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Conserved domains on  [gi|17553978|ref|NP_499370|]
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Putative H/ACA ribonucleoprotein complex subunit 4 [Caenorhabditis elegans]

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 ...
 44-369 5.66e-174

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: 490.05  E-value: 5.66e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978    44 LKNYDKLNVRTNHYTPHVEGVSPLKRDIKNYISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVC 123
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   124 IDRTTRLAKSQQGAGKEYICIFKLHEEVEDDRkVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDPaqQMGI 203
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEED-ILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDG--KDVL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGiCDENENMVTMHDVLDAQYLLDTQKDESYMRHIVRPLEALLTQ 283
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSG-CFGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   284 HKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVIMERDV 363
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 17553978   364 YGRKWG 369
Cdd:TIGR00425 317 YPRMWK 322
 
Name Accession Description Interval E-value
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 44-369 5.66e-174

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: 490.05  E-value: 5.66e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978    44 LKNYDKLNVRTNHYTPHVEGVSPLKRDIKNYISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVC 123
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   124 IDRTTRLAKSQQGAGKEYICIFKLHEEVEDDRkVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDPaqQMGI 203
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEED-ILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDG--KDVL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGiCDENENMVTMHDVLDAQYLLDTQKDESYMRHIVRPLEALLTQ 283
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSG-CFGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   284 HKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVIMERDV 363
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 17553978   364 YGRKWG 369
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 76-258 4.25e-127

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: 365.43  E-value: 4.25e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  76 SSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEEVeDDR 155
Cdd:cd02572   1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDV-DEE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 156 KVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDPAQQMGIFNCICESGTYVRTICVHLGLILGCGGQMQELR 235
Cdd:cd02572  80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                       170       180
                ....*....|....*....|...
gi 17553978 236 RNRSGICDENENMVTMHDVLDAQ 258
Cdd:cd02572 160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
63-359 1.08e-122

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 358.79  E-value: 1.08e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   63 GVSPLKRDIKNYISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYI 142
Cdd:PRK04270   8 GCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  143 CIFKLHEEVeDDRKVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDpaQQMGIFNCICESGTYVRTICVHLG 222
Cdd:PRK04270  88 CVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID--GRDVLFRVRCESGTYIRKLCHDIG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  223 LILGCGGQMQELRRNRSGICDEnENMVTMHDVLDAQYLLDTQKDESYMRHIVRPLEALLTQHKRVVVKDSCINAICYGAK 302
Cdd:PRK04270 165 LALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAIAHGAP 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 17553978  303 ILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVIM 359
Cdd:PRK04270 244 LYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 78-358 1.23e-51

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: 175.62  E-value: 1.23e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  78 GFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEE------- 150
Cdd:COG0130   1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLGVEtdtddae 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 151 ---VE-------DDRKVKQALEKLTGALFQRPPLISAVK-----------------RQLRIRTVYENKFIEYDPAQqmGI 203
Cdd:COG0130  81 gevVEtspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--LT 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGICDEnENMVTMHDVldaqylldTQKDESYMRHIVRPLEALLTQ 283
Cdd:COG0130 159 LEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTRVGPFTL-EDAVTLEEL--------EELAEGALDALLLPVDEALAD 229

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17553978 284 HKRVVVKDSCINAICYGAKILIPGILrydddieVGKEIVIMSTKGEAICIAIaqmntstiasVDHGVVaKSKRVI 358
Cdd:COG0130 230 LPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFLALGE----------IEDGRL-KPKRVF 286
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 37-94 1.97e-35

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: 125.02  E-value: 1.97e-35
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 17553978    37 ASQWPLLLKNYDKLNVRTNHYTPHVEGVSPLKRDIKNYISSGFFNLDKPSNPSSHEVV 94
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
285-359 8.08e-19

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 80.38  E-value: 8.08e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17553978    285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVD-HGVVAKSKRVIM 359
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRAVM 76
 
Name Accession Description Interval E-value
CBF5 TIGR00425
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
 44-369 5.66e-174

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: 490.05  E-value: 5.66e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978    44 LKNYDKLNVRTNHYTPHVEGVSPLKRDIKNYISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVC 123
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   124 IDRTTRLAKSQQGAGKEYICIFKLHEEVEDDRkVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDPaqQMGI 203
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEED-ILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDG--KDVL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGiCDENENMVTMHDVLDAQYLLDTQKDESYMRHIVRPLEALLTQ 283
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSG-CFGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   284 HKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVIMERDV 363
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 17553978   364 YGRKWG 369
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 76-258 4.25e-127

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: 365.43  E-value: 4.25e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  76 SSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEEVeDDR 155
Cdd:cd02572   1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDV-DEE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 156 KVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDPAQQMGIFNCICESGTYVRTICVHLGLILGCGGQMQELR 235
Cdd:cd02572  80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                       170       180
                ....*....|....*....|...
gi 17553978 236 RNRSGICDENENMVTMHDVLDAQ 258
Cdd:cd02572 160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
63-359 1.08e-122

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 358.79  E-value: 1.08e-122
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   63 GVSPLKRDIKNYISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYI 142
Cdd:PRK04270   8 GCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  143 CIFKLHEEVeDDRKVKQALEKLTGALFQRPPLISAVKRQLRIRTVYENKFIEYDpaQQMGIFNCICESGTYVRTICVHLG 222
Cdd:PRK04270  88 CVMHLHGDV-PEEDIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID--GRDVLFRVRCESGTYIRKLCHDIG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  223 LILGCGGQMQELRRNRSGICDEnENMVTMHDVLDAQYLLDTQKDESYMRHIVRPLEALLTQHKRVVVKDSCINAICYGAK 302
Cdd:PRK04270 165 LALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAIAHGAP 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 17553978  303 ILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVIM 359
Cdd:PRK04270 244 LYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 78-254 8.19e-68

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: 215.10  E-value: 8.19e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  78 GFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLH--------- 148
Cdd:cd00506   1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGqatdtfdat 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 149 ----EEVEDDR----KVKQALEKLTGALFQRPPLISAVKRQ-----------------LRIRTVYENKFIEYDPAQQMGI 203
Cdd:cd00506  81 gqviEETPYDHitheQLERALETLTGDIQQVPPLYSAVKRQgqrayelarrgllvpdeARPPTIYELLCIRFNPPHFLLE 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 17553978 204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGICdENENMVTMHDV 254
Cdd:cd00506 161 VEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPF-KVENAVTLHHL 210
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 78-358 1.23e-51

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: 175.62  E-value: 1.23e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  78 GFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEE------- 150
Cdd:COG0130   1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLGVEtdtddae 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 151 ---VE-------DDRKVKQALEKLTGALFQRPPLISAVK-----------------RQLRIRTVYENKFIEYDPAQqmGI 203
Cdd:COG0130  81 gevVEtspvprlTEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--LT 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGICDEnENMVTMHDVldaqylldTQKDESYMRHIVRPLEALLTQ 283
Cdd:COG0130 159 LEVTCSKGTYIRSLARDLGEALGCGAHLSALRRTRVGPFTL-EDAVTLEEL--------EELAEGALDALLLPVDEALAD 229

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17553978 284 HKRVVVKDSCINAICYGAKILIPGILrydddieVGKEIVIMSTKGEAICIAIaqmntstiasVDHGVVaKSKRVI 358
Cdd:COG0130 230 LPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFLALGE----------IEDGRL-KPKRVF 286
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 78-250 3.33e-46

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: 158.76  E-value: 3.33e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  78 GFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEE------- 150
Cdd:cd02573   1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLGEAtdtddae 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 151 ---VE-------DDRKVKQALEKLTGALFQRPPLISAVK----------RQ-----LRIR--TVYENKFIEYDPAQQMGI 203
Cdd:cd02573  81 geiIEtsppprlTEEEIEAALKAFTGEIEQVPPMYSAVKvdgkrlyelaRAgeeveRPPRkvTIYSLELLSFDPENPEAD 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 17553978 204 FNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGICDEnENMVT 250
Cdd:cd02573 161 FEVHCSKGTYIRSLARDLGKALGCGAHLSALRRTRSGPFTL-EQAIT 206
PUA_Cbf5 cd21148
PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5; The RNA-binding ...
 284-357 6.32e-40

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: 137.60  E-value: 6.32e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17553978 284 HKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRV 357
Cdd:cd21148   2 LPRIVIKDSAVNAICYGAKLAIPGVLRYEDGIEKGDEVVIMTTKGEAVALGIALMTTAEIATCDHGIVAKIKRV 75
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 37-94 1.97e-35

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: 125.02  E-value: 1.97e-35
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 17553978    37 ASQWPLLLKNYDKLNVRTNHYTPHVEGVSPLKRDIKNYISSGFFNLDKPSNPSSHEVV 94
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 98-214 2.24e-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: 122.59  E-value: 2.24e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978    98 KRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEEVE----------------DDRKVKQAL 161
Cdd:pfam01509   1 KRILGAKKVGHTGTLDPLATGVLPVCVGEATKLLQYLLDADKEYVATIRLGVATDtldaegeiveesvdhiTEEKIEEVL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   162 EKLTGALFQRPPLISAVK-----------------RQLRIRTVYENKFIEYDPAQqmGIFNCICESGTYV 214
Cdd:pfam01509  81 ASFTGEIEQVPPMYSAVKvngkrlyelaregieveRPPRPVTIYSLELLEFDLPE--VTFRVTCSKGTYI 148
TruB TIGR00431
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
 78-240 3.73e-32

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: 121.32  E-value: 3.73e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978    78 GFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLHEEVEDD--- 154
Cdd:TIGR00431   3 GVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLGVRTDTLdpd 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   155 -------------RKVKQALEKLTGALFQRPPLISAVK-----------------RQLRIRTVYENKFIEYDpaQQMGIF 204
Cdd:TIGR00431  83 gqivetrpvnpttEDVEAALPTFRGEIEQIPPMYSALKvngkrlyeyarqgieveRKARPVTVYDLQFLKYE--GPELTL 160

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 17553978   205 NCICESGTYVRTICVHLGLILGCGGQMQELRRNRSG 240
Cdd:TIGR00431 161 EVHCSKGTYIRTLARDLGEKLGCGAYVSHLRRTAVG 196
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 215-281 4.72e-28

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: 105.64  E-value: 4.72e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17553978   215 RTICVHLGLILGCGGQMQELRRNRSGICDENeNMVTMHDVLDAQYLLDTqKDESYMRHIVRPLEALL 281
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEA-DMVTLHDLLDAYLLYKE-GDESYLRRVLLPLESAL 65
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 285-358 9.66e-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: 88.31  E-value: 9.66e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17553978   285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRVI 358
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTEKGELVAVGLANYSSEELAKIEGGKAVKVRRVL 74
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
285-359 8.08e-19

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 80.38  E-value: 8.08e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17553978    285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVD-HGVVAKSKRVIM 359
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRAVM 76
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 285-353 4.63e-14

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: 66.94  E-value: 4.63e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17553978 285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAK 353
Cdd:cd07953   1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSEGGRPLAIGVAEMSSDEMKEELKGIAVR 69
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 82-245 2.05e-13

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 70.17  E-value: 2.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   82 LDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKLH------------E 149
Cdd:PRK02193   5 LYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIKFGfisttydsegqiI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  150 EVEDDRKV-----KQALEKLTGALFQRPPLISAVKrqLRIRTVYE----NKFIE---------------YDPAQQMGIFN 205
Cdd:PRK02193  85 NVSQNIKVtkenlEEALNNLVGSQKQVPPVFSAKK--VNGKRAYDlarqGKQIElkpieikiskiellnFDEKLQNCVFM 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 17553978  206 CICESGTYVRTICVHLGLILGCGGQMQELRRNRSGICDEN 245
Cdd:PRK02193 163 WVVSRGTYIRSLIHDLGKMLKTGAYMSDLERTKIGNLDKN 202
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 75-304 1.02e-12

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 68.90  E-value: 1.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978   75 ISSGFFNLDKPSNPSSHEVVSWIKRILRCEKTGHSGTLDPKVSGCLIVCIDRTTRLAKSQQGAGKEYICIFKL------- 147
Cdd:PRK14846   1 MSNYWLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFgmqtnsg 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  148 ---------HEEVEDDRKVKQALEKLTGALFQRPPLISAVK---------------RQLRIR--TVYENKFIEYDPAQQM 201
Cdd:PRK14846  81 dcagkviatKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKvngvrayklaregkkVELKPRniTIYDLKCLNFDEKNAT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  202 GIFNCICESGTYVRTICVHLGLILGCGGQMQELRRNRSGIC-DENENMVTMHDVLDAQYLldtqkDESYMRhivrpLEAL 280
Cdd:PRK14846 161 ATYYTECSKGTYIRTLAEDLALSLQSLGFVIELRRTQVGIFkEENAIRIKSPDEITKNAL-----EEKSIK-----IEAI 230

                        250       260
                 ....*....|....*....|....
gi 17553978  281 LTQHKRVVVKDSCINAICYGAKIL 304
Cdd:PRK14846 231 LDDILVLDATDSQAQQIKYGQKCL 254
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 78-181 4.40e-10

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: 60.53  E-value: 4.40e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  78 GFFNLDKPSNPSSHEVVSWIKRILRCE-----------------------------KTGHSGTLDPKVSGCLIVCIDRTT 128
Cdd:cd02867   1 GVFAINKPSGITSAQVLNDLKPLFLNSalfkdkiqravakrgkkarrrkgrkrsklKIGHGGTLDPLATGVLVVGVGAGT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 129 RLAKSQQGAGKEYICIFKL-HEEVEDDR----------------KVKQALEKLTGALFQRPPLISAVKRQ 181
Cdd:cd02867  81 KQLQDYLSCSKTYEATGLFgASTTTYDRegkilkkkpyshitreDIEEVLAKFRGDIKQVPPLYSALKMD 150
PRK13794 PRK13794
hypothetical protein; Provisional
 273-389 1.43e-07

hypothetical protein; Provisional


Pssm-ID: 237509 [Multi-domain]  Cd Length: 479  Bit Score: 53.52  E-value: 1.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  273 IVRPLEALL---TQHKR-VVVKDSCINAI-CYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVD 347
Cdd:PRK13794 109 IPRPEGARRlipTAKKKfIVVKDDVPKFIrNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEEIVNME 188

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 17553978  348 HGVVAKSKRVIMERDvYGRKWGLGPVASKKKQMVK--DGLLDKF 389
Cdd:PRK13794 189 KGMVVKVRKSEEPKN-SNILSEYGPGEETWKDMVEanKNVLDKY 231
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 274-354 2.05e-07

Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441619 [Multi-domain]  Cd Length: 154  Bit Score: 50.17  E-value: 2.05e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978 274 VRPLEALLTQHKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMS-TKGEAICIAIAQMNTSTIASVDHGVVA 352
Cdd:COG2016  63 LRGLLKYPPEKPVVTVDMGAVKFVSNGADVMRPGIVEADGEIKEGDIVVIVEeKHGKPLAVGRALVDGEEMVEGKKGKAV 142


                ..
gi 17553978 353 KS 354
Cdd:COG2016 143 KN 144
PRK13795 PRK13795
hypothetical protein; Provisional
 270-357 7.54e-07

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 51.53  E-value: 7.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  270 MRHIVRPLE---ALLTQHKR---VVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTI 343
Cdd:PRK13795 106 LRWRFEPRLegaKRLLKKRLkkwVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMDGDDM 185

                         90
                 ....*....|....
gi 17553978  344 ASVDHGVVAKSKRV 357
Cdd:PRK13795 186 IKRFRGRAVKVRKS 199
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 285-354 1.39e-06

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: 45.96  E-value: 1.39e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17553978 285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMS-TKGEAICIAIAQMNTSTIASVDHGVVAKS 354
Cdd:cd21154   3 PRVVVDMGAVKFVANGADVMRPGIVEADEEIKKGDIVVVVDeRHGKPLAVGIALMSGEEMVEMKKGKAVKN 73
unchar_dom_2 TIGR00451
uncharacterized domain 2; This uncharacterized domain is found a number of enzymes and ...
 280-353 5.02e-06

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: 45.12  E-value: 5.02e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17553978   280 LLTQHKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMS-TKGEAICIAIAQMNTSTIASVDHGVVAK 353
Cdd:TIGR00451  26 LMEDKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEGDDVVVVDeNKDRPLAVGIALMSGEEMKEMDKGKAVK 100
arCOG00985 TIGR03684
arCOG04150 universal archaeal PUA-domain protein; This universal archaeal protein contains a ...
 285-354 1.80e-05

arCOG04150 universal archaeal PUA-domain protein; This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).


Pssm-ID: 274723 [Multi-domain]  Cd Length: 150  Bit Score: 44.52  E-value: 1.80e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17553978   285 KRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMS-TKGEAICIAIAQMNTSTIASVDHGVVAKS 354
Cdd:TIGR03684  70 NVVVVDEGAVKFIINGADIMAPGIVEADPSIKEGDIVFVVDeTHGKPLAVGIALMDAEEMVEEKKGKAVKN 140
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 274-354 3.52e-05

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 44.07  E-value: 3.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17553978  274 VRPLEALLTQHKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMS-TKGEAICIAIAQMNTSTIASVDHGVVA 352
Cdd:PRK14560  66 LRGALKLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEeTHGKPLAVGRALMDGDEMVEEKKGKAV 145


                 ..
gi 17553978  353 KS 354
Cdd:PRK14560 146 KN 147
PUA_archaeosine_TGT cd21149
PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase; The RNA-binding PUA ...
 284-357 3.48e-04

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: 39.13  E-value: 3.48e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17553978 284 HKRVVVKDSCINAICYGAKILIPGILRYDDDIEVGKEIVIMSTKGEAICIAIAQMNTSTIASVDHGVVAKSKRV 357
Cdd:cd21149   2 ENRVVVNKESAPFVRKGGSVFAKGVVDADENIRPGDEVLVVDEDDRLLAVGRAVLSGKEMKEFERGVAVKVRHG 75
PUA_TruB_thermotogae cd21905
PUA RNA-binding domain of the thermotogae tRNA pseudouridine synthase B; The RNA-binding PUA ...
 286-358 3.66e-03

PUA RNA-binding domain of the thermotogae tRNA pseudouridine synthase B; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of the thermotogae subfamily of pseudouridine synthases TruB 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. The pseudouridine synthase TruB (also called tRNA pseudouridylate synthase B or Psi55 synthase) is responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of elongator tRNAs.


Pssm-ID: 409300 [Multi-domain]  Cd Length: 78  Bit Score: 36.06  E-value: 3.66e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17553978 286 RVVVKDSCINAICYGAKILIPGILRYDDDiEVGKEIVIMSTKGEAICIAIAQMNTSTIASV----DHGVVAKSKRVI 358
Cdd:cd21905   3 KVVVNEESSKRVLNGSQIHLEDVIEVEGF-FKGELVRIFDEEGNLLAIARAERNSSFLETLkkheRNERVAKLKKVF 78
 
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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