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Conserved domains on  [gi|4503337|ref|NP_001354|]
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H/ACA ribonucleoprotein complex subunit DKC1 isoform 1 [Homo sapiens]

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 ...
 56-381 0e+00

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: 547.83  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337     56 LKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVC 135
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    136 IERATRLVKSQQSAGKEYVGIVRLHNAIEGgTQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERrlGI 215
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKE-EDILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    216 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEkDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTS 295
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    296 HKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDT 375
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 4503337    376 YPRKWG 381
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 ...
 56-381 0e+00

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: 547.83  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337     56 LKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVC 135
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    136 IERATRLVKSQQSAGKEYVGIVRLHNAIEGgTQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERrlGI 215
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKE-EDILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    216 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEkDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTS 295
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    296 HKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDT 375
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 4503337    376 YPRKWG 381
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 88-270 6.45e-124

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: 359.65  E-value: 6.45e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   88 RTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAiEGGT 167
Cdd:cd02572   1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD-VDEE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  168 QLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELR 247
Cdd:cd02572  80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                       170       180
                ....*....|....*....|...
gi 4503337  248 RVRSGVMSEKDHMVTMHDVLDAQ 270
Cdd:cd02572 160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
75-371 2.38e-117

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 347.61  E-value: 2.38e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    75 GSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYV 154
Cdd:PRK04270   8 GCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   155 GIVRLHNAIEGGtQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDpERRLgIFWVSCEAGTYIRTLCVHLG 234
Cdd:PRK04270  88 CVMHLHGDVPEE-DIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID-GRDV-LFRVRCESGTYIRKLCHDIG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   235 LLLGVGGQMQELRRVRSGVMSEKDhMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTSHKRLVMKDSAVNAICYGAK 314
Cdd:PRK04270 165 LALGTGAHMQELRRTRTGPFTEED-LVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAIAHGAP 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 4503337   315 IMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIM 371
Cdd:PRK04270 244 LYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 90-346 3.05e-44

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: 157.52  E-value: 3.05e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   90 GFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNA-----IE 164
Cdd:COG0130   1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLGVEtdtddAE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  165 G------------GTQLSRALETLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPERrlGI 215
Cdd:COG0130  81 GevvetspvprltEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--LT 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  216 FWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSGVMSEKDhMVTMHDVLDAqwlydnhkDESYLRRV 285
Cdd:COG0130 159 LEVTCSKGTYIRSLARdlgealgcgaH----------LSALRRTRVGPFTLED-AVTLEELEEL--------AEGALDAL 219

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4503337  286 VYPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPGVLryedgieVNQEIVVITTKGEAICMA 346
Cdd:COG0130 220 LLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFLALG 273
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 49-106 1.48e-36

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: 129.25  E-value: 1.48e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 4503337     49 TSQWPLLLKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVV 106
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
297-371 2.13e-16

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 73.83  E-value: 2.13e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4503337     297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCD-HGIVAKIKRVIM 371
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 ...
 56-381 0e+00

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: 547.83  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337     56 LKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVC 135
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    136 IERATRLVKSQQSAGKEYVGIVRLHNAIEGgTQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERrlGI 215
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKE-EDILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    216 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEkDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTS 295
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    296 HKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDT 375
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 4503337    376 YPRKWG 381
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 88-270 6.45e-124

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: 359.65  E-value: 6.45e-124
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   88 RTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAiEGGT 167
Cdd:cd02572   1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD-VDEE 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  168 QLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELR 247
Cdd:cd02572  80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                       170       180
                ....*....|....*....|...
gi 4503337  248 RVRSGVMSEKDHMVTMHDVLDAQ 270
Cdd:cd02572 160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
75-371 2.38e-117

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 347.61  E-value: 2.38e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    75 GSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYV 154
Cdd:PRK04270   8 GCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   155 GIVRLHNAIEGGtQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDpERRLgIFWVSCEAGTYIRTLCVHLG 234
Cdd:PRK04270  88 CVMHLHGDVPEE-DIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID-GRDV-LFRVRCESGTYIRKLCHDIG 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   235 LLLGVGGQMQELRRVRSGVMSEKDhMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTSHKRLVMKDSAVNAICYGAK 314
Cdd:PRK04270 165 LALGTGAHMQELRRTRTGPFTEED-LVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAIAHGAP 243

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 4503337   315 IMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIM 371
Cdd:PRK04270 244 LYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 90-266 8.69e-78

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: 242.83  E-value: 8.69e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   90 GFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIE----- 164
Cdd:cd00506   1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDtfdat 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  165 ------------GGTQLSRALETLTGALFQRPPLIAAVKRQ-----------------LRVRTIYESKMIEYDPERRLGI 215
Cdd:cd00506  81 gqvieetpydhiTHEQLERALETLTGDIQQVPPLYSAVKRQgqrayelarrgllvpdeARPPTIYELLCIRFNPPHFLLE 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 4503337  216 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMsEKDHMVTMHDV 266
Cdd:cd00506 161 VEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPF-KVENAVTLHHL 210
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 90-346 3.05e-44

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: 157.52  E-value: 3.05e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   90 GFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNA-----IE 164
Cdd:COG0130   1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLGVEtdtddAE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  165 G------------GTQLSRALETLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPERrlGI 215
Cdd:COG0130  81 GevvetspvprltEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--LT 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  216 FWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSGVMSEKDhMVTMHDVLDAqwlydnhkDESYLRRV 285
Cdd:COG0130 159 LEVTCSKGTYIRSLARdlgealgcgaH----------LSALRRTRVGPFTLED-AVTLEELEEL--------AEGALDAL 219

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4503337  286 VYPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPGVLryedgieVNQEIVVITTKGEAICMA 346
Cdd:COG0130 220 LLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP-------ADGLVRVYDPDGRFLALG 273
PUA_Cbf5 cd21148
PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5; The RNA-binding ...
 295-369 9.26e-42

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: 9.26e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4503337  295 SHKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRV 369
Cdd:cd21148   1 HLPRIVIKDSAVNAICYGAKLAIPGVLRYEDGIEKGDEVVIMTTKGEAVALGIALMTTAEIATCDHGIVAKIKRV 75
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 90-262 1.05e-37

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: 137.58  E-value: 1.05e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   90 GFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNA-----IE 164
Cdd:cd02573   1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLGEAtdtddAE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  165 GGT------------QLSRALETLTGALFQRPPLIAAVK----------RQ-----LRVR--TIYESKMIEYDPERRLGI 215
Cdd:cd02573  81 GEIietsppprlteeEIEAALKAFTGEIEQVPPMYSAVKvdgkrlyelaRAgeeveRPPRkvTIYSLELLSFDPENPEAD 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 4503337  216 FWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSGVMSEKDhMVT 262
Cdd:cd02573 161 FEVHCSKGTYIRSLARdlgkalgcgaH----------LSALRRTRSGPFTLEQ-AIT 206
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 49-106 1.48e-36

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: 129.25  E-value: 1.48e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 4503337     49 TSQWPLLLKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVV 106
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 110-226 3.12e-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: 123.36  E-value: 3.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    110 RRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNA-----IEGGT-----------QLSRAL 173
Cdd:pfam01509   1 KRILGAKKVGHTGTLDPLATGVLPVCVGEATKLLQYLLDADKEYVATIRLGVAtdtldAEGEIveesvdhiteeKIEEVL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    174 ETLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKMIEYDPERRLgiFWVSCEAGTYI 226
Cdd:pfam01509  81 ASFTGEIEQVPPMYSAVKvngkrlyelaregieveRPPRPVTIYSLELLEFDLPEVT--FRVTCSKGTYI 148
TruB TIGR00431
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
 90-260 3.77e-29

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: 114.00  E-value: 3.77e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337     90 GFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRL---------- 159
Cdd:TIGR00431   3 GVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLgvrtdtldpd 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    160 ------HNAIEGGTQLSRALETLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKMIEYD-PERRLgi 215
Cdd:TIGR00431  83 gqivetRPVNPTTEDVEAALPTFRGEIEQIPPMYSALKvngkrlyeyarqgieveRKARPVTVYDLQFLKYEgPELTL-- 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 4503337    216 fWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEKDHM 260
Cdd:TIGR00431 161 -EVHCSKGTYIRTLARDLGEKLGCGAYVSHLRRTAVGDFPLDQSV 204
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 297-370 2.34e-20

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: 84.84  E-value: 2.34e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4503337    297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVI 370
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTEKGELVAVGLANYSSEELAKIEGGKAVKVRRVL 74
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 227-293 3.92e-18

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: 78.29  E-value: 3.92e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4503337    227 RTLCVHLGLLLGVGGQMQELRRVRSGVMSEkDHMVTMHDVLDAQWLYDNHkDESYLRRVVYPLEKLL 293
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDE-ADMVTLHDLLDAYLLYKEG-DESYLRRVLLPLESAL 65
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
297-371 2.13e-16

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 73.83  E-value: 2.13e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4503337     297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCD-HGIVAKIKRVIM 371
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRAVM 76
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 91-258 1.24e-12

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 68.90  E-value: 1.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    91 FINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGTQLS 170
Cdd:PRK14846   5 WLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFGMQTNSGDCAG 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   171 RALET----------------LTGALFQRPPLIAAVK---------------RQLRVR--TIYESKMIEYDPERRLGIFW 217
Cdd:PRK14846  85 KVIATkdcipsqeeayavcskFIGNVTQIPPAFSALKvngvrayklaregkkVELKPRniTIYDLKCLNFDEKNATATYY 164

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 4503337   218 VSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEKD 258
Cdd:PRK14846 165 TECSKGTYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEEN 205
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 90-229 8.68e-11

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: 63.22  E-value: 8.68e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   90 GFINLDKPSNPSSHEVVAWI--------------------------RRILRVE---KTGHSGTLDPKVTGCLIVCIERAT 140
Cdd:cd02867   1 GVFAINKPSGITSAQVLNDLkplflnsalfkdkiqravakrgkkarRRKGRKRsklKIGHGGTLDPLATGVLVVGVGAGT 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  141 RLVKSQQSAGKEYVGIVRLHNAIEGG-----------------TQLSRALETLTGALFQRPPLIAAVKRQ---------- 193
Cdd:cd02867  81 KQLQDYLSCSKTYEATGLFGASTTTYdregkilkkkpyshitrEDIEEVLAKFRGDIKQVPPLYSALKMDgkrlyeyare 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 4503337  194 ---------LRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTL 229
Cdd:cd02867 161 gkplprpieRRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERSV 205
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 94-258 3.88e-09

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 57.84  E-value: 3.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    94 LDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYV-----GIVRLHNAIEG--- 165
Cdd:PRK02193   5 LYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIakikfGFISTTYDSEGqii 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   166 ---------GTQLSRALETLTGALFQRPPLIAAVK----------RQ--------LRVRtIYESKMIEYDPERRLGIFWV 218
Cdd:PRK02193  85 nvsqnikvtKENLEEALNNLVGSQKQVPPVFSAKKvngkraydlaRQgkqielkpIEIK-ISKIELLNFDEKLQNCVFMW 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 4503337   219 SCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEKD 258
Cdd:PRK02193 164 VVSRGTYIRSLIHDLGKMLKTGAYMSDLERTKIGNLDKNF 203
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 297-366 1.20e-07

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: 48.83  E-value: 1.20e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337  297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKI 366
Cdd:cd07953   1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSEGGRPLAIGVAEMSSDEMKEELKGIAVRV 70
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 297-365 2.20e-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: 45.57  E-value: 2.20e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4503337  297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNqEIVVIT--TKGEAICMAIALMTTAVISTCDHGIVAK 365
Cdd:cd21154   3 PRVVVDMGAVKFVANGADVMRPGIVEADEEIKKG-DIVVVVdeRHGKPLAVGIALMSGEEMVEMKKGKAVK 72
PRK13795 PRK13795
hypothetical protein; Provisional
 297-369 5.35e-06

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 49.22  E-value: 5.35e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4503337   297 KRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRV 369
Cdd:PRK13795 127 KWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMDGDDMIKRFRGRAVKVRKS 199
unchar_dom_2 TIGR00451
uncharacterized domain 2; This uncharacterized domain is found a number of enzymes and ...
 266-365 5.15e-04

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: 39.72  E-value: 5.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337    266 VLDAQWLYDNHKDESYLRrvVYPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNqEIVVITTKGE--AI 343
Cdd:TIGR00451   2 LVDGEPLYFIYDDKVIPS--LKGALKLMEDKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEG-DDVVVVDENKdrPL 78

                          90       100
                  ....*....|....*....|..
gi 4503337    344 CMAIALMTTAVISTCDHGIVAK 365
Cdd:TIGR00451  79 AVGIALMSGEEMKEMDKGKAVK 100
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 286-365 1.96e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 39.06  E-value: 1.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4503337   286 VYPLEKLLTSH---KRLVMKDS-AVNAICYGAKIMLPGVLRYEDGIEVNqEIVVITTK--GEAICMAIALMTTAVISTCD 359
Cdd:PRK14560  62 LFPTLRGALKLkpeKRRVVVDAgAVKFVSNGADVMAPGIVEADEDIKEG-DIVFVVEEthGKPLAVGRALMDGDEMVEEK 140


                 ....*.
gi 4503337   360 HGIVAK 365
Cdd:PRK14560 141 KGKAVK 146
PUA_archaeosine_TGT cd21149
PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase; The RNA-binding PUA ...
 296-369 7.81e-03

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: 35.28  E-value: 7.81e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4503337  296 HKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRV 369
Cdd:cd21149   2 ENRVVVNKESAPFVRKGGSVFAKGVVDADENIRPGDEVLVVDEDDRLLAVGRAVLSGKEMKEFERGVAVKVRHG 75
 
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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