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Conserved domains on  [gi|225007597|ref|NP_001028279|]
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H/ACA ribonucleoprotein complex subunit DKC1 [Danio rerio]

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 ...
 51-376 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: 534.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597   51 LKNFDKLNIRTAHYTPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVC 130
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  131 VERATRLVKSQQSAGKEYVGIVRLHNALENEhQLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDPERrlGI 210
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  211 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLGEkDNLVTMHDVLDAQWQFDHNKDETYLRRVIFPLEKLLIS 290
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  291 HKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIMERDT 370
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 225007597  371 YPRKWG 376
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 ...
 51-376 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: 534.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597   51 LKNFDKLNIRTAHYTPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVC 130
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  131 VERATRLVKSQQSAGKEYVGIVRLHNALENEhQLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDPERrlGI 210
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  211 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLGEkDNLVTMHDVLDAQWQFDHNKDETYLRRVIFPLEKLLIS 290
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  291 HKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIMERDT 370
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 225007597  371 YPRKWG 376
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 83-265 2.35e-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: 360.81  E-value: 2.35e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  83 RSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRLHNAlENEH 162
Cdd:cd02572    1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD-VDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 163 QLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELR 242
Cdd:cd02572   80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                        170       180
                 ....*....|....*....|...
gi 225007597 243 RVRSGVLGEKDNLVTMHDVLDAQ 265
Cdd:cd02572  160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
65-366 7.48e-117

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 346.07  E-value: 7.48e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  65 TPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSA 144
Cdd:PRK04270   3 TNPEYGCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLES 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 145 GKEYVGIVRLHNALENEhQLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDpERRLgIFWVSCEAGTYIRTL 224
Cdd:PRK04270  83 GKEYVCVMHLHGDVPEE-DIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID-GRDV-LFRVRCESGTYIRKL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 225 CVHLGLLLGVGGQMQELRRVRSGVLGEkDNLVTMHDVLDAQWQFDHNKDETYLRRVIFPLEKLLISHKRIVMKDSAVNAI 304
Cdd:PRK04270 160 CHDIGLALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAI 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 225007597 305 CYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIM 366
Cdd:PRK04270 239 AHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 85-316 5.80e-45

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: 159.45  E-value: 5.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  85 GFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL---------- 154
Cdd:COG0130    1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLgvetdtddae 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 155 --------HNALeNEHQLARALECLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKLIEYDPERrlG 209
Cdd:COG0130   81 gevvetspVPRL-TEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--L 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 210 IFWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSGVLGEkDNLVTMHDVLDAqwqfdhnkDETYLRR 279
Cdd:COG0130  158 TLEVTCSKGTYIRSLARdlgealgcgaH----------LSALRRTRVGPFTL-EDAVTLEELEEL--------AEGALDA 218

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 225007597 280 VIFPLEKLLISHKRIVMKDSAVNAICYGAKIMLPGVL 316
Cdd:COG0130  219 LLLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP 255
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 44-101 1.07e-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: 129.64  E-value: 1.07e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 225007597   44 TSQWPLLLKNFDKLNIRTAHYTPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVV 101
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
292-366 3.28e-16

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 73.45  E-value: 3.28e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 225007597   292 KRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCD-HGVVAKIKRVIM 366
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 ...
 51-376 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: 534.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597   51 LKNFDKLNIRTAHYTPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVC 130
Cdd:TIGR00425   1 LKNFENLIVKEEHYTNIDYGCNPLKRDIEEYISYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVC 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  131 VERATRLVKSQQSAGKEYVGIVRLHNALENEhQLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDPERrlGI 210
Cdd:TIGR00425  81 IERATRLVKSQQEAPKEYVCLMRLHRDAKEE-DILRVLKEFTGRIFQRPPLKSAVKRQLRVRTIYESELLEKDGKD--VL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  211 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLGEkDNLVTMHDVLDAQWQFDHNKDETYLRRVIFPLEKLLIS 290
Cdd:TIGR00425 158 FRVSCEAGTYIRKLCVDIGEALGTGAHMQELRRTRSGCFGE-DDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRH 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  291 HKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIMERDT 370
Cdd:TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGT 316


                  ....*.
gi 225007597  371 YPRKWG 376
Cdd:TIGR00425 317 YPRMWK 322
PseudoU_synth_hDyskerin cd02572
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
 83-265 2.35e-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: 360.81  E-value: 2.35e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  83 RSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRLHNAlENEH 162
Cdd:cd02572    1 KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD-VDEE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 163 QLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELR 242
Cdd:cd02572   80 KVRRVLEEFTGAIFQRPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAHMQELR 159

                        170       180
                 ....*....|....*....|...
gi 225007597 243 RVRSGVLGEKDNLVTMHDVLDAQ 265
Cdd:cd02572  160 RTRSGPFSEEDNMVTLHDVLDAQ 182
PRK04270 PRK04270
RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;
65-366 7.48e-117

RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5;


Pssm-ID: 179806 [Multi-domain]  Cd Length: 300  Bit Score: 346.07  E-value: 7.48e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  65 TPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSA 144
Cdd:PRK04270   3 TNPEYGCPPEKRPIEELIKFGVVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLES 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 145 GKEYVGIVRLHNALENEhQLARALECLTGALFQRPPLIAAVKRQLRVRTIYESKLIEYDpERRLgIFWVSCEAGTYIRTL 224
Cdd:PRK04270  83 GKEYVCVMHLHGDVPEE-DIRKVFKEFTGEIYQKPPLKSAVKRRLRVRTIYELEILEID-GRDV-LFRVRCESGTYIRKL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 225 CVHLGLLLGVGGQMQELRRVRSGVLGEkDNLVTMHDVLDAQWQFDHNKDETYLRRVIFPLEKLLISHKRIVMKDSAVNAI 304
Cdd:PRK04270 160 CHDIGLALGTGAHMQELRRTRTGPFTE-EDLVTLQDLADAYYFWKEDGDEEELRRVILPMEYALSHLPKIIIKDSAVDAI 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 225007597 305 CYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIM 366
Cdd:PRK04270 239 AHGAPLYAPGIAKLEKGIKKGDLVAVFTLKGELVALGKALMDSDEILKAEKGIVVDLERVFM 300
PseudoU_synth_TruB_like cd00506
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
 85-261 8.92e-74

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: 232.43  E-value: 8.92e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  85 GFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRLHNALENEH-- 162
Cdd:cd00506    1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDTFDat 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 163 ---------------QLARALECLTGALFQRPPLIAAVKRQ-----------------LRVRTIYESKLIEYDPERRLGI 210
Cdd:cd00506   81 gqvieetpydhitheQLERALETLTGDIQQVPPLYSAVKRQgqrayelarrgllvpdeARPPTIYELLCIRFNPPHFLLE 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 225007597 211 FWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLgEKDNLVTMHDV 261
Cdd:cd00506  161 VEVVCETGTYIRTLIHDLGLELGVGAHVTELRRTRVGPF-KVENAVTLHHL 210
TruB COG0130
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
 85-316 5.80e-45

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: 159.45  E-value: 5.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  85 GFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL---------- 154
Cdd:COG0130    1 GILLLDKPAGMTSHDVVQKVRRLLGAKKVGHTGTLDPLATGVLPICLGEATKLSQYLLDADKTYRATIRLgvetdtddae 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 155 --------HNALeNEHQLARALECLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKLIEYDPERrlG 209
Cdd:COG0130   81 gevvetspVPRL-TEEEIEAALASFTGEIEQVPPMYSAIKvdgkrlyelarageeveRPPRPVTIYSLELLSFDAPE--L 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 210 IFWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSGVLGEkDNLVTMHDVLDAqwqfdhnkDETYLRR 279
Cdd:COG0130  158 TLEVTCSKGTYIRSLARdlgealgcgaH----------LSALRRTRVGPFTL-EDAVTLEELEEL--------AEGALDA 218

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 225007597 280 VIFPLEKLLISHKRIVMKDSAVNAICYGAKIMLPGVL 316
Cdd:COG0130  219 LLLPVDEALADLPAVELDEEEAKRLRNGQRLPLPGLP 255
PUA_Cbf5 cd21148
PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5; The RNA-binding ...
 290-364 4.45e-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: 144.53  E-value: 4.45e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 225007597 290 SHKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRV 364
Cdd:cd21148    1 HLPRIVIKDSAVNAICYGAKLAIPGVLRYEDGIEKGDEVVIMTTKGEAVALGIALMTTAEIATCDHGIVAKIKRV 75
PseudoU_synth_EcTruB cd02573
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
 85-247 4.45e-39

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: 141.04  E-value: 4.45e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  85 GFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL---------- 154
Cdd:cd02573    1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLgeatdtddae 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 155 -------HNALENEHQLARALECLTGALFQRPPLIAAVK----------RQ-----LRVR--TIYESKLIEYDPERRLGI 210
Cdd:cd02573   81 geiietsPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKvdgkrlyelaRAgeeveRPPRkvTIYSLELLSFDPENPEAD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 225007597 211 FWVSCEAGTYIRTLCV----------HlglllgvggqMQELRRVRSG 247
Cdd:cd02573  161 FEVHCSKGTYIRSLARdlgkalgcgaH----------LSALRRTRSG 197
DKCLD pfam08068
DKCLD (NUC011) domain; This is a TruB_N/PUA domain associated N-terminal domain of ...
 44-101 1.07e-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: 129.64  E-value: 1.07e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 225007597   44 TSQWPLLLKNFDKLNIRTAHYTPLPHGSNPLKRGIHDYVRSGFINLDKPANPSSHEVV 101
Cdd:pfam08068   1 TSEWPLLLKNYDKLNVRTGHYTPLPYGCSPLKRPIEEYIKYGVINLDKPSNPSSHEVV 58
TruB_N pfam01509
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
 105-221 2.29e-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: 123.74  E-value: 2.29e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  105 KRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRLH----------------NALENEHQLARAL 168
Cdd:pfam01509   1 KRILGAKKVGHTGTLDPLATGVLPVCVGEATKLLQYLLDADKEYVATIRLGvatdtldaegeiveesVDHITEEKIEEVL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  169 ECLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKLIEYDPERRLgiFWVSCEAGTYI 221
Cdd:pfam01509  81 ASFTGEIEQVPPMYSAVKvngkrlyelaregieveRPPRPVTIYSLELLEFDLPEVT--FRVTCSKGTYI 148
TruB TIGR00431
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
 85-247 1.50e-28

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: 112.46  E-value: 1.50e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597   85 GFINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL---------- 154
Cdd:TIGR00431   3 GVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLgvrtdtldpd 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  155 ------HNALENEHQLARALECLTGALFQRPPLIAAVK-----------------RQLRVRTIYESKLIEYD-PERRLgi 210
Cdd:TIGR00431  83 gqivetRPVNPTTEDVEAALPTFRGEIEQIPPMYSALKvngkrlyeyarqgieveRKARPVTVYDLQFLKYEgPELTL-- 160

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 225007597  211 fWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSG 247
Cdd:TIGR00431 161 -EVHCSKGTYIRTLARDLGEKLGCGAYVSHLRRTAVG 196
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 292-365 4.24e-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: 84.07  E-value: 4.24e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 225007597  292 KRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVI 365
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTEKGELVAVGLANYSSEELAKIEGGKAVKVRRVL 74
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
292-366 3.28e-16

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 73.45  E-value: 3.28e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 225007597   292 KRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCD-HGVVAKIKRVIM 366
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIVDEKGEPLGIGLANMSSEEIARIKgKGLAVKVRRAVM 76
TruB_C_2 pfam16198
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
 222-288 1.86e-15

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: 70.58  E-value: 1.86e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 225007597  222 RTLCVHLGLLLGVGGQMQELRRVRSGVLGEKDnLVTMHDVLDAQWQFDhNKDETYLRRVIFPLEKLL 288
Cdd:pfam16198   1 RTLCEDIGEALGCGAHMAELRRTRVGPFDEAD-MVTLHDLLDAYLLYK-EGDESYLRRVLLPLESAL 65
truB PRK14846
tRNA pseudouridine synthase B; Provisional
 86-253 3.78e-12

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 237834 [Multi-domain]  Cd Length: 345  Bit Score: 67.75  E-value: 3.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  86 FINLDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL----------- 154
Cdd:PRK14846   5 WLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFgmqtnsgdcag 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 155 -----HNALENEHQLARALECLTGALFQRPPLIAAVK---------------RQLRVR--TIYESKLIEYDPERRLGIFW 212
Cdd:PRK14846  85 kviatKDCIPSQEEAYAVCSKFIGNVTQIPPAFSALKvngvrayklaregkkVELKPRniTIYDLKCLNFDEKNATATYY 164

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 225007597 213 VSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLGEKD 253
Cdd:PRK14846 165 TECSKGTYIRTLAEDLALSLQSLGFVIELRRTQVGIFKEEN 205
PseudoU_synth_TruB_4 cd02867
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
 85-224 4.77e-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: 63.99  E-value: 4.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  85 GFINLDKPANPSSHEVVAWIKRILRVE-----------------------------KTGHSGTLDPKVTGCLIVCVERAT 135
Cdd:cd02867    1 GVFAINKPSGITSAQVLNDLKPLFLNSalfkdkiqravakrgkkarrrkgrkrsklKIGHGGTLDPLATGVLVVGVGAGT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 136 RLVKSQQSAGKEYVGIVRLHNALEN-------------EH----QLARALECLTGALFQRPPLIAAVKRQ---------- 188
Cdd:cd02867   81 KQLQDYLSCSKTYEATGLFGASTTTydregkilkkkpySHitreDIEEVLAKFRGDIKQVPPLYSALKMDgkrlyeyare 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 225007597 189 ---------LRVRTIYESKLIEYDPERRLGIFWVSCEAGTYIRTL 224
Cdd:cd02867  161 gkplprpieRRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERSV 205
truB PRK02193
tRNA pseudouridine synthase B; Provisional
 89-253 3.90e-09

tRNA pseudouridine synthase B; Provisional


Pssm-ID: 179381 [Multi-domain]  Cd Length: 279  Bit Score: 57.84  E-value: 3.90e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597  89 LDKPANPSSHEVVAWIKRILRVEKTGHSGTLDPKVTGCLIVCVERATRLVKSQQSAGKEYVGIVRL-------------H 155
Cdd:PRK02193   5 LYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIKFgfisttydsegqiI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 156 NALEN----EHQLARALECLTGALFQRPPLIAAVK----------RQ--------LRVRtIYESKLIEYDPERRLGIFWV 213
Cdd:PRK02193  85 NVSQNikvtKENLEEALNNLVGSQKQVPPVFSAKKvngkraydlaRQgkqielkpIEIK-ISKIELLNFDEKLQNCVFMW 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 225007597 214 SCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVLGEKD 253
Cdd:PRK02193 164 VVSRGTYIRSLIHDLGKMLKTGAYMSDLERTKIGNLDKNF 203
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 292-361 9.08e-08

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: 49.22  E-value: 9.08e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 292 KRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKI 361
Cdd:cd07953    1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSEGGRPLAIGVAEMSSDEMKEELKGIAVRV 70
PRK13795 PRK13795
hypothetical protein; Provisional
 286-364 5.22e-07

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 52.30  E-value: 5.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 286 KLLISHKR---IVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIK 362
Cdd:PRK13795 118 KRLLKKRLkkwVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEVVGVGRAKMDGDDMIKRFRGRAVKVR 197


                 ..
gi 225007597 363 RV 364
Cdd:PRK13795 198 KS 199
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 292-360 6.61e-07

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: 47.11  E-value: 6.61e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 225007597 292 KRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNqDIVVIT--TKGEAICTAVALMTTAVISTCDHGVVAK 360
Cdd:cd21154    3 PRVVVDMGAVKFVANGADVMRPGIVEADEEIKKG-DIVVVVdeRHGKPLAVGIALMSGEEMVEMKKGKAVK 72
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 281-360 7.63e-05

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 43.30  E-value: 7.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 281 IFPLEKLLISH---KRIVMKDS-AVNAICYGAKIMLPGVLRYEDGIEVNqDIVVITTK--GEAICTAVALMTTAVISTCD 354
Cdd:PRK14560  62 LFPTLRGALKLkpeKRRVVVDAgAVKFVSNGADVMAPGIVEADEDIKEG-DIVFVVEEthGKPLAVGRALMDGDEMVEEK 140


                 ....*.
gi 225007597 355 HGVVAK 360
Cdd:PRK14560 141 KGKAVK 146
unchar_dom_2 TIGR00451
uncharacterized domain 2; This uncharacterized domain is found a number of enzymes and ...
 286-360 1.63e-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: 40.88  E-value: 1.63e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 225007597  286 KLLISHKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNqDIVVITTKGE--AICTAVALMTTAVISTCDHGVVAK 360
Cdd:TIGR00451  25 KLMEDKKIVVVDNGAVKFLKNGADVMRPGIVDADEDIKEG-DDVVVVDENKdrPLAVGIALMSGEEMKEMDKGKAVK 100
PRK13794 PRK13794
hypothetical protein; Provisional
 292-395 1.87e-04

hypothetical protein; Provisional


Pssm-ID: 237509 [Multi-domain]  Cd Length: 479  Bit Score: 43.89  E-value: 1.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 225007597 292 KRIVMKDSAVNAI-CYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRVIMERD- 369
Cdd:PRK13794 125 KFIVVKDDVPKFIrNKGASVLRPGVAEASEDIEEGDDVIILDENGDVVGVGRARMSYEEIVNMEKGMVVKVRKSEEPKNs 204

                         90       100
                 ....*....|....*....|....*.
gi 225007597 370 TYPRKWGLGPKASQKKMMIQKGLLDK 395
Cdd:PRK13794 205 NILSEYGPGEETWKDMVEANKNVLDK 230
PUA_archaeosine_TGT cd21149
PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase; The RNA-binding PUA ...
 291-364 1.49e-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: 37.21  E-value: 1.49e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 225007597 291 HKRIVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQDIVVITTKGEAICTAVALMTTAVISTCDHGVVAKIKRV 364
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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