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Conserved domains on  [gi|386768562|ref|NP_001246490|]
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nucleolar protein at 60B, isoform G [Drosophila melanogaster]

Protein Classification

pseudouridine synthase family protein; tRNA pseudouridine(13) synthase TruD( domain architecture ID 10547395)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines| tRNA pseudouridine(13) synthase TruD catalyzes the isomerization of uridines at positions 13 in tRNA 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 ...
 86-214 3.09e-88

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 cd02572:

Pssm-ID: 469624  Cd Length: 182  Bit Score: 258.35  E-value: 3.09e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  86 KTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVeSVA 165
Cdd:cd02572    1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDV-DEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 386768562 166 KVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDETRNMDLL 214
Cdd:cd02572   80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLF 128
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 47-104 1.64e-39

DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins.


:

Pssm-ID: 462353  Cd Length: 58  Bit Score: 130.02  E-value: 1.64e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 386768562   47 TSQWPLLLKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVV 104
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
 
Name Accession Description Interval E-value
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 86-214 3.09e-88

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: 258.35  E-value: 3.09e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  86 KTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVeSVA 165
Cdd:cd02572    1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDV-DEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 386768562 166 KVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDETRNMDLL 214
Cdd:cd02572   80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLF 128
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 54-209 1.20e-83

rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273073 [Multi-domain]  Cd Length: 322  Bit Score: 251.61  E-value: 1.20e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562   54 LKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVC 133
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386768562  134 IDRATRLVKSQQSAGKEYVAIFKLHGAVESvAKVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDETR 209
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKE-EDILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD 155
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
68-216 1.40e-65

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 204.71  E-value: 1.40e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  68 TPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSA 147
Cdd:PRK04270   3 TNPEYGCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLES 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386768562 148 GKEYVAIFKLHGAVeSVAKVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDEtrnMDLLIR 216
Cdd:PRK04270  83 GKEYVCVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEIDG---RDVLFR 147
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 47-104 1.64e-39

DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins.


Pssm-ID: 462353  Cd Length: 58  Bit Score: 130.02  E-value: 1.64e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 386768562   47 TSQWPLLLKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVV 104
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 88-209 1.74e-33

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: 121.70  E-value: 1.74e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  88 GFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL---------H 158
Cdd:COG0130    1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLgvetdtddaE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386768562 159 GAVE--------SVAKVRQGLEKLRGALFQRPPLISAVK-----------------RQLRVRTVYDSKLLDYDETR 209
Cdd:COG0130   81 GEVVetspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE 156
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 108-207 4.40e-33

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: 116.43  E-value: 4.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  108 KKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVES----------------VAKVRQGL 171
Cdd:pfam01509   1 KRILGAKKVGHTGTLDPLATGVLPVCVGEATKLLQYLLDADKEYVATIRLGVATDTldaegeiveesvdhitEEKIEEVL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 386768562  172 EKLRGALFQRPPLISAVK-----------------RQLRVRTVYDSKLLDYDE 207
Cdd:pfam01509  81 ASFTGEIEQVPPMYSAVKvngkrlyelaregieveRPPRPVTIYSLELLEFDL 133
 
Name Accession Description Interval E-value
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 86-214 3.09e-88

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: 258.35  E-value: 3.09e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  86 KTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVeSVA 165
Cdd:cd02572    1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDV-DEE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 386768562 166 KVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDETRNMDLL 214
Cdd:cd02572   80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLF 128
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 54-209 1.20e-83

rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273073 [Multi-domain]  Cd Length: 322  Bit Score: 251.61  E-value: 1.20e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562   54 LKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVC 133
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386768562  134 IDRATRLVKSQQSAGKEYVAIFKLHGAVESvAKVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDETR 209
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKE-EDILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD 155
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
68-216 1.40e-65

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 204.71  E-value: 1.40e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  68 TPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSA 147
Cdd:PRK04270   3 TNPEYGCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLES 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386768562 148 GKEYVAIFKLHGAVeSVAKVRQGLEKLRGALFQRPPLISAVKRQLRVRTVYDSKLLDYDEtrnMDLLIR 216
Cdd:PRK04270  83 GKEYVCVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEIDG---RDVLFR 147
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 88-210 1.01e-44

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: 148.46  E-value: 1.01e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  88 GFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVE----- 162
Cdd:cd00506    1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDtfdat 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386768562 163 ------------SVAKVRQGLEKLRGALFQRPPLISAVKRQ-----------------LRVRTVYDSKLLDYDETRN 210
Cdd:cd00506   81 gqvieetpydhiTHEQLERALETLTGDIQQVPPLYSAVKRQgqrayelarrgllvpdeARPPTIYELLCIRFNPPHF 157
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 47-104 1.64e-39

DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins.


Pssm-ID: 462353  Cd Length: 58  Bit Score: 130.02  E-value: 1.64e-39
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 386768562   47 TSQWPLLLKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVV 104
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 88-209 1.74e-33

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: 121.70  E-value: 1.74e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  88 GFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL---------H 158
Cdd:COG0130    1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLgvetdtddaE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386768562 159 GAVE--------SVAKVRQGLEKLRGALFQRPPLISAVK-----------------RQLRVRTVYDSKLLDYDETR 209
Cdd:COG0130   81 GEVVetspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE 156
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 108-207 4.40e-33

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: 116.43  E-value: 4.40e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  108 KKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVES----------------VAKVRQGL 171
Cdd:pfam01509   1 KRILGAKKVGHTGTLDPLATGVLPVCVGEATKLLQYLLDADKEYVATIRLGVATDTldaegeiveesvdhitEEKIEEVL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 386768562  172 EKLRGALFQRPPLISAVK-----------------RQLRVRTVYDSKLLDYDE 207
Cdd:pfam01509  81 ASFTGEIEQVPPMYSAVKvngkrlyelaregieveRPPRPVTIYSLELLEFDL 133
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 88-210 2.09e-32

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: 116.77  E-value: 2.09e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  88 GFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL---------H 158
Cdd:cd02573    1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLgeatdtddaE 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386768562 159 GAVE--------SVAKVRQGLEKLRGALFQRPPLISAVK----------RQ-----LRVR--TVYDSKLLDYDETRN 210
Cdd:cd02573   81 GEIIetsppprlTEEEIEAALKAFTGEIEQVPPMYSAVKvdgkrlyelaRAgeeveRPPRkvTIYSLELLSFDPENP 157
TruB TIGR00431
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
 88-206 3.92e-25

tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129523  Cd Length: 209  Bit Score: 97.82  E-value: 3.92e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562   88 GFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL---------H 158
Cdd:TIGR00431   3 GVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLgvrtdtldpD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386768562  159 GAV-------ESVAKVRQGLEKLRGALFQRPPLISAVK-----------------RQLRVRTVYDSKLLDYD 206
Cdd:TIGR00431  83 GQIvetrpvnPTTEDVEAALPTFRGEIEQIPPMYSALKvngkrlyeyarqgieveRKARPVTVYDLQFLKYE 154
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 88-207 4.15e-12

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: 63.99  E-value: 4.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  88 GFINLDKPSNPSSHEVVAWIKKILKVE-----------------------------KTGHSGTLDPKVTGCLIVCIDRAT 138
Cdd:cd02867    1 GVFAINKPSGITSAQVLNDLKPLFLNSalfkdkiqravakrgkkarrrkgrkrsklKIGHGGTLDPLATGVLVVGVGAGT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562 139 RLVKSQQSAGKEYVAIfKLHGA----------------VESVAK--VRQGLEKLRGALFQRPPLISAVKRQ--------- 191
Cdd:cd02867   81 KQLQDYLSCSKTYEAT-GLFGAstttydregkilkkkpYSHITRedIEEVLAKFRGDIKQVPPLYSALKMDgkrlyeyar 159

                        170       180
                 ....*....|....*....|....*.
gi 386768562 192 ----------LRVRTVYDSKLLDYDE 207
Cdd:cd02867  160 egkplprpieRRQVVVSELLVKDWIE 185
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 92-189 2.30e-08

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 53.22  E-value: 2.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  92 LDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL---------HGAVE 162
Cdd:PRK02193   5 LYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIKFgfisttydsEGQII 84

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 386768562 163 SVA--------KVRQGLEKLRGALFQRPPLISAVK 189
Cdd:PRK02193  85 NVSqnikvtkeNLEEALNNLVGSQKQVPPVFSAKK 119
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 85-207 7.63e-08

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 51.95  E-value: 7.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768562  85 MKTGFINLDKPSNPSSHEVVAWIKKILKVEKTGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKL------- 157
Cdd:PRK14846   1 MSNYWLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFgmqtnsg 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386768562 158 ---------HGAVESVAKVRQGLEKLRGALFQRPPLISAVK---------------RQLRVR--TVYDSKLLDYDE 207
Cdd:PRK14846  81 dcagkviatKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKvngvrayklaregkkVELKPRniTIYDLKCLNFDE 156
 
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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