Psyllid ID: psy1176

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230--
NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
cccccccccccccccccccccccccHHHcccccEEEEEccccccHHHHHHHHHHHHccccccccccccccccEEcccEEccccccccHHHccccEEEEEEEEccccccccccccHHHHHHHHHHHcccccccccccccEEEEccccccccEEEEEEEEEEcccccEEEEEEEEcccHHHHHHHHHHHHHcccccEEcccEEEEEccccccccHHHHHHHHHHHHHHHHHccc
ccccEEEEcccccccccccccccccHHHHHHccEEEcccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccEEEEEEEEcccccccccccccHHHHHHHHHHHccHHcccccHHHHHHHHHHHcEEEEEEHccEEEEcccccEEEEEEEccccHHHHHHHHHHHHHHcccHHHHHHHHHHccccccccccEEHHHHHHHHHHHHHHHcc
nfdklnvrtnhytplpfgksplQRTIQEYIRAGyvnldkpsnpssHEVVAWIKRILRCektghsgtldpktsgcliVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQglldkhgkpnentpaSYLAELeaapnkkptymksnlissdvtLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIElrrnrsgiqseedGLVTFRQEHMFEHIVSTWVLC
nfdklnvrtnhytplpfgksplqRTIQEYIRAGyvnldkpsnpsSHEVVAWIKRILRCEKtghsgtldpktsgcLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQglldkhgkpneNTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
***********YTPLPFGKSPLQRTIQEYIRAGYVNLD*******HEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENV**********************************************NLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGI***EDGLVTFRQEHMFEHIVSTWVL*
NFDKLNVRTNHYTPLPFG**PL*R*IQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
*FDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMFEHIVSTWVLC
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query232 2.2.26 [Sep-21-2011]
O44081 508 H/ACA ribonucleoprotein c yes N/A 0.887 0.405 0.620 1e-74
Q60YA8 445 Putative H/ACA ribonucleo N/A N/A 0.887 0.462 0.583 4e-64
P33322 483 H/ACA ribonucleoprotein c yes N/A 0.866 0.416 0.561 4e-64
O17919 445 Putative H/ACA ribonucleo yes N/A 0.939 0.489 0.557 4e-64
Q54T81 540 Probable H/ACA ribonucleo yes N/A 0.887 0.381 0.550 8e-64
Q9ESX5 509 H/ACA ribonucleoprotein c yes N/A 0.887 0.404 0.578 5e-63
P40615 509 H/ACA ribonucleoprotein c yes N/A 0.922 0.420 0.530 1e-62
O60832 514 H/ACA ribonucleoprotein c yes N/A 0.887 0.400 0.574 3e-62
Q5ZJH9 516 H/ACA ribonucleoprotein c yes N/A 0.887 0.399 0.569 3e-62
O43100 481 Centromere/microtubule-bi yes N/A 0.892 0.430 0.541 5e-62
>sp|O44081|DKC1_DROME H/ACA ribonucleoprotein complex subunit 4 OS=Drosophila melanogaster GN=Nop60B PE=1 SV=1 Back     alignment and function desciption
 Score =  279 bits (713), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 134/216 (62%), Positives = 163/216 (75%), Gaps = 10/216 (4%)

Query: 1   NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
           NFDKLN+R+NHYTPL  G SPL R I+EY++ G++NLDKPSNPSSHEVVAWIK+IL+ EK
Sbjct: 56  NFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEK 115

Query: 61  TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
           TGHSGTLDPK +GCLIVCIDRATRLVKSQQSAGKEY++IFKLH AVE+VAK       ++
Sbjct: 116 TGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVESVAK-------VR 168

Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVR 180
           QGL    G   +  P     + +    +  T   S L+  D T + G+ W+ C+AG+Y+R
Sbjct: 169 QGLEKLRGALFQRPPLISAVKRQL---RVRTVYDSKLLDYDETRNMGVFWVSCEAGSYIR 225

Query: 181 TYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTF 216
           T CVH+GLVLGVG QM+ELRR RSGIQSE DG+VT 
Sbjct: 226 TMCVHLGLVLGVGGQMLELRRVRSGIQSERDGMVTM 261
Plays a central role in ribosomal RNA processing. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Pseudouridine ('psi') residues may serve to stabilize the conformation of rRNAs. Required for maintenance of the germline stem cell lineage during spermatogenesis.
Drosophila melanogaster (taxid: 7227)
EC: 5EC: .EC: 4EC: .EC: 9EC: 9EC: .EC: -
>sp|Q60YA8|DKC1_CAEBR Putative H/ACA ribonucleoprotein complex subunit 4 OS=Caenorhabditis briggsae GN=CBG18316 PE=3 SV=1 Back     alignment and function description
>sp|P33322|CBF5_YEAST H/ACA ribonucleoprotein complex subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CBF5 PE=1 SV=1 Back     alignment and function description
>sp|O17919|DKC1_CAEEL Putative H/ACA ribonucleoprotein complex subunit 4 OS=Caenorhabditis elegans GN=K01G5.5 PE=3 SV=1 Back     alignment and function description
>sp|Q54T81|DKC1_DICDI Probable H/ACA ribonucleoprotein complex subunit 4 OS=Dictyostelium discoideum GN=nola4 PE=1 SV=1 Back     alignment and function description
>sp|Q9ESX5|DKC1_MOUSE H/ACA ribonucleoprotein complex subunit 4 OS=Mus musculus GN=Dkc1 PE=1 SV=4 Back     alignment and function description
>sp|P40615|DKC1_RAT H/ACA ribonucleoprotein complex subunit 4 OS=Rattus norvegicus GN=Dkc1 PE=1 SV=4 Back     alignment and function description
>sp|O60832|DKC1_HUMAN H/ACA ribonucleoprotein complex subunit 4 OS=Homo sapiens GN=DKC1 PE=1 SV=3 Back     alignment and function description
>sp|Q5ZJH9|DKC1_CHICK H/ACA ribonucleoprotein complex subunit 4 OS=Gallus gallus GN=DKC1 PE=2 SV=1 Back     alignment and function description
>sp|O43100|CBF5_EMENI Centromere/microtubule-binding protein CBF5 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=cbf5 PE=2 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query232
170041155 515 H/ACA ribonucleoprotein complex subunit 0.887 0.4 0.620 2e-73
170029441 521 H/ACA ribonucleoprotein complex subunit 0.887 0.395 0.620 2e-73
195023790 509 GH20974 [Drosophila grimshawi] gi|193901 0.887 0.404 0.625 3e-73
375065910 534 FI18403p1 [Drosophila melanogaster] 0.887 0.385 0.620 4e-73
157136797 527 centromere/microtubule binding protein c 0.887 0.390 0.615 4e-73
157816752 489 LD07711p [Drosophila melanogaster] 0.887 0.421 0.620 5e-73
195341866 502 GM18314 [Drosophila sechellia] gi|194132 0.887 0.410 0.620 6e-73
195586327 508 GD11839 [Drosophila simulans] gi|1941949 0.887 0.405 0.620 6e-73
17975520 508 nucleolar protein at 60B, isoform A [Dro 0.887 0.405 0.620 7e-73
19528063 468 AT23018p, partial [Drosophila melanogast 0.887 0.440 0.620 7e-73
>gi|170041155|ref|XP_001848339.1| H/ACA ribonucleoprotein complex subunit 4 [Culex quinquefasciatus] gi|167864704|gb|EDS28087.1| H/ACA ribonucleoprotein complex subunit 4 [Culex quinquefasciatus] Back     alignment and taxonomy information
 Score =  281 bits (718), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/216 (62%), Positives = 166/216 (76%), Gaps = 10/216 (4%)

Query: 1   NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
           NFD+LNVRTNHYTPLPFG SPL R I++Y+ +G++NLDKPSNPSSHEVVAWIK+IL+ EK
Sbjct: 57  NFDRLNVRTNHYTPLPFGSSPLNRKIKDYVTSGFINLDKPSNPSSHEVVAWIKKILKVEK 116

Query: 61  TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
           TGHSGTLDPK +GCLIVCIDRATRLVKSQQSAGKEY+++FKLHSAVE+VAK       + 
Sbjct: 117 TGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAVFKLHSAVESVAK-------VN 169

Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVR 180
           QGL    G   +  P   ++ ++     +  Y  S L+  D   + G+ W+ C+AG+Y+R
Sbjct: 170 QGLEKLRGALFQRPP--LISAVKRQLRVRTVY-DSKLLDYDDQRNMGVFWVSCEAGSYIR 226

Query: 181 TYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTF 216
           T CVH+GLV GVG QM+ELRR RSGIQSE+DG+VT 
Sbjct: 227 TMCVHLGLVTGVGGQMLELRRVRSGIQSEKDGMVTM 262

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|170029441|ref|XP_001842601.1| H/ACA ribonucleoprotein complex subunit 4 [Culex quinquefasciatus] gi|167862432|gb|EDS25815.1| H/ACA ribonucleoprotein complex subunit 4 [Culex quinquefasciatus] Back     alignment and taxonomy information
>gi|195023790|ref|XP_001985751.1| GH20974 [Drosophila grimshawi] gi|193901751|gb|EDW00618.1| GH20974 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|375065910|gb|AFA28436.1| FI18403p1 [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|157136797|ref|XP_001656912.1| centromere/microtubule binding protein cbf5 [Aedes aegypti] gi|108880941|gb|EAT45166.1| AAEL003514-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|157816752|gb|ABV82369.1| LD07711p [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|195341866|ref|XP_002037526.1| GM18314 [Drosophila sechellia] gi|194132376|gb|EDW53944.1| GM18314 [Drosophila sechellia] Back     alignment and taxonomy information
>gi|195586327|ref|XP_002082929.1| GD11839 [Drosophila simulans] gi|194194938|gb|EDX08514.1| GD11839 [Drosophila simulans] Back     alignment and taxonomy information
>gi|17975520|ref|NP_525120.1| nucleolar protein at 60B, isoform A [Drosophila melanogaster] gi|62471759|ref|NP_001014547.1| nucleolar protein at 60B, isoform B [Drosophila melanogaster] gi|281364183|ref|NP_001163286.1| nucleolar protein at 60B, isoform C [Drosophila melanogaster] gi|281364189|ref|NP_001163289.1| nucleolar protein at 60B, isoform F [Drosophila melanogaster] gi|3914156|sp|O44081.1|DKC1_DROME RecName: Full=H/ACA ribonucleoprotein complex subunit 4; AltName: Full=Nucleolar protein AT band 60B; AltName: Full=Protein minifly gi|2661227|gb|AAC97117.1| nucleolar protein at band 60B [Drosophila melanogaster] gi|4322557|gb|AAD16092.1| minifly protein [Drosophila melanogaster] gi|7291757|gb|AAF47178.1| nucleolar protein at 60B, isoform A [Drosophila melanogaster] gi|61678336|gb|AAX52682.1| nucleolar protein at 60B, isoform B [Drosophila melanogaster] gi|112382762|gb|ABI17547.1| MFL protein [Drosophila melanogaster] gi|272432682|gb|ACZ94558.1| nucleolar protein at 60B, isoform C [Drosophila melanogaster] gi|272432685|gb|ACZ94561.1| nucleolar protein at 60B, isoform F [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|19528063|gb|AAL90146.1| AT23018p, partial [Drosophila melanogaster] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query232
FB|FBgn0259937 508 Nop60B "Nucleolar protein at 6 0.883 0.403 0.623 3.5e-68
UNIPROTKB|F1RZ24 521 DKC1 "Uncharacterized protein" 0.883 0.393 0.590 1.4e-62
UNIPROTKB|E2R6Q8 464 DKC1 "Uncharacterized protein" 0.883 0.441 0.590 1.8e-62
UNIPROTKB|F6XRK3 517 DKC1 "Uncharacterized protein" 0.883 0.396 0.590 1.8e-62
UNIPROTKB|A7YWH5 506 DKC1 "Uncharacterized protein" 0.883 0.405 0.590 1.8e-62
ZFIN|ZDB-GENE-031118-120 507 dkc1 "dyskeratosis congenita 1 0.922 0.422 0.557 2.3e-62
MGI|MGI:1861727 509 Dkc1 "dyskeratosis congenita 1 0.883 0.402 0.590 3e-62
RGD|621780 509 Dkc1 "dyskeratosis congenita 1 0.922 0.420 0.539 3.8e-62
UNIPROTKB|O60832 514 DKC1 "H/ACA ribonucleoprotein 0.883 0.398 0.586 1.3e-61
UNIPROTKB|F1P0Q8 470 DKC1 "H/ACA ribonucleoprotein 0.883 0.436 0.581 1.6e-61
FB|FBgn0259937 Nop60B "Nucleolar protein at 60B" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 692 (248.7 bits), Expect = 3.5e-68, P = 3.5e-68
 Identities = 134/215 (62%), Positives = 165/215 (76%)

Query:     1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
             NFDKLN+R+NHYTPL  G SPL R I+EY++ G++NLDKPSNPSSHEVVAWIK+IL+ EK
Sbjct:    56 NFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTGFINLDKPSNPSSHEVVAWIKKILKVEK 115

Query:    61 TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
             TGHSGTLDPK +GCLIVCIDRATRLVKSQQSAGKEY++IFKLH AVE+VAK       ++
Sbjct:   116 TGHSGTLDPKVTGCLIVCIDRATRLVKSQQSAGKEYVAIFKLHGAVESVAK-------VR 168

Query:   121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVR 180
             QGL    G   +  P   ++ ++     +  Y  S L+  D T + G+ W+ C+AG+Y+R
Sbjct:   169 QGLEKLRGALFQRPPL--ISAVKRQLRVRTVY-DSKLLDYDETRNMGVFWVSCEAGSYIR 225

Query:   181 TYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVT 215
             T CVH+GLVLGVG QM+ELRR RSGIQSE DG+VT
Sbjct:   226 TMCVHLGLVLGVGGQMLELRRVRSGIQSERDGMVT 260
GO:0005730 "nucleolus" evidence=ISS;NAS;IDA
GO:0042254 "ribosome biogenesis" evidence=IMP
GO:0006364 "rRNA processing" evidence=NAS;IMP
GO:0001522 "pseudouridine synthesis" evidence=IMP
GO:0005634 "nucleus" evidence=NAS
GO:0004730 "pseudouridylate synthase activity" evidence=ISS
GO:0007281 "germ cell development" evidence=IMP
GO:0003723 "RNA binding" evidence=IEA
GO:0009982 "pseudouridine synthase activity" evidence=IEA
GO:0035220 "wing disc development" evidence=IMP
GO:0022008 "neurogenesis" evidence=IMP
UNIPROTKB|F1RZ24 DKC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E2R6Q8 DKC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|F6XRK3 DKC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|A7YWH5 DKC1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-031118-120 dkc1 "dyskeratosis congenita 1, dyskerin" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
MGI|MGI:1861727 Dkc1 "dyskeratosis congenita 1, dyskerin" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|621780 Dkc1 "dyskeratosis congenita 1, dyskerin" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|O60832 DKC1 "H/ACA ribonucleoprotein complex subunit 4" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1P0Q8 DKC1 "H/ACA ribonucleoprotein complex subunit 4" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
P40615DKC1_RAT5, ., 4, ., 9, 9, ., -0.53070.92240.4204yesN/A
O26140TRUB_METTH5, ., 4, ., 9, 9, ., 2, 50.36910.84910.6080yesN/A
P33322CBF5_YEAST5, ., 4, ., 9, 9, ., -0.56100.86630.4161yesN/A
O43102CBF5_ASPFUNo assigned EC number0.54160.89220.4250yesN/A
O13473CBF5_KLULANo assigned EC number0.56190.86200.4219yesN/A
O44081DKC1_DROME5, ., 4, ., 9, 9, ., -0.62030.88790.4055yesN/A
O14007CBF5_SCHPO5, ., 4, ., 9, 9, ., -0.50430.92670.4535yesN/A
O17919DKC1_CAEEL5, ., 4, ., 9, 9, ., -0.55700.93960.4898yesN/A
Q5ZJH9DKC1_CHICK5, ., 4, ., 9, 9, ., -0.56940.88790.3992yesN/A
O43100CBF5_EMENINo assigned EC number0.54160.89220.4303yesN/A
O60832DKC1_HUMAN5, ., 4, ., 9, 9, ., -0.57400.88790.4007yesN/A
Q54T81DKC1_DICDI5, ., 4, ., 9, 9, ., -0.55090.88790.3814yesN/A
Q6AJY7TRUB_DESPS5, ., 4, ., 9, 9, ., 2, 50.31130.77580.7317yesN/A
Q9ESX5DKC1_MOUSE5, ., 4, ., 9, 9, ., -0.57870.88790.4047yesN/A
O30001TRUB_ARCFU5, ., 4, ., 9, 9, ., 2, 50.34280.84910.6061yesN/A
Q9LD90CBF5_ARATH5, ., 4, ., 9, 9, ., -0.56010.88790.3646yesN/A

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer5.4.99LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query232
cd02572182 cd02572, PseudoU_synth_hDyskerin, Pseudouridine sy 1e-80
TIGR00425 322 TIGR00425, CBF5, rRNA pseudouridine synthase, puta 3e-80
PRK04270300 PRK04270, PRK04270, H/ACA RNA-protein complex comp 6e-55
COG0130271 COG0130, TruB, Pseudouridine synthase [Translation 7e-50
cd00506210 cd00506, PseudoU_synth_TruB_like, Pseudouridine sy 9e-49
cd02573213 cd02573, PseudoU_synth_EcTruB, Pseudouridine synth 7e-31
pfam0806859 pfam08068, DKCLD, DKCLD (NUC011) domain 2e-24
TIGR00431209 TIGR00431, TruB, tRNA pseudouridine(55) synthase 1e-21
PRK00130290 PRK00130, truB, tRNA pseudouridine synthase B; Pro 2e-19
pfam01509149 pfam01509, TruB_N, TruB family pseudouridylate syn 4e-19
PRK14124308 PRK14124, PRK14124, tRNA pseudouridine synthase B; 1e-18
PRK03287298 PRK03287, truB, tRNA pseudouridine synthase B; Pro 2e-16
PRK01851303 PRK01851, truB, tRNA pseudouridine synthase B; Pro 1e-14
PRK01550 304 PRK01550, truB, tRNA pseudouridine synthase B; Pro 1e-14
PRK00020244 PRK00020, truB, tRNA pseudouridine synthase B; Pro 4e-14
PRK02484294 PRK02484, truB, tRNA pseudouridine synthase B; Pro 4e-14
PRK14123305 PRK14123, PRK14123, tRNA pseudouridine synthase B; 2e-13
PRK14122 312 PRK14122, PRK14122, tRNA pseudouridine synthase B; 6e-13
PRK02755295 PRK02755, truB, tRNA pseudouridine synthase B; Pro 8e-13
PRK01528292 PRK01528, truB, tRNA pseudouridine synthase B; Pro 8e-12
PRK02193279 PRK02193, truB, tRNA pseudouridine synthase B; Pro 3e-11
PRK14846 345 PRK14846, truB, tRNA pseudouridine synthase B; Pro 4e-11
PRK05389305 PRK05389, truB, tRNA pseudouridine synthase B; Pro 6e-11
PRK00989230 PRK00989, truB, tRNA pseudouridine synthase B; Pro 3e-10
PRK05033 312 PRK05033, truB, tRNA pseudouridine synthase B; Pro 3e-09
PRK04642300 PRK04642, truB, tRNA pseudouridine synthase B; Pro 1e-08
PRK04099273 PRK04099, truB, tRNA pseudouridine synthase B; Pro 4e-06
cd02867312 cd02867, PseudoU_synth_TruB_4, Pseudouridine synth 2e-05
PRK01550304 PRK01550, truB, tRNA pseudouridine synthase B; Pro 4e-04
PRK02484294 PRK02484, truB, tRNA pseudouridine synthase B; Pro 0.001
PRK05033312 PRK05033, truB, tRNA pseudouridine synthase B; Pro 0.004
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human dyskerin like Back     alignment and domain information 
 Score =  238 bits (610), Expect = 1e-80
 Identities = 99/200 (49%), Positives = 117/200 (58%), Gaps = 41/200 (20%)

Query: 31  RAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQ 90
           + G +NLDKPS PSSHEVVAWIKRIL  EKTGHSGTLDPK +GCL VCIDRATRLVKSQQ
Sbjct: 1   KYGVINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQ 60

Query: 91  SAGKEYISIFKLHSAV--ENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNK 148
            AGKEY+ + +LH  V  E V +                           L E   A  +
Sbjct: 61  EAGKEYVCVMRLHDDVDEEKVRRV--------------------------LEEFTGAIFQ 94

Query: 149 KP-------------TYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQ 195
           +P             T  +S L+  D      +  + C+AGTY+RT CVH+GL+LGVGA 
Sbjct: 95  RPPLISAVKRQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVHIGLLLGVGAH 154

Query: 196 MIELRRNRSGIQSEEDGLVT 215
           M ELRR RSG  SEED +VT
Sbjct: 155 MQELRRTRSGPFSEEDNMVT 174

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. Length = 182
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative Back     alignment and domain information
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB family Back     alignment and domain information
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>gnl|CDD|203846 pfam08068, DKCLD, DKCLD (NUC011) domain Back     alignment and domain information
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase Back     alignment and domain information
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal domain) Back     alignment and domain information
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4 Back     alignment and domain information
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 232
TIGR00431209 TruB tRNA pseudouridine 55 synthase. TruB, the tRN 100.0
TIGR00425 322 CBF5 rRNA pseudouridine synthase, putative. This f 100.0
PRK00020244 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 100.0
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14123305 tRNA pseudouridine synthase B; Provisional 100.0
PRK14124308 tRNA pseudouridine synthase B; Provisional 100.0
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 100.0
cd00506210 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudo 100.0
PRK00989230 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 100.0
PRK14846 345 truB tRNA pseudouridine synthase B; Provisional 100.0
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 100.0
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 100.0
cd02572182 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Li 100.0
PRK14122312 tRNA pseudouridine synthase B; Provisional 100.0
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 100.0
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 100.0
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 100.0
cd02868226 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Li 100.0
PF01509149 TruB_N: TruB family pseudouridylate synthase (N te 100.0
KOG2529|consensus 395 100.0
KOG2559|consensus318 99.95
PF0806859 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 99.56
TIGR01213388 conserved hypothetical protein TIGR01213. Members 99.37
cd0129187 PseudoU_synth PseudoU_synth: Pseudouridine synthas 99.23
PRK14554422 putative pseudouridylate synthase; Provisional 99.23
COG1258398 Predicted pseudouridylate synthase [Translation, r 98.76
cd02566168 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridi 98.53
cd02553167 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridi 98.26
cd02554164 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudo 98.16
PRK10700289 23S rRNA pseudouridylate synthase B; Provisional 98.12
cd02556167 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridi 98.11
PRK10475290 23S rRNA pseudouridine synthase F; Provisional 98.03
PRK11394217 23S rRNA pseudouridine synthase E; Provisional 98.03
cd02555177 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup 97.79
TIGR01621217 RluA-like pseudouridine synthase Rlu family protei 97.78
PRK10158219 23S rRNA/tRNA pseudouridine synthase A; Provisiona 97.77
cd02558246 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup 97.73
PRK10839232 16S rRNA pseudouridylate synthase A; Provisional 97.72
cd02557213 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Ps 97.72
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 97.66
COG0564289 RluA Pseudouridylate synthases, 23S RNA-specific [ 97.57
cd02563223 PseudoU_synth_TruC tRNA pseudouridine isomerase C: 97.53
TIGR00005299 rluA_subfam pseudouridine synthase, RluA family. m 97.39
COG1187248 RsuA 16S rRNA uridine-516 pseudouridylate synthase 97.32
cd02550154 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: 97.28
PRK11180325 rluD 23S rRNA pseudouridine synthase D; Provisiona 97.27
PRK11112257 tRNA pseudouridine synthase C; Provisional 97.27
PRK11025317 23S rRNA pseudouridylate synthase C; Provisional 97.14
PF00849164 PseudoU_synth_2: RNA pseudouridylate synthase This 97.01
cd02869185 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: 96.89
cd02870146 PseudoU_synth_RsuA_like Pseudouridine synthases ar 96.61
KOG1919|consensus371 96.06
TIGR00093128 pseudouridine synthase. This model identifies pane 95.87
KOG2529|consensus395 91.71
>TIGR00431 TruB tRNA pseudouridine 55 synthase Back     alignment and domain information 
Probab=100.00  E-value=1.5e-69  Score=469.61  Aligned_cols=184  Identities=26%  Similarity=0.407  Sum_probs=174.9

Q ss_pred             cceEEEEeCCCCCCHHHHHHHHHHHhccccccCCCCCCCCceEEEEEEEccccccchhhhcCCceEEEEEEecceecccc
Q psy1176          31 RAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVA  110 (232)
Q Consensus        31 ~~Gil~v~KP~G~tS~~vv~~ik~~l~~~KvGH~GTLDP~AtGvLvv~iG~aTkl~~~l~~~~K~Y~a~~~lG~~tdt~~  110 (232)
                      +||||+||||+||||||||+++||.++.+||||+|||||+|||||++|+|+|||+++|+++.+|+|+++++||.+|||.|
T Consensus         1 ~~G~l~v~KP~g~tS~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~~G~~TdT~D   80 (209)
T TIGR00431         1 INGVLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLGVRTDTLD   80 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHhhhhHHHcCCCCeEEEEEEECCcCCCCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             c---------ccCcHHHHHHHHhcCccCceecCCccCccceeeCC----------------CCccEEEEEEeeEeeCCCc
Q psy1176         111 K---------ASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAP----------------NKKPTYMKSNLISSDVTLS  165 (232)
Q Consensus       111 ~---------v~~t~e~l~~~l~~f~G~i~Q~PP~~~ySAvK~~G----------------~R~v~Iy~i~l~~~~~~~~  165 (232)
                      .         ..++.|+|++++++|+|+++|+||+  |||+|++|                +|+++||++++++|+.  |
T Consensus        81 ~~G~i~~~~~~~~~~~~l~~~l~~f~G~~~Q~PP~--ySA~Kv~G~raYelAR~g~~v~~~~r~v~I~~i~ll~~~~--~  156 (209)
T TIGR00431        81 PDGQIVETRPVNPTTEDVEAALPTFRGEIEQIPPM--YSALKVNGKRLYEYARQGIEVERKARPVTVYDLQFLKYEG--P  156 (209)
T ss_pred             CCCCEEEecCCCCCHHHHHHHHHHccCcEEEECCh--hhEEeeCCHhHHHHHHCCCccccCcceeEEEEEEEEEEcC--C
Confidence            2         2357899999999999999999999  99999998                4689999999999976  7


Q ss_pred             eEEEEEEeeCCcchHHHHHHHHhhcCCcEEEeeEEEEEEeCccCcccccChHHH
Q psy1176         166 TGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQE  219 (232)
Q Consensus       166 ~~~~~v~cs~GTYIRsL~~DiG~~Lg~~A~l~~LrRt~~G~f~l~da~~~l~~l  219 (232)
                      .+.|+|+||+||||||||+|||.+|||+|||++||||++|+|+++|| +++|||
T Consensus       157 ~~~~~v~cs~GTYIRsL~~Dig~~L~~~a~l~~L~Rt~~G~f~~~~a-~~l~~l  209 (209)
T TIGR00431       157 ELTLEVHCSKGTYIRTLARDLGEKLGCGAYVSHLRRTAVGDFPLDQS-VTLEEL  209 (209)
T ss_pred             cEEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEeEEECCCcHHHc-CChhhC
Confidence            99999999999999999999999999999999999999999999996 899875

TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of 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
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information
>PRK00020 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family Back     alignment and domain information
>PRK00989 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>PRK14122 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like Back     alignment and domain information
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones Back     alignment and domain information
>KOG2529|consensus Back     alignment and domain information
>KOG2559|consensus Back     alignment and domain information
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [] Back     alignment and domain information
>TIGR01213 conserved hypothetical protein TIGR01213 Back     alignment and domain information
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>PRK14554 putative pseudouridylate synthase; Provisional Back     alignment and domain information
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE Back     alignment and domain information
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like Back     alignment and domain information
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>PRK11394 23S rRNA pseudouridine synthase E; Provisional Back     alignment and domain information
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family Back     alignment and domain information
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621 Back     alignment and domain information
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional Back     alignment and domain information
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi) Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11112 tRNA pseudouridine synthase C; Provisional Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family Back     alignment and domain information
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family Back     alignment and domain information
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA Back     alignment and domain information
>KOG1919|consensus Back     alignment and domain information
>TIGR00093 pseudouridine synthase Back     alignment and domain information
>KOG2529|consensus Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query232
3u28_A 400 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From 4e-65
2aus_C 334 Crystal Structure Of The Archaeal Box HACA SRNP NOP 6e-37
3hjw_A 327 Structure Of A Functional Ribonucleoprotein Pseudou 5e-35
3mqk_A 328 Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Cont 6e-35
2ey4_A333 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Leng 6e-35
3lwo_A 340 Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONT 6e-35
2hvy_A 346 Crystal Structure Of An HACA BOX RNP FROM PYROCOCCU 6e-35
2rfk_A 334 Substrate Rna Positioning In The Archaeal HACA Ribo 7e-34
2apo_A 357 Crystal Structure Of The Methanococcus Jannaschii C 2e-27
1sgv_A316 Structure Of Trna Psi55 Pseudouridine Synthase (Tru 2e-15
1r3e_A309 Crystal Structure Of Trna Pseudouridine Synthase Tr 3e-13
1ze1_A309 Conformational Change Of Pseudouridine 55 Synthase 3e-13
1ze2_A309 Conformational Change Of Pseudouridine 55 Synthase 3e-13
2ab4_A309 Dissecting The Roles Of A Strictly Conserved Tyrosi 8e-13
1k8w_A327 Crystal Structure Of The E. Coli Pseudouridine Synt 7e-10
1r3f_A314 Crystal Structure Of Trna Pseudouridine Synthase Tr 7e-10
1zl3_A327 Coupling Of Active Site Motions And Rna Binding Len 3e-09
3zv0_C195 Structure Of The Shq1p-Cbf5p Complex Length = 195 7e-09
>pdb|3U28|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From Saccharomyces Cerevisiae Length = 400 Back     alignment and structure 
Iteration: 1

 Score =  244 bits (622), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 122/216 (56%), Positives = 150/216 (69%), Gaps = 10/216 (4%)
Query: 1   NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
           NFDKL VR+ HYTP+P G SPL+R ++ YI +G +NLDKPSNPSSHEVVAWIKRILRCEK
Sbjct: 28  NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEK 87
Query: 61  TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIK 120
           TGHSGTLDPK +GCLIVCIDRATRLVKSQQ AGKEY+ I +LH A+       K +  + 
Sbjct: 88  TGHSGTLDPKVTGCLIVCIDRATRLVKSQQGAGKEYVCIVRLHDAL-------KDEKDLG 140
Query: 121 QGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVR 180
           + L +  G   +  P     + +    +  T  +SNLI  D   + G+ W  C+AGTY+R
Sbjct: 141 RSLENLTGALFQRPPLISAVKRQL---RVRTIYESNLIEFDNKRNLGVFWASCEAGTYMR 197
Query: 181 TYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTF 216
           T CVH+G++LGVG  M ELRR RSG  SE D +VT 
Sbjct: 198 TLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTL 233
>pdb|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5 Complex Length = 334 Back     alignment and structure
>pdb|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine Synthase Bound To A Substrate Rna Length = 327 Back     alignment and structure
>pdb|3MQK|A Chain A, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing Aca Trinucleotide Length = 328 Back     alignment and structure
>pdb|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Length = 333 Back     alignment and structure
>pdb|3LWO|A Chain A, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING 5BRU Length = 340 Back     alignment and structure
>pdb|2HVY|A Chain A, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS FURIOSUS Length = 346 Back     alignment and structure
>pdb|2RFK|A Chain A, Substrate Rna Positioning In The Archaeal HACA Ribonucleoprotein Complex Length = 334 Back     alignment and structure
>pdb|2APO|A Chain A, Crystal Structure Of The Methanococcus Jannaschii Cbf5 Nop10 Complex Length = 357 Back     alignment and structure
>pdb|1SGV|A Chain A, Structure Of Trna Psi55 Pseudouridine Synthase (Trub) Length = 316 Back     alignment and structure
>pdb|1R3E|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And Its Rna Complex: Rna-Protein Recognition Through A Combination Of Rigid Docking And Induced Fit Length = 309 Back     alignment and structure
>pdb|1ZE1|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon Its Association With Rna Substrate Length = 309 Back     alignment and structure
>pdb|1ZE2|A Chain A, Conformational Change Of Pseudouridine 55 Synthase Upon Its Association With Rna Substrate Length = 309 Back     alignment and structure
>pdb|2AB4|A Chain A, Dissecting The Roles Of A Strictly Conserved Tyrosine In Substrate Recognition And Catalysis By Pseudouridine 55 Synthase Length = 309 Back     alignment and structure
>pdb|1K8W|A Chain A, Crystal Structure Of The E. Coli Pseudouridine Synthase Trub Bound To A T Stem-Loop Rna Length = 327 Back     alignment and structure
>pdb|1R3F|A Chain A, Crystal Structure Of Trna Pseudouridine Synthase Trub And Its Rna Complex: Rna-Protein Recognition Through A Combination Of Rigid Docking And Induced Fit Length = 314 Back     alignment and structure
>pdb|1ZL3|A Chain A, Coupling Of Active Site Motions And Rna Binding Length = 327 Back     alignment and structure
>pdb|3ZV0|C Chain C, Structure Of The Shq1p-Cbf5p Complex Length = 195 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query232
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 3e-77
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 3e-75
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 1e-07
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 3e-74
1r3e_A 309 TRNA pseudouridine synthase B; RNA modification, p 3e-22
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 1e-07
1sgv_A 316 TRNA pseudouridine synthase B; hinged motion, tRNA 4e-22
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 1e-07
1k8w_A 327 TRNA pseudouridine synthase B; protein-RNA complex 2e-21
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 2e-07
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 6e-09
3zv0_C195 H/ACA ribonucleoprotein complex subunit 4; cell cy 4e-08
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Length = 357 Back     alignment and structure
 Score =  235 bits (602), Expect = 3e-77
 Identities = 72/221 (32%), Positives = 112/221 (50%), Gaps = 20/221 (9%)

Query: 1   NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEK 60
           + ++L V+    T   +G +P +R I++ I+ G V +DKP  P+SHEV  W+K+IL  +K
Sbjct: 35  DKEELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDK 94

Query: 61  TGHSGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAV--ENVAKASKK-KM 117
            GH GTLDPK +G L V ++RAT+ +       KEY+ +  LH     E++ +  K+   
Sbjct: 95  AGHGGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHRDASEEDILRVFKEFTG 154

Query: 118 MIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGT 177
            I Q             P    A ++     +  + +  L+  D      +  +KCQ+GT
Sbjct: 155 RIYQ------------RPPLKAA-VKRRLRIRKIH-ELELLDKD--GKDVLFRVKCQSGT 198

Query: 178 YVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQ 218
           Y+R  C  +G  LG  A M ELRR +SG   E+D  V  + 
Sbjct: 199 YIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKD-AVYLQD 238
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Length = 400 Back     alignment and structure
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Length = 400 Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Length = 334 Back     alignment and structure
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Length = 309 Back     alignment and structure
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Length = 309 Back     alignment and structure
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Length = 316 Back     alignment and structure
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Length = 316 Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Length = 327 Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Length = 327 Back     alignment and structure
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens} Length = 530 Back     alignment and structure
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP assembly, X-linked dyskeratosis congenita; 2.80A {Saccharomyces cerevisiae} Length = 195 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query232
3u28_A 400 H/ACA ribonucleoprotein complex subunit 4; pseudou 100.0
2apo_A 357 Probable tRNA pseudouridine synthase B; protein-pr 100.0
2aus_C 334 Pseudouridine synthase; isomerase, structural prot 100.0
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 100.0
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 100.0
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 100.0
2v9k_A530 Uncharacterized protein FLJ32312; pseudouridine sy 99.35
3dh3_A290 Ribosomal large subunit pseudouridine synthase F; 98.73
1v9k_A228 Ribosomal large subunit pseudouridine synthase C; 97.88
2gml_A237 Ribosomal large subunit pseudouridine synthase F; 97.86
1vio_A243 Ribosomal small subunit pseudouridine synthase A; 97.32
2i82_A217 Ribosomal large subunit pseudouridine synthase A; 97.28
1ksk_A234 Ribosomal small subunit pseudouridine synthase A; 97.24
1v9f_A325 Ribosomal large subunit pseudouridine synthase D; 97.17
2oml_A189 Ribosomal large subunit pseudouridine synthase E; 97.08
2olw_A217 Ribosomal large subunit pseudouridine synthase E; 96.94
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A Back     alignment and structure
Probab=100.00  E-value=2.6e-73  Score=530.52  Aligned_cols=212  Identities=57%  Similarity=0.951  Sum_probs=200.4

Q ss_pred             CCcccceeccCCCCCCCCCCCCccchhhhccceEEEEeCCCCCCHHHHHHHHHHHhccccccCCCCCCCCceEEEEEEEc
Q psy1176           1 NFDKLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCID   80 (232)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gil~v~KP~G~tS~~vv~~ik~~l~~~KvGH~GTLDP~AtGvLvv~iG   80 (232)
                      |||+|++|++++||+++|+.|.+|++.+++.+|||+||||+||||||||+|+|++|+.+|+||+|||||+||||||||+|
T Consensus        28 ~~~~~~~~~~~~t~~~~g~~p~~r~~~~~~~~Gil~ldKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~iG  107 (400)
T 3u28_A           28 NFDKLLVRSGHYTPIPAGSSPLKRDLKSYISSGVINLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCID  107 (400)
T ss_dssp             TGGGSEESCSCCCCCCCSCCGGGCCHHHHHHTEEEEEEECSSSCHHHHHHHHHHHHTCSCEEESSCCCTTCEEEEEEEEG
T ss_pred             chHheeeecccccCCccCCCcCcCCHHHhccCcEEEEECCCCCCHHHHHHHHHHHhCcCcccccCCCCCCCeEEEEEEEC
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccchhhhcCCceEEEEEEecceecccccccCcHHHHHHHHhcCccCceecCCccCccceeeCCCCccEEEEEEeeEe
Q psy1176          81 RATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISS  160 (232)
Q Consensus        81 ~aTkl~~~l~~~~K~Y~a~~~lG~~tdt~~~v~~t~e~l~~~l~~f~G~i~Q~PP~~~ySAvK~~G~R~v~Iy~i~l~~~  160 (232)
                      +|||+++|+++.+|+|+++++||.+++       ++++|++++++|+|.|+|+||+  |||+|++ .|+++||++++++|
T Consensus       108 ~aTKl~~~l~~~~K~Y~a~~~lG~~~~-------~~~~i~~~l~~f~G~i~Q~PP~--ySAvK~~-~R~v~I~~i~ll~~  177 (400)
T 3u28_A          108 RATRLVKSQQGAGKEYVCIVRLHDALK-------DEKDLGRSLENLTGALFQRPPL--ISAVKRQ-LRVRTIYESNLIEF  177 (400)
T ss_dssp             GGGGGHHHHHHSCEEEEEEEEESSCCS-------STTHHHHHHHHTCEEEEECCC-------CCC-CEEEEEEEEEEEEE
T ss_pred             hHHhHhHHhcCCCcEEEEEEEeCCCCC-------CHHHHHHHHHhCcCceEEECCc--eecccCC-ceeEEEEEEEEEEE
Confidence            999999999999999999999999874       6788999999999999999999  9999998 89999999999999


Q ss_pred             eCCCceEEEEEEeeCCcchHHHHHHHHhhcCCcEEEeeEEEEEEeCccCcccccChHHHHhc
Q psy1176         161 DVTLSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMF  222 (232)
Q Consensus       161 ~~~~~~~~~~v~cs~GTYIRsL~~DiG~~Lg~~A~l~~LrRt~~G~f~l~da~~~l~~l~~~  222 (232)
                      +.+.+.++|+|+||+||||||||+|||++|||+|||++||||++|+|+++|+++||+||.+.
T Consensus       178 ~~~~~~~~~~V~CskGTYIRsL~~DiG~~LG~gahm~~LrRt~~G~F~~~~a~vtL~~l~~~  239 (400)
T 3u28_A          178 DNKRNLGVFWASCEAGTYMRTLCVHLGMLLGVGGHMQELRRVRSGALSENDNMVTLHDVMDA  239 (400)
T ss_dssp             ETTTTEEEEEEEECTTCCHHHHHHHHHHHHSSCEEEEEEEEEEETTEETTSSCBCHHHHHHH
T ss_pred             cCCCceEEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEEEEEEEcCcchhhhcCCHHHHHHh
Confidence            87667899999999999999999999999999999999999999999999988999999753
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A Back     alignment and structure
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A Back     alignment and structure
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2 Back     alignment and structure
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A Back     alignment and structure
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens} Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A Back     alignment and structure
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli} Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli} Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli} Back     alignment and structure
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 232
d2apoa2230 d.265.1.2 (A:17-246) Pseudouridine synthase II Tru 3e-47
d2ey4a2245 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB 3e-44
d1sgva2233 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB 1e-35
d1r3ea2228 d.265.1.2 (A:10-237) Pseudouridine synthase II Tru 2e-34
d1k8wa5242 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB 6e-33
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 230 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  154 bits (389), Expect = 3e-47
 Identities = 69/208 (33%), Positives = 102/208 (49%), Gaps = 13/208 (6%)

Query: 4   KLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGH 63
           +L V+    T   +G +P +R I++ I+ G V +DKP  P+SHEV  W+K+IL  +K GH
Sbjct: 1   ELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAGH 60

Query: 64  SGTLDPKTSGCLIVCIDRATRLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGL 123
            GTLDPK +G L V ++RAT+ +       KEY+ +  LH            +  I +  
Sbjct: 61  GGTLDPKVTGVLPVALERATKTIPMWHIPPKEYVCLMHLHR--------DASEEDILRVF 112

Query: 124 LDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVTLSTGIIWLKCQAGTYVRTYC 183
            +  G+  +  P     +      K        L   D      +  +KCQ+GTY+R  C
Sbjct: 113 KEFTGRIYQRPPLKAAVKRRLRIRKIH-----ELELLDKDGKDVLFRVKCQSGTYIRKLC 167

Query: 184 VHMGLVLGVGAQMIELRRNRSGIQSEED 211
             +G  LG  A M ELRR +SG   E+D
Sbjct: 168 EDIGEALGTSAHMQELRRTKSGCFEEKD 195
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 245 Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Length = 233 Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Length = 228 Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Length = 242 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query232
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 100.0
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 100.0
d1sgva2233 Pseudouridine synthase II TruB {Mycobacterium tube 100.0
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 100.0
d1r3ea2228 Pseudouridine synthase II TruB {Thermotoga maritim 100.0
d1vioa1174 Ribosomal small subunit pseudouridine 516 synthase 98.42
d1kska4172 Ribosomal small subunit pseudouridine 516 synthase 98.22
d1v9fa_250 Ribosomal large subunit pseudouridine synthase D, 97.51
d1v9ka_227 Ribosomal large subunit pseudouridine synthase C, 97.4
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Pseudouridine synthase
superfamily: Pseudouridine synthase
family: Pseudouridine synthase II TruB
domain: Pseudouridine synthase II TruB
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=1.3e-72  Score=491.80  Aligned_cols=205  Identities=34%  Similarity=0.570  Sum_probs=186.2

Q ss_pred             ccceeccCCCCCCCCCCCCccchhhhccceEEEEeCCCCCCHHHHHHHHHHHhccccccCCCCCCCCceEEEEEEEcccc
Q psy1176           4 KLNVRTNHYTPLPFGKSPLQRTIQEYIRAGYVNLDKPSNPSSHEVVAWIKRILRCEKTGHSGTLDPKTSGCLIVCIDRAT   83 (232)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Gil~v~KP~G~tS~~vv~~ik~~l~~~KvGH~GTLDP~AtGvLvv~iG~aT   83 (232)
                      +|.++++..|+..+|.+|.+|++.+++.+|||+||||.|||||+||+++||+++.+||||+|||||+||||||||+|+||
T Consensus         1 ~~~~~~~~~~~~~~g~~p~~r~i~~~~~~G~l~idKP~G~TS~~vv~~ikk~l~~kKvGH~GTLDP~AtGvL~v~iG~aT   80 (230)
T d2apoa2           1 ELIVKEEVETNWDYGCNPYERKIEDLIKYGVVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERAT   80 (230)
T ss_dssp             CEEESSCCCCCTTSSCCGGGCCHHHHHHTEEEEEEECSSSCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGG
T ss_pred             CeEeccCCcCCcccCCCcccCCHHHHhcCcEEEEECCCCCCHHHHHHHHHHHcCCCCCCcccccCccceeeeeeeecHHH
Confidence            46788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhhcCCceEEEEEEecceecccccccCcHHHHHHHHhcCccCceecCCccCccceeeCCCCccEEEEEEeeEeeCC
Q psy1176          84 RLVKSQQSAGKEYISIFKLHSAVENVAKASKKKMMIKQGLLDKHGKPNENTPASYLAELEAAPNKKPTYMKSNLISSDVT  163 (232)
Q Consensus        84 kl~~~l~~~~K~Y~a~~~lG~~tdt~~~v~~t~e~l~~~l~~f~G~i~Q~PP~~~ySAvK~~G~R~v~Iy~i~l~~~~~~  163 (232)
                      |+++|++..+|+|++++.||..|++        ++|++++++|.|+++|+||+  |||+|++ .|.++||++++++++. 
T Consensus        81 Kl~~~~~~~~K~Y~~~~~~g~~t~~--------~di~~~l~~f~G~i~Q~PP~--ySAiK~~-~r~~~i~~l~l~~~~~-  148 (230)
T d2apoa2          81 KTIPMWHIPPKEYVCLMHLHRDASE--------EDILRVFKEFTGRIYQRPPL--KAAVKRR-LRIRKIHELELLDKDG-  148 (230)
T ss_dssp             GGGGGTTSSCEEEEEEEEESSCCCH--------HHHHHHHHHHSEEEECC--------------CEEEEEEEEEEEEET-
T ss_pred             HHHHHHhccCceEEEEEEeeccccH--------hHHHHHHHhccCcccccCCe--eeeeccc-cceeeeEEeeeccccC-
Confidence            9999999999999999999999964        45889999999999999999  9999998 7899999999999987 


Q ss_pred             CceEEEEEEeeCCcchHHHHHHHHhhcCCcEEEeeEEEEEEeCccCcccccChHHHHhc
Q psy1176         164 LSTGIIWLKCQAGTYVRTYCVHMGLVLGVGAQMIELRRNRSGIQSEEDGLVTFRQEHMF  222 (232)
Q Consensus       164 ~~~~~~~v~cs~GTYIRsL~~DiG~~Lg~~A~l~~LrRt~~G~f~l~da~~~l~~l~~~  222 (232)
                       |.+.|+|+||+||||||||+|||++|||+|||++||||++|+|+++|| ++|+||.+.
T Consensus       149 -~~~~~~V~CSkGTYIRSLa~DlG~~Lg~~a~l~~LrRt~~G~f~l~~a-i~l~dl~~a  205 (230)
T d2apoa2         149 -KDVLFRVKCQSGTYIRKLCEDIGEALGTSAHMQELRRTKSGCFEEKDA-VYLQDLLDA  205 (230)
T ss_dssp             -TEEEEEEEECTTCCHHHHHHHHHHHTTSCEEEEEEEEEEETTEEGGGC-BCHHHHHHH
T ss_pred             -CeEEEEEEECCCccHHHHHHHHHHHcCCEEEEeECcCCccCCcCHHHc-cCHHHHHHH
Confidence             799999999999999999999999999999999999999999999996 899999764
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1sgva2 d.265.1.2 (A:3-235) Pseudouridine synthase II TruB {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1k8wa5 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r3ea2 d.265.1.2 (A:10-237) Pseudouridine synthase II TruB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1vioa1 d.265.1.3 (A:58-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska4 d.265.1.3 (A:60-231) Ribosomal small subunit pseudouridine 516 synthase RsuA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9fa_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase D, RluD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v9ka_ d.265.1.3 (A:) Ribosomal large subunit pseudouridine synthase C, RluC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure