067215155 126 VEGIPSEEklAALRAGVALNDGMtlpagARIMDDPAVWPRNP-----PIRERREIPTCWLEITIVEGRNRQVRRMTAH 198
Cdd:pfam00849  81 VDKPEEEE--GTIKSPIKKEKNK-----SPFRKEEELGGKKAvthlkVLKSGSKGDYSLLELELVTGRKHQIRAHLAA 151
PHA03378 PHA03378
EBNA-3B; Provisional
 164-300 8.58e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 37.74  E-value: 8.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 164 PRNPPIRERREIPTCWLEITIVEGRNRQVrrmtahiGHPTLRLIRYAIGEWTLDGLAPGEsraLPAPELAPAP--RPAAT 241
Cdd:PHA03378  651 PHQPPQVEITPYKPTWTQIGHIPYQPSPT-------GANTMLPIQWAPGTMQPPPRAPTP---MRPPAAPPGRaqRPAAA 720

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2067215155 242 QGKARASAAAggTGRSAPRTARPTDQDPPQGRERRgADPRQANRSGGRTTARRPARTKP 300
Cdd:PHA03378  721 TGRARPPAAA--PGRARPPAAAPGRARPPAAAPGR-ARPPAAAPGRARPPAAAPGAPTP 776
 
Name Accession Description Interval E-value
PseudoU_synth_RluE cd02566
Pseudouridine synthase, Escherichia coli RluE; This group is comprised of bacterial proteins ...
 54-219 2.57e-89

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: 263.47  E-value: 2.57e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEG-GRETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:cd02566     1 LILFNKPYGVLSQFTDESeKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDGRLQHRITDPSFKHPKTYYVQVEGVPTE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 133 EKLAALRAGVALNDGMTLPAGARIMDDPA-VWPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAI 211
Cdd:cd02566    81 DALEQLRNGVELGDGLTLPAKVEKVDEPPwLWEREPPIRFRKNIPTSWIEITICEGKNRQVRRMTAAVGFPTLRLIRVSI 160


                  ....*...
gi 2067215155 212 GEWTLDGL 219
Cdd:cd02566   161 GDIGLDNL 168
PRK11394 PRK11394
23S rRNA pseudouridine(2457) synthase RluE;
42-225 3.59e-82

23S rRNA pseudouridine(2457) synthase RluE;


Pssm-ID: 183115  Cd Length: 217  Bit Score: 247.35  E-value: 3.59e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  42 ERKPATAPVdrKLLLLNKPYMVLCQFTDEGGRETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKT 121
Cdd:PRK11394   31 RRKPENQPT--RVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKI 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 122 YWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPA-VWPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIG 200
Cdd:PRK11394  109 YYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAwLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVG 188

                         170       180
                  ....*....|....*....|....*
gi 2067215155 201 HPTLRLIRYAIGEWTLDGLAPGESR 225
Cdd:PRK11394  189 FPTLRLIRYAMGDYSLDNLANGEWR 213
RsuA COG1187
Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ...
 44-227 1.24e-59

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: 189.86  E-value: 1.24e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  44 KPATAPVDRKLLLLNKPYMVLCQFTDEGGRETLKDYITE---PGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPK 120
Cdd:COG1187    54 KPLKLPEEPVYLLLNKPAGVVSTTKDPEGRPTVFDLLPEarkERLFPVGRLDKDTEGLLLLTNDGELAHRLTHPKYGVEK 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 121 TYWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPAvwprnppirerreipTCWLEITIVEGRNRQVRRMTAHIG 200
Cdd:COG1187   134 EYLVRVDGPVTEEDLERLREGVELEDGPTKPAKVEILSGEA---------------NTWLRITLTEGRNRQVRRMFEAVG 198

                         170       180
                  ....*....|....*....|....*..
gi 2067215155 201 HPTLRLIRYAIGEWTLDGLAPGESRAL 227
Cdd:COG1187   199 LPVVRLKRVRIGPLTLGDLPPGEWREL 225
TIGR00093 TIGR00093
pseudouridine synthase; This model identifies panels of pseudouridine synthase enzymes that ...
 88-227 2.47e-56

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: 177.91  E-value: 2.47e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  88 AGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVALNDGMTLPAGARIMDDPavwprnp 167
Cdd:TIGR00093   1 VGRLDRDSEGLLLLTNDGELVHRLTHPGHHHEKEYLVTVEGPVTDEDLEALRKGVQLEDGKTKPAKLKVITEP------- 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 168 pirerrEIPTcWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAIGEWTLDGLAPGESRAL 227
Cdd:TIGR00093  74 ------GFPT-WLRVTLSEGRNRQVRRMFAAVGFPVLRLHRVRIGDVSLNGLPPGEWRPL 126
PseudoU_synth_RsuA_like cd02870
Pseudouridine synthases, RsuA subfamily; Pseudouridine synthases are responsible for the ...
 55-211 1.02e-55

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: 176.92  E-value: 1.02e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  55 LLLNKPYMVLCQFTDEGGRETLKDYI--TEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:cd02870     2 LLLNKPRGVVSTVRDPEGRPTVLDLLkdVGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVRGVPSE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2067215155 133 EKLAALRAGVALNDGMTLPAGARIMDdpavwprnppirerREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAI 211
Cdd:cd02870    82 EELRRLRAGVELDDGKTAPAKVKVLS--------------RDPKNTLLEVTLHEGRNRQVRRMFEAVGHPVLRLKRVRI 146
PseudoU_synth_RsuA cd02553
Pseudouridine synthase, Escherichia coli RsuA like; This group is comprised of eukaryotic and ...
 55-232 7.33e-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: 142.27  E-value: 7.33e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  55 LLLNKPYMVLCQFTDEGGR---ETLKDYITEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPS 131
Cdd:cd02553     3 LMLNKPAGVVCATKDPHHPtviDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLAGPLT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 132 EEKLAALRAGVALNDG-MTLPAGARIMDDpavwprnppirerreiptCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYA 210
Cdd:cd02553    83 EDDIEAFAEGVLLHDGyPTKPAKLEILSP------------------TTVRLTITEGKYHQVKRMFAAVGNKVVALHRIR 144

                         170       180
                  ....*....|....*....|...
gi 2067215155 211 IGEWTLD-GLAPGESRALPAPEL 232
Cdd:cd02553   145 IGGLELDdDLAPGEWRPLTEEEL 167
PseudoU_synth_Rsu_Rlu_like cd02550
Pseudouridine synthase, Rsu/Rlu family; This group is comprised of eukaryotic, bacterial and ...
 54-211 3.09e-34

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: 122.10  E-value: 3.09e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEGGRETLKDYITEPG---IYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIP 130
Cdd:cd02550     1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHgprVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVRGEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 131 SEEKLAALrAGVALNDGmtlpAGARIMDDPAvwPRNPPIRERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRYA 210
Cdd:cd02550    81 DEEGIEDL-ATVRRGRL----SGLVDEGVPL--AVTKVRVIGEHGGTGRLRLTLKTGRTHQIRRHCAAVGFPVLRLHRVR 153


                  .
gi 2067215155 211 I 211
Cdd:cd02550   154 I 154
PseudoU_synth_RluF cd02554
Pseudouridine synthase, Escherichia coli RluF like; This group is comprised of bacterial ...
 55-233 5.68e-34

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: 121.65  E-value: 5.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  55 LLLNKPYMVLCQfTDEGGRETLKDYIT-EPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSEE 133
Cdd:cd02554     3 IAYNKPVGIDCT-LERADEDNIIDFVNpPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTVNKPITDE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 134 KLAALRAGVALNDGMTLPAgarimddpavwprnppiRERREIPTCwLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAIGE 213
Cdd:cd02554    82 FIEGMSNGVVILGTVTKPC-----------------KVERLAKDK-FRIVLTQGLNRQIRRMCEALGYRVTDLKRVRIMN 143

                         170       180
                  ....*....|....*....|
gi 2067215155 214 WTLDGLAPGESRALPAPELA 233
Cdd:cd02554   144 IELGDLAPGEWRPLTDAELF 163
PseudoU_synth_RluB cd02556
Pseudouridine synthase, Escherichia coli RluB like; This group is comprised of bacterial and ...
 53-228 1.35e-32

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: 118.18  E-value: 1.35e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  53 KLLLLNKPYMVLCQFTDEGGRETLKDYITEPGI---YAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGI 129
Cdd:cd02556     1 RVLIYHKPEGLICTRKDPKGRPTVFDLLPKLGIprwISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVFGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 130 PSEEKLAALRAGVALNDGMTLPAGARImddpavwprnppirERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLIRY 209
Cdd:cd02556    81 VTDEQLKSLKKGVELEDGFAGFKSIQL--------------EGGEGKNSWYRVTLREGRNREVRRLWEAFGLQVSRLIRI 146

                         170       180
                  ....*....|....*....|
gi 2067215155 210 AIGEWTL-DGLAPGESRALP 228
Cdd:cd02556   147 RYGPIFLpGNLKRGQWEELP 166
PRK10839 PRK10839
16S rRNA pseudouridine(516) synthase RsuA;
56-233 3.15e-25

16S rRNA pseudouridine(516) synthase RsuA;


Pssm-ID: 236774 [Multi-domain]  Cd Length: 232  Bit Score: 100.57  E-value: 3.15e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  56 LLNKPYMVLCQfTDEGGRETLKDYITEPGIY---AAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:PRK10839   64 MLNKPQGYVCS-TDDPDHPTVLYFLDEPVAYklhAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVAD 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 133 EKLAALRAGVALNDGMTL--PAGARIMDDPAVwprnppirerreiptcwlEITIVEGRNRQVRRMTAHIGHPTLRLIRYA 210
Cdd:PRK10839  143 DTAEQFAKGVQLHNEKDLtkPAVLEVITPTQV------------------RLTISEGRYHQVKRMFAAVGNHVVELHRER 204

                         170       180
                  ....*....|....*....|....
gi 2067215155 211 IGEWTLD-GLAPGESRALPAPELA 233
Cdd:PRK10839  205 IGAITLDaDLAPGEYRPLTEEEIA 228
PRK10475 PRK10475
23S rRNA pseudouridine(2604) synthase RluF;
54-277 2.89e-23

23S rRNA pseudouridine(2604) synthase RluF;


Pssm-ID: 236698 [Multi-domain]  Cd Length: 290  Bit Score: 96.72  E-value: 2.89e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQfTDEGGRETLKDYITEPG-IYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSE 132
Cdd:PRK10475   69 LIALNKPVGIVST-TEDGERDNIVDFVNHSKrVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITD 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 133 EKLAALRAGVALNDGMTlpagarimddpavwprnPPIRERREIPTCWlEITIVEGRNRQVRRMTAHIGHPTLRLIRYAIG 212
Cdd:PRK10475  148 EFIRGMGAGVPILGTVT-----------------KKCKVKKEAPFVF-RITLVQGLNRQIRRMCEHFGYEVTKLERTRIM 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 213 EWTLDGLAPGESRALPAPELA------------PAPRPAATQGKARASAAAGGTGRSAPRTARPTDQDPP---QGRERRG 277
Cdd:PRK10475  210 NVSLSGIPLGEWRDLTDDELIdlfklienssseAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRftsPGRKKKG 289
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 54-198 4.30e-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: 90.16  E-value: 4.30e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEGGRETLKDYI------TEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQ--PGEKTPKTYWVQ 125
Cdd:pfam00849   1 YIVVNKPAGVPVHPTDSLTKLLSLLALllrrelGVKRLYPVHRLDKNTSGLLLLAKDGEAANKLNKlfPERKIEKEYLAL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2067215155 126 VEGIPSEEklAALRAGVALNDGMtlpagARIMDDPAVWPRNP-----PIRERREIPTCWLEITIVEGRNRQVRRMTAH 198
Cdd:pfam00849  81 VDKPEEEE--GTIKSPIKKEKNK-----SPFRKEEELGGKKAvthlkVLKSGSKGDYSLLELELVTGRKHQIRAHLAA 151
PRK10700 PRK10700
23S rRNA pseudouridine(2605) synthase RluB;
53-216 2.44e-15

23S rRNA pseudouridine(2605) synthase RluB;


Pssm-ID: 182659 [Multi-domain]  Cd Length: 289  Bit Score: 74.80  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  53 KLLLLNKPYMVLCQFTDEGGRETLKDYItePGI-----YAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVE 127
Cdd:PRK10700   68 RVLAYYKPEGELCTRNDPEGRPTVFDRL--PKLrgarwIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 128 GIPSEEKLAALRAGVALNDGmtlPAGARIMDdpavwprnppiRERREIPTCWLEITIVEGRNRQVRRMTAHIGHPTLRLI 207
Cdd:PRK10700  146 GQVDDAKLRQLSRGVQLEDG---PAAFKTIK-----------FSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLI 211


                  ....*....
gi 2067215155 208 RYAIGEWTL 216
Cdd:PRK10700  212 RVRYGDIPL 220
PSSA_1 cd02555
Pseudouridine synthase, a subgroup of the RsuA family; This group is comprised of bacterial ...
 84-231 2.50e-11

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: 61.27  E-value: 2.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  84 GIYAAGRLDRDSEGLLLLTNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVALnDGMTLPAGArimddpAVW 163
Cdd:cd02555    46 RLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLNHGLTY-DGRELPPAK------VSW 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2067215155 164 prnppIRERReiptcwLEITIVEGRNRQVRRMTAHIGHPTLRLIRYAIGEWTLDGLAPGESRALPAPE 231
Cdd:cd02555   119 -----QNEQR------LRFALKEPQPGQIRRMCESVGLEVVALRRIRIGRVSLGKLPLGQWRYLTTGE 175
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 54-202 2.97e-08

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: 52.72  E-value: 2.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  54 LLLLNKPYMVLCQFTDEGGRETLKDYI--------TEPGIYAAGRLDRDSEGLLLLTNDGKLQARLTQ--PGEKTPKTYW 123
Cdd:cd02869     1 LLVVNKPAGLPVHPGPGHLTGTLVNALlklllllgEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKqfKERKVKKTYL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 124 VQVEGIPSEEKlaalragvALNDGMTLPAGARIMDDPAVWPRNPPIR-----ERREIPTCWLEITIVEGRNRQVRRMTAH 198
Cdd:cd02869    81 ALVDGKPPEDE--------GTIDAPLGRKKRKKRARVVVSEDGKPAIthykvLERFGNVTLVELQLETGRTHQIRVHLAS 152


                  ....
gi 2067215155 199 IGHP 202
Cdd:cd02869   153 IGHP 156
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 85-204 1.00e-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: 42.71  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155  85 IYAAGRLDRDSEGLLLLTNDGKLQARLTQ--PGEKTPKTYWVQVEGIPSE---------EKLAALRAGVALNDGMTLPA- 152
Cdd:cd02563    46 VYPVHRLDRPTSGVLLFALSSEVARKLGEqfTEHRVHKTYLAVVRGYVPEsgtidyplsEELDKLADKFASDDKAPQAAt 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2067215155 153 ----GARIMDDPAVWPRNPPIRerreipTCWLEITIVEGRNRQVRRMTAHIGHPTL 204
Cdd:cd02563   126 thyrLLAVEELPVVVGKYPTSR------YSLVELTPHTGRKHQLRRHLAHIRHPII 175
PHA03378 PHA03378
EBNA-3B; Provisional
 164-300 8.58e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 37.74  E-value: 8.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2067215155 164 PRNPPIRERREIPTCWLEITIVEGRNRQVrrmtahiGHPTLRLIRYAIGEWTLDGLAPGEsraLPAPELAPAP--RPAAT 241
Cdd:PHA03378  651 PHQPPQVEITPYKPTWTQIGHIPYQPSPT-------GANTMLPIQWAPGTMQPPPRAPTP---MRPPAAPPGRaqRPAAA 720

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2067215155 242 QGKARASAAAggTGRSAPRTARPTDQDPPQGRERRgADPRQANRSGGRTTARRPARTKP 300
Cdd:PHA03378  721 TGRARPPAAA--PGRARPPAAAPGRARPPAAAPGR-ARPPAAAPGRARPPAAAPGAPTP 776
 
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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