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Conserved domains on  [gi|1958648062|ref|XP_038940651|]
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pseudouridylate synthase TRUB1 isoform X4 [Rattus norvegicus]

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
TruB super family cl33772
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 34-121 1.78e-35

tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG0130:

Pssm-ID: 439900 [Multi-domain]  Cd Length: 288  Bit Score: 125.16  E-value: 1.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQPPFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELTRTK 113
Cdd:COG0130   115 YSAIKVDGKRLYELARAGEEVE-RPPRPVTIYSLELLSFDAPELTLEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTR 193


                  ....*...
gi 1958648062 114 QGPFTLAQ 121
Cdd:COG0130   194 VGPFTLED 201
 
Name Accession Description Interval E-value
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 34-121 1.78e-35

tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439900 [Multi-domain]  Cd Length: 288  Bit Score: 125.16  E-value: 1.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQPPFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELTRTK 113
Cdd:COG0130   115 YSAIKVDGKRLYELARAGEEVE-RPPRPVTIYSLELLSFDAPELTLEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTR 193


                  ....*...
gi 1958648062 114 QGPFTLAQ 121
Cdd:COG0130   194 VGPFTLED 201
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 34-179 3.02e-32

Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).


Pssm-ID: 211344 [Multi-domain]  Cd Length: 312  Bit Score: 117.54  E-value: 3.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEARPARPVTVHSISLLKYQP---PFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELT 110
Cdd:cd02867   144 YSALKMDGKRLYEYAREGKPLPRPIERRQVVVSELLVKDWIepgPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVTELT 223

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958648062 111 RTKQGPFTLAQHALPEDRWTINDIAQSlKRCTSLLPEELTFKKSKSE-------PSSDQALSCGYITLRETKREDD 179
Cdd:cd02867   224 ATAEGDPVEEVEATHEESKRKSEVEEE-ANEKSLGPEARSLESDAGRgsfspaaMVRLARVGQGTYIRQDVKLIRT 298
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 34-89 3.08e-20

TruB family pseudouridylate synthase (N terminal domain); 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 TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.


Pssm-ID: 426297  Cd Length: 148  Bit Score: 82.14  E-value: 3.08e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQPPFFTLDVECGGGFYI 89
Cdd:pfam01509  94 YSAVKVNGKRLYELAREGIEVE-RPPRPVTIYSLELLEFDLPEVTFRVTCSKGTYI 148
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 34-117 8.01e-10

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 56.30  E-value: 8.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEARPArPVTVHSISLLKYQPPFFTLDVE--CGGGFYIRSLVSDIGKELSSCATVLELTR 111
Cdd:PRK02193  115 FSAKKVNGKRAYDLARQGKQIELKPI-EIKISKIELLNFDEKLQNCVFMwvVSRGTYIRSLIHDLGKMLKTGAYMSDLER 193


                  ....*.
gi 1958648062 112 TKQGPF 117
Cdd:PRK02193  194 TKIGNL 199
 
Name Accession Description Interval E-value
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 34-121 1.78e-35

tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439900 [Multi-domain]  Cd Length: 288  Bit Score: 125.16  E-value: 1.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQPPFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELTRTK 113
Cdd:COG0130   115 YSAIKVDGKRLYELARAGEEVE-RPPRPVTIYSLELLSFDAPELTLEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTR 193


                  ....*...
gi 1958648062 114 QGPFTLAQ 121
Cdd:COG0130   194 VGPFTLED 201
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 34-179 3.02e-32

Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).


Pssm-ID: 211344 [Multi-domain]  Cd Length: 312  Bit Score: 117.54  E-value: 3.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEARPARPVTVHSISLLKYQP---PFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELT 110
Cdd:cd02867   144 YSALKMDGKRLYEYAREGKPLPRPIERRQVVVSELLVKDWIepgPLFTRTVEEEGKQYERSVVKMLGKELKTFAEVTELT 223

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958648062 111 RTKQGPFTLAQHALPEDRWTINDIAQSlKRCTSLLPEELTFKKSKSE-------PSSDQALSCGYITLRETKREDD 179
Cdd:cd02867   224 ATAEGDPVEEVEATHEESKRKSEVEEE-ANEKSLGPEARSLESDAGRgsfspaaMVRLARVGQGTYIRQDVKLIRT 298
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 34-121 1.28e-31

Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.


Pssm-ID: 211339 [Multi-domain]  Cd Length: 213  Bit Score: 113.31  E-value: 1.28e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQP--PFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELTR 111
Cdd:cd02573   115 YSAVKVDGKRLYELARAGEEVE-RPPRKVTIYSLELLSFDPenPEADFEVHCSKGTYIRSLARDLGKALGCGAHLSALRR 193

                          90
                  ....*....|
gi 1958648062 112 TKQGPFTLAQ 121
Cdd:cd02573   194 TRSGPFTLEQ 203
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 32-129 5.85e-26

Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dyskerin cause X-linked dyskeratosis congenitas.


Pssm-ID: 211323 [Multi-domain]  Cd Length: 210  Bit Score: 98.77  E-value: 5.85e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  32 ICYSALKKDGQRLSTLMKRGETVEARPaRPVTVHSISLLKYQPPFFTLDVE--CGGGFYIRSLVSDIGKELSSCATVLEL 109
Cdd:cd00506   113 PLYSAVKRQGQRAYELARRGLLVPDEA-RPPTIYELLCIRFNPPHFLLEVEvvCETGTYIRTLIHDLGLELGVGAHVTEL 191

                          90       100
                  ....*....|....*....|
gi 1958648062 110 TRTKQGPFTLaQHALPEDRW 129
Cdd:cd00506   192 RRTRVGPFKV-ENAVTLHHL 210
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 34-89 3.08e-20

TruB family pseudouridylate synthase (N terminal domain); 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 TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.


Pssm-ID: 426297  Cd Length: 148  Bit Score: 82.14  E-value: 3.08e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEaRPARPVTVHSISLLKYQPPFFTLDVECGGGFYI 89
Cdd:pfam01509  94 YSAVKVNGKRLYELAREGIEVE-RPPRPVTIYSLELLEFDLPEVTFRVTCSKGTYI 148
PseudoU_synth_hTruB2_like cd02868
Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine ...
 57-138 1.21e-12

Pseudouridine synthase, humanTRUB2_like; This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).


Pssm-ID: 211345 [Multi-domain]  Cd Length: 226  Bit Score: 63.56  E-value: 1.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  57 RPA--RPVTVHSISLLKYQPPFFTLDVECGGGF--YIRSLVSDIGKELSSCATVLELTRTKQGPFTLaQHALPEDRWTIN 132
Cdd:cd02868   142 RPAdkSPPIIYGIRLLEFRPPEFTLEVQCINETqeYLRKLIHEIGLELRSSAVCTQVRRTRDGPFTV-DDALLRKQWNLQ 220


                  ....*.
gi 1958648062 133 DIAQSL 138
Cdd:cd02868   221 NIISNI 226
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 34-117 8.01e-10

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 56.30  E-value: 8.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEARPArPVTVHSISLLKYQPPFFTLDVE--CGGGFYIRSLVSDIGKELSSCATVLELTR 111
Cdd:PRK02193  115 FSAKKVNGKRAYDLARQGKQIELKPI-EIKISKIELLNFDEKLQNCVFMwvVSRGTYIRSLIHDLGKMLKTGAYMSDLER 193


                  ....*.
gi 1958648062 112 TKQGPF 117
Cdd:PRK02193  194 TKIGNL 199
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 34-117 4.70e-08

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 51.57  E-value: 4.70e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  34 YSALKKDGQRLSTLMKRGETVEARPaRPVTVHSISLLKYQPPFFTLD--VECGGGFYIRSLVSDIGKELSSCATVLELTR 111
Cdd:PRK14846  117 FSALKVNGVRAYKLAREGKKVELKP-RNITIYDLKCLNFDEKNATATyyTECSKGTYIRTLAEDLALSLQSLGFVIELRR 195


                  ....*.
gi 1958648062 112 TKQGPF 117
Cdd:PRK14846  196 TQVGIF 201
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
56-118 5.95e-07

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 48.31  E-value: 5.95e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958648062  56 ARPARPVTVHSISLLKYQPPFFTLDVECGGGFYIRSLVSDIGKELSSCATVLELTRTKQGPFT 118
Cdd:PRK04270  123 KRRLRVRTIYELEILEIDGRDVLFRVRCESGTYIRKLCHDIGLALGTGAHMQELRRTRTGPFT 185
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 56-118 2.15e-05

Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl results in miniflies that suffer abnormalities.


Pssm-ID: 211338  Cd Length: 182  Bit Score: 43.02  E-value: 2.15e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958648062  56 ARPARPVTVHSISLLKYQPPF--FTLDVECGGGFYIRSLVSDIGKELSSCATVLELTRTKQGPFT 118
Cdd:cd02572   103 KRQLRVRTIYESKLLEYDGERrlVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELRRTRSGPFS 167
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 90-149 4.45e-04

tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset of TruB_B protein family members pfam01509. It is found from bacteria and archaea to fungi, plants and human.


Pssm-ID: 465060 [Multi-domain]  Cd Length: 65  Bit Score: 37.07  E-value: 4.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958648062  90 RSLVSDIGKELSSCATVLELTRTKQGPFTLAqhalpeDRWTINDIAQSLKRCTSLLPEEL 149
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEA------DMVTLHDLLDAYLLYKEGDESYL 54
 
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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