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Conserved domains on  [gi|119874623|gb|ABM05788|]
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dyskerin, partial [Archispirostreptus gigas]

Protein Classification

CBF5 family protein( domain architecture ID 1001675)

CBF5 (centromere-binding factor 5) family protein such as Homo sapiens H/ACA ribonucleoprotein complex subunit DKC1, which is the catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA

Gene Ontology:  GO:0003723|GO:0006364
PubMed:  21149572|18178425

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CBF5 super family cl36650
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 1-233 2.65e-127

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]


The actual alignment was detected with superfamily member TIGR00425:

Pssm-ID: 273073 [Multi-domain]  Cd Length: 322  Bit Score: 362.55  E-value: 2.65e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623    1 DRATRLVKSQQSAGKEYVCILKLHEAVESEkQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQnmVIF 80
Cdd:TIGR00425  82 ERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VLF 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   81 WVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTMHDLLDAQWLYDNHKDESLLRRVIKPLEALLVSH 160
Cdd:TIGR00425 159 RVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHL 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119874623  161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:TIGR00425 238 KRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRV 310
 
Name Accession Description Interval E-value
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 1-233 2.65e-127

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: 362.55  E-value: 2.65e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623    1 DRATRLVKSQQSAGKEYVCILKLHEAVESEkQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQnmVIF 80
Cdd:TIGR00425  82 ERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VLF 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   81 WVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTMHDLLDAQWLYDNHKDESLLRRVIKPLEALLVSH 160
Cdd:TIGR00425 159 RVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHL 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119874623  161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:TIGR00425 238 KRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRV 310
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
2-233 4.06e-94

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 277.51  E-value: 4.06e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEAVeSEKQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQnmVIFW 81
Cdd:PRK04270  71 KATKVVQALLESGKEYVCVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEIDGRD--VLFR 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  82 VKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTMHDLLDAQWLYDNHKDESLLRRVIKPLEALLVSHK 161
Cdd:PRK04270 148 VRCESGTYIRKLCHDIGLALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLP 226

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119874623 162 RIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:PRK04270 227 KIIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERV 298
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 1-134 3.24e-87

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: 256.03  E-value: 3.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   1 DRATRLVKSQQSAGKEYVCILKLHEAVeSEKQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQNMVIF 80
Cdd:cd02572   50 DRATRLVKSQQEAGKEYVCVMRLHDDV-DEEKVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLF 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119874623  81 WVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEHDNLVTMHDLLDAQ 134
Cdd:cd02572  129 RVSCEAGTYIRTLCVHIGLLLGVGAHMQELRRTRSGPFSEEDNMVTLHDVLDAQ 182
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 2-210 4.62e-30

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: 112.84  E-value: 4.62e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEA----------VE-------SEKQIALALETLTGAQFQRPPLISAVK--------- 55
Cdd:COG0130   49 EATKLSQYLLDADKTYRATIRLGVEtdtddaegevVEtspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyel 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  56 --------RQLRIRTIYESKLLEYnsEQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTM 127
Cdd:COG0130  129 arageeveRPPRPVTIYSLELLSF--DAPELTLEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTRVGPFTL-EDAVTL 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 128 HDLLDAqwlydnhkDESLLRRVIKPLEALLVSHKRIIVKDSAVNAICYGAKIMLPGVLrydngieLNQEIVIVTTKGEAV 207
Cdd:COG0130  206 EELEEL--------AEGALDALLLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFL 270


                 ...
gi 119874623 208 ALA 210
Cdd:COG0130  271 ALG 273
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 91-157 6.12e-29

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: 103.32  E-value: 6.12e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119874623   91 RTLCVHLGLVLGVGGKMQELRRVRSGIQSEHDnLVTMHDLLDAQWLYDNHkDESLLRRVIKPLEALL 157
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEAD-MVTLHDLLDAYLLYKEG-DESYLRRVLLPLESAL 65
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
161-233 9.17e-18

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 74.99  E-value: 9.17e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119874623   161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCD-HGVVAKIKRV 233
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRA 74
 
Name Accession Description Interval E-value
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 1-233 2.65e-127

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: 362.55  E-value: 2.65e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623    1 DRATRLVKSQQSAGKEYVCILKLHEAVESEkQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQnmVIF 80
Cdd:TIGR00425  82 ERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VLF 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   81 WVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTMHDLLDAQWLYDNHKDESLLRRVIKPLEALLVSH 160
Cdd:TIGR00425 159 RVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHL 237

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119874623  161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:TIGR00425 238 KRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRV 310
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
2-233 4.06e-94

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 277.51  E-value: 4.06e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEAVeSEKQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQnmVIFW 81
Cdd:PRK04270  71 KATKVVQALLESGKEYVCVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEIDGRD--VLFR 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  82 VKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTMHDLLDAQWLYDNHKDESLLRRVIKPLEALLVSHK 161
Cdd:PRK04270 148 VRCESGTYIRKLCHDIGLALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLP 226

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 119874623 162 RIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:PRK04270 227 KIIIKDSAVDAIAHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERV 298
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 1-134 3.24e-87

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: 256.03  E-value: 3.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   1 DRATRLVKSQQSAGKEYVCILKLHEAVeSEKQIALALETLTGAQFQRPPLISAVKRQLRIRTIYESKLLEYNSEQNMVIF 80
Cdd:cd02572   50 DRATRLVKSQQEAGKEYVCVMRLHDDV-DEEKVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLF 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119874623  81 WVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEHDNLVTMHDLLDAQ 134
Cdd:cd02572  129 RVSCEAGTYIRTLCVHIGLLLGVGAHMQELRRTRSGPFSEEDNMVTLHDVLDAQ 182
PUA_Cbf5 cd21148
PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5; The RNA-binding ...
 159-233 1.44e-44

PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of the archaeal and eukaryotic subfamily of pseudouridine synthases, including Cbf5 (dyskerin in humans) and similar proteins, are modules that assist in the binding and positioning (guide and/or substrate) of RNA to the pseudouridine synthase complex. Pseudouridine synthases are enzymes that are responsible for post-translational modifications of RNAs by specifically isomerizing uracil residues. In Pyrococcus furiosus H/ACA ribonucleoprotein (RNP) assembly with a single-hairpin H/ACA RNA, the lower stem and the ACA motif of the guide RNA are anchored at the PUA domain of Cbf5. In addition, the N-terminal extension of Cbf5, which is a hot spot for dyskeratosis congenita (a rare genetic form of bone marrow failure) mutation, forms an extra structural layer on the PUA domain.


Pssm-ID: 409290 [Multi-domain]  Cd Length: 75  Bit Score: 143.76  E-value: 1.44e-44
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 119874623 159 SHKRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:cd21148    1 HLPRIVIKDSAVNAICYGAKLAIPGVLRYEDGIEKGDEVVIMTTKGEAVALGIALMTTAEIATCDHGIVAKIKRV 75
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 2-130 8.62e-41

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: 138.83  E-value: 8.62e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEAVESE-----------------KQIALALETLTGAQFQRPPLISAVKRQ------- 57
Cdd:cd00506   49 KATKLLKHLLAATKDYTAIGRLGQATDTFdatgqvieetpydhithEQLERALETLTGDIQQVPPLYSAVKRQgqrayel 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  58 ----------LRIRTIYESKLLEYNSEQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTM 127
Cdd:cd00506  129 arrgllvpdeARPPTIYELLCIRFNPPHFLLEVEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPFKV-ENAVTL 207


                 ...
gi 119874623 128 HDL 130
Cdd:cd00506  208 HHL 210
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 2-210 4.62e-30

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: 112.84  E-value: 4.62e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEA----------VE-------SEKQIALALETLTGAQFQRPPLISAVK--------- 55
Cdd:COG0130   49 EATKLSQYLLDADKTYRATIRLGVEtdtddaegevVEtspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyel 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  56 --------RQLRIRTIYESKLLEYnsEQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEhDNLVTM 127
Cdd:COG0130  129 arageeveRPPRPVTIYSLELLSF--DAPELTLEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTRVGPFTL-EDAVTL 205

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 128 HDLLDAqwlydnhkDESLLRRVIKPLEALLVSHKRIIVKDSAVNAICYGAKIMLPGVLrydngieLNQEIVIVTTKGEAV 207
Cdd:COG0130  206 EELEEL--------AEGALDALLLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFL 270


                 ...
gi 119874623 208 ALA 210
Cdd:COG0130  271 ALG 273
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 91-157 6.12e-29

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: 103.32  E-value: 6.12e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119874623   91 RTLCVHLGLVLGVGGKMQELRRVRSGIQSEHDnLVTMHDLLDAQWLYDNHkDESLLRRVIKPLEALL 157
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEAD-MVTLHDLLDAYLLYKEG-DESYLRRVLLPLESAL 65
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 2-116 7.47e-24

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: 94.82  E-value: 7.47e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   2 RATRLVKSQQSAGKEYVCILKLHEA----------VE-------SEKQIALALETLTGAQFQRPPLISAVKRQ------- 57
Cdd:cd02573   49 EATKLSQYLLDADKTYRATVRLGEAtdtddaegeiIEtsppprlTEEEIEAALKAFTGEIEQVPPMYSAVKVDgkrlyel 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 119874623  58 --------LRIR--TIYESKLLEYNSEQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSG 116
Cdd:cd02573  129 arageeveRPPRkvTIYSLELLSFDPENPEADFEVHCSKGTYIRSLARDLGKALGCGAHLSALRRTRSG 197
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 161-233 8.73e-22

PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain.


Pssm-ID: 426278 [Multi-domain]  Cd Length: 74  Bit Score: 85.23  E-value: 8.73e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 119874623  161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTEKGELVAVGLANYSSEELAKIEGGKAVKVRRV 73
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 2-90 9.66e-19

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: 79.45  E-value: 9.66e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623    2 RATRLVKSQQSAGKEYVCILKLHEAVES----------------EKQIALALETLTGAQFQRPPLISAVK---------- 55
Cdd:pfam01509  29 EATKLLQYLLDADKEYVATIRLGVATDTldaegeiveesvdhitEEKIEEVLASFTGEIEQVPPMYSAVKvngkrlyela 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 119874623   56 -------RQLRIRTIYESKLLEYNSEQnmVIFWVKCEAGTYI 90
Cdd:pfam01509 109 regieveRPPRPVTIYSLELLEFDLPE--VTFRVTCSKGTYI 148
TruB TIGR00431
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
 2-116 6.58e-18

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: 78.95  E-value: 6.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623    2 RATRLVKSQQSAGKEYVCILKLH----------EAVESEK------QIALALETLTGAQFQRPPLISAVK---------- 55
Cdd:TIGR00431  51 KATKLSPYLTDLDKEYRAEIRLGvrtdtldpdgQIVETRPvnptteDVEAALPTFRGEIEQIPPMYSALKvngkrlyeya 130

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119874623   56 -------RQLRIRTIYESKLLEYNseQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSG 116
Cdd:TIGR00431 131 rqgieveRKARPVTVYDLQFLKYE--GPELTLEVHCSKGTYIRTLARDLGEKLGCGAYVSHLRRTAVG 196
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
161-233 9.17e-18

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 74.99  E-value: 9.17e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119874623   161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCD-HGVVAKIKRV 233
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRA 74
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 161-230 2.37e-10

PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, and a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was also found in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in regulating the expression of other genes. It has been shown that the PUA domain acts as an RNA binding domain in at least some of the proteins involved in RNA metabolism.


Pssm-ID: 409289 [Multi-domain]  Cd Length: 73  Bit Score: 54.99  E-value: 2.37e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKI 230
Cdd:cd07953    1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSEGGRPLAIGVAEMSSDEMKEELKGIAVRV 70
PRK13795 PRK13795
hypothetical protein; Provisional
 142-233 5.93e-10

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 58.47  E-value: 5.93e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 142 DESLLRRVIKPLE---ALLVSHKR---IIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMT 215
Cdd:PRK13795 102 DLLELRWRFEPRLegaKRLLKKRLkkwVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMD 181

                         90
                 ....*....|....*...
gi 119874623 216 TATIASCDHGVVAKIKRV 233
Cdd:PRK13795 182 GDDMIKRFRGRAVKVRKS 199
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 161-229 2.69e-09

PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this mostly archaeal family have not been characterized functionally; they may bind to RNA. This family includes Pyrococcus horikoshii PH0734 where the N-terminal domain may modulate the binding target of the C-terminal PUA domain using its characteristic electropositive surface.


Pssm-ID: 409296 [Multi-domain]  Cd Length: 84  Bit Score: 52.51  E-value: 2.69e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVT-TKGEAVALAIALMTTATIASCDHGVVAK 229
Cdd:cd21154    3 PRVVVDMGAVKFVANGADVMRPGIVEADEEIKKGDIVVVVDeRHGKPLAVGIALMSGEEMVEMKKGKAVK 72
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 31-116 1.25e-07

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 50.91  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  31 KQIALALETLTGAQFQRPPLISAVK----------RQ--------LRIRtIYESKLLEYNSEQNMVIFWVKCEAGTYIRT 92
Cdd:PRK02193  95 ENLEEALNNLVGSQKQVPPVFSAKKvngkraydlaRQgkqielkpIEIK-ISKIELLNFDEKLQNCVFMWVVSRGTYIRS 173

                         90       100
                 ....*....|....*....|....
gi 119874623  93 LCVHLGLVLGVGGKMQELRRVRSG 116
Cdd:PRK02193 174 LIHDLGKMLKTGAYMSDLERTKIG 197
PRK13794 PRK13794
hypothetical protein; Provisional
 161-232 1.03e-05

hypothetical protein; Provisional


Pssm-ID: 237509 [Multi-domain]  Cd Length: 479  Bit Score: 45.81  E-value: 1.03e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119874623 161 KRII-VKDSAVNAI-CYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKR 232
Cdd:PRK13794 124 KKFIvVKDDVPKFIrNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEEIVNMEKGMVVKVRK 197
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 9-181 2.02e-05

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 44.64  E-value: 2.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623   9 SQQSAGKEYVCILKLHEAVESEKQIALALETLTGAQFQRPPLISAVKR---------------QLRIR--TIYESKLLEY 71
Cdd:PRK14846  75 MQTNSGDCAGKVIATKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKVngvrayklaregkkvELKPRniTIYDLKCLNF 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  72 NSEQNMVIFWVKCEAGTYIRTLCVHLGLVLGVGGKMQELRRVRSGIQSEHDNL-VTMHDLLDAQWLYDNHkdesllrrvI 150
Cdd:PRK14846 155 DEKNATATYYTECSKGTYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEENAIrIKSPDEITKNALEEKS---------I 225

                        170       180       190
                 ....*....|....*....|....*....|.
gi 119874623 151 KpLEALLVSHKRIIVKDSAVNAICYGAKIML 181
Cdd:PRK14846 226 K-IEAILDDILVLDATDSQAQQIKYGQKCLF 255
PUA_archaeosine_TGT cd21149
PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase; The RNA-binding PUA ...
 160-233 4.04e-05

PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this archaeosine tRNA-guanine transglycosylase (TGT) family are responsible for the exchange of a guanine residue in archaeal tRNAs with a preQ0 base (7-cyano-7-deazaguanine), which constitutes the initial step in archaeosine biosynthesis. Archaeosine is a modified RNA base specific to archaea (7-formamidino-7deazaguanosine), found at position 15 in tRNAs. It has been shown that the PUA domain of archaeosine TGT is not required for its specificity for position 15.


Pssm-ID: 409291 [Multi-domain]  Cd Length: 75  Bit Score: 40.67  E-value: 4.04e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119874623 160 HKRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVTTKGEAVALAIALMTTATIASCDHGVVAKIKRV 233
Cdd:cd21149    2 ENRVVVNKESAPFVRKGGSVFAKGVVDADENIRPGDEVLVVDEDDRLLAVGRAVLSGKEMKEFERGVAVKVRHG 75
unchar_dom_2 TIGR00451
uncharacterized domain 2; This uncharacterized domain is found a number of enzymes and ...
 130-229 4.98e-05

uncharacterized domain 2; This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.


Pssm-ID: 129543 [Multi-domain]  Cd Length: 107  Bit Score: 41.26  E-value: 4.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  130 LLDAQWLYDNHKDESLLRrvIKPLEALLVSHKRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVT-TKGEAVA 208
Cdd:TIGR00451   2 LVDGEPLYFIYDDKVIPS--LKGALKLMEDKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDeNKDRPLA 79

                          90       100
                  ....*....|....*....|.
gi 119874623  209 LAIALMTTATIASCDHGVVAK 229
Cdd:TIGR00451  80 VGIALMSGEEMKEMDKGKAVK 100
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 161-229 7.79e-05

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 41.76  E-value: 7.79e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623 161 KRIIVKDSAVNAICYGAKIMLPGVLRYDNGIELNQEIVIVT-TKGEAVALAIALMTTATIASCDHGVVAK 229
Cdd:PRK14560  77 RRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEeTHGKPLAVGRALMDGDEMVEEKKGKAVK 146
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 32-128 1.21e-03

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: 39.34  E-value: 1.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119874623  32 QIALALETLTGAQFQRPPLISAVKRQ-------------------LRIRTIYESKLLEYNSEQNMVIFWVKCEAGTYIRT 92
Cdd:cd02867  125 DIEEVLAKFRGDIKQVPPLYSALKMDgkrlyeyaregkplprpieRRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERS 204

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 119874623  93 LCVHLGLVLGVGGKMQELRRVRSGIQSEHDNLVTMH 128
Cdd:cd02867  205 VVKMLGKELKTFAEVTELTATAEGDPVEEVEATHEE 240
 
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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