Psyllid ID: psy1178

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 (MEMSAT_SVM) ?
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----
MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS
ccccEEEEEEcccccccEEHHHHHHHHHHHHHHccccHHcccEEEEccccccccccEEEcccHHHHHHcccccccccEEEcccccccccEEEEEEccccEEEEEEEEccccccccccccEEEEEEEEEEccccccccccccccc
cHHHHHHcccccccccccEEHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccEEEEEccHHHHHHHccHEEcccEEEEccccccccEEEEEEccHHHHHHHHHHccHHHHHcccccEEEEEEEEEEccccccccccccccc
mielrrnrsgiqseedglvTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAqimlpgvlryedgiemdEEIVIVSTKGEAVALALAQMTTstmatcdhGVVAKIKRVImdrdtyprkwglgpks
mielrrnrsgiqseedglvTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTtstmatcdhgvvakikrvimdrdtyprkwglgpks
MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS
*****************LVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKW******
*IELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLG***
***********QSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS
***********Q**EDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGL****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS
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 ?
Query144 2.2.26 [Sep-21-2011]
O44081 508 H/ACA ribonucleoprotein c yes N/A 1.0 0.283 0.798 9e-67
O60832 514 H/ACA ribonucleoprotein c yes N/A 1.0 0.280 0.708 1e-60
Q9ESX5 509 H/ACA ribonucleoprotein c yes N/A 1.0 0.282 0.701 5e-60
P40615 509 H/ACA ribonucleoprotein c yes N/A 1.0 0.282 0.701 3e-59
Q5ZJH9 516 H/ACA ribonucleoprotein c yes N/A 1.0 0.279 0.708 3e-58
Q54T81 540 Probable H/ACA ribonucleo yes N/A 1.0 0.266 0.680 4e-57
O14007 474 H/ACA ribonucleoprotein c yes N/A 1.0 0.303 0.673 7e-57
O13473 474 Centromere/microtubule-bi yes N/A 0.986 0.299 0.676 1e-55
O43101 479 Centromere/microtubule-bi N/A N/A 0.986 0.296 0.647 9e-55
O43102 487 Centromere/microtubule-bi yes N/A 0.986 0.291 0.654 1e-54
>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 =  251 bits (641), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 115/144 (79%), Positives = 135/144 (93%)

Query: 1   MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
           M+ELRR RSGIQSE DG+VT+HD+ DAM+LY+ HKDES+LRRVI+PLEGLLV HKRII+K
Sbjct: 241 MLELRRVRSGIQSERDGMVTMHDVLDAMWLYENHKDESMLRRVIKPLEGLLVNHKRIIMK 300

Query: 61  DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
           DS+VNAVCYGA+I LPGVLRYEDGIE+D+EIVI +TKGEA+ LA+A MTT+TMA+CDHGV
Sbjct: 301 DSSVNAVCYGAKITLPGVLRYEDGIEIDQEIVICTTKGEAICLAIALMTTATMASCDHGV 360

Query: 121 VAKIKRVIMDRDTYPRKWGLGPKS 144
           VAKIKRVIM+RDTYPRKWGLGPK+
Sbjct: 361 VAKIKRVIMERDTYPRKWGLGPKA 384
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|O60832|DKC1_HUMAN H/ACA ribonucleoprotein complex subunit 4 OS=Homo sapiens GN=DKC1 PE=1 SV=3 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|Q5ZJH9|DKC1_CHICK H/ACA ribonucleoprotein complex subunit 4 OS=Gallus gallus GN=DKC1 PE=2 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|O14007|CBF5_SCHPO H/ACA ribonucleoprotein complex subunit 4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cbf5 PE=3 SV=1 Back     alignment and function description
>sp|O13473|CBF5_KLULA Centromere/microtubule-binding protein CBF5 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=CBF5 PE=3 SV=1 Back     alignment and function description
>sp|O43101|CBF5_CANAL Centromere/microtubule-binding protein CBF5 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=CBF5 PE=3 SV=1 Back     alignment and function description
>sp|O43102|CBF5_ASPFU Centromere/microtubule-binding protein cbf5 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 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 ?
Query144
157136797 527 centromere/microtubule binding protein c 1.0 0.273 0.833 1e-67
195431316 1467 GK15777 [Drosophila willistoni] gi|19415 1.0 0.098 0.798 6e-67
289741503 613 pseudouridine synthase [Glossina morsita 1.0 0.234 0.798 3e-66
312373002 500 hypothetical protein AND_19384 [Anophele 1.0 0.288 0.826 5e-66
158297969 521 AGAP004739-PA [Anopheles gambiae str. PE 1.0 0.276 0.812 6e-66
223950515 534 MIP05689p [Drosophila melanogaster] 1.0 0.269 0.798 4e-65
375065910 534 FI18403p1 [Drosophila melanogaster] 1.0 0.269 0.798 5e-65
157816752 489 LD07711p [Drosophila melanogaster] 1.0 0.294 0.798 5e-65
19528063 468 AT23018p, partial [Drosophila melanogast 1.0 0.307 0.798 6e-65
4406198 508 minifly protein [Drosophila melanogaster 1.0 0.283 0.798 6e-65
>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
 Score =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 120/144 (83%), Positives = 138/144 (95%)

Query: 1   MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
           M+ELRR RSGIQSE+DG+VT+HD+ DA YLYD HKDE++LRRVI+PLEGLLVGHKRII+K
Sbjct: 247 MLELRRVRSGIQSEKDGMVTMHDVLDAQYLYDNHKDETMLRRVIKPLEGLLVGHKRIIMK 306

Query: 61  DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
           DS+VNAVCYGA+IMLPGVLRYEDGIEMD+EIVIV+TKGEAVALA+A MTT+TMA+CDHGV
Sbjct: 307 DSSVNAVCYGAKIMLPGVLRYEDGIEMDQEIVIVTTKGEAVALAIALMTTATMASCDHGV 366

Query: 121 VAKIKRVIMDRDTYPRKWGLGPKS 144
            AKIKRVIM+RDTYPRKWGLGPK+
Sbjct: 367 CAKIKRVIMERDTYPRKWGLGPKA 390

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|195431316|ref|XP_002063689.1| GK15777 [Drosophila willistoni] gi|194159774|gb|EDW74675.1| GK15777 [Drosophila willistoni] Back     alignment and taxonomy information
>gi|289741503|gb|ADD19499.1| pseudouridine synthase [Glossina morsitans morsitans] Back     alignment and taxonomy information
>gi|312373002|gb|EFR20835.1| hypothetical protein AND_19384 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|158297969|ref|XP_318082.4| AGAP004739-PA [Anopheles gambiae str. PEST] gi|157014582|gb|EAA13199.5| AGAP004739-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|223950515|gb|ACN29341.1| MIP05689p [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|375065910|gb|AFA28436.1| FI18403p1 [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|157816752|gb|ABV82369.1| LD07711p [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|19528063|gb|AAL90146.1| AT23018p, partial [Drosophila melanogaster] Back     alignment and taxonomy information
>gi|4406198|gb|AAD19897.1| minifly protein [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 ?
Query144
FB|FBgn0259937 508 Nop60B "Nucleolar protein at 6 1.0 0.283 0.798 1.2e-60
UNIPROTKB|E2R6Q8464 DKC1 "Uncharacterized protein" 1.0 0.310 0.715 5.3e-56
UNIPROTKB|F6XRK3 517 DKC1 "Uncharacterized protein" 1.0 0.278 0.715 5.3e-56
UNIPROTKB|A7YWH5 506 DKC1 "Uncharacterized protein" 1.0 0.284 0.708 1.1e-55
UNIPROTKB|H7C2Q2208 DKC1 "H/ACA ribonucleoprotein 1.0 0.692 0.708 1.1e-55
UNIPROTKB|O60832 514 DKC1 "H/ACA ribonucleoprotein 1.0 0.280 0.708 1.1e-55
UNIPROTKB|F1RZ24 521 DKC1 "Uncharacterized protein" 1.0 0.276 0.715 1.1e-55
MGI|MGI:1861727 509 Dkc1 "dyskeratosis congenita 1 1.0 0.282 0.701 2.3e-55
RGD|621780 509 Dkc1 "dyskeratosis congenita 1 1.0 0.282 0.701 9.9e-55
UNIPROTKB|F1P0Q8 470 DKC1 "H/ACA ribonucleoprotein 1.0 0.306 0.708 7e-54
FB|FBgn0259937 Nop60B "Nucleolar protein at 60B" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 621 (223.7 bits), Expect = 1.2e-60, P = 1.2e-60
 Identities = 115/144 (79%), Positives = 135/144 (93%)

Query:     1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
             M+ELRR RSGIQSE DG+VT+HD+ DAM+LY+ HKDES+LRRVI+PLEGLLV HKRII+K
Sbjct:   241 MLELRRVRSGIQSERDGMVTMHDVLDAMWLYENHKDESMLRRVIKPLEGLLVNHKRIIMK 300

Query:    61 DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
             DS+VNAVCYGA+I LPGVLRYEDGIE+D+EIVI +TKGEA+ LA+A MTT+TMA+CDHGV
Sbjct:   301 DSSVNAVCYGAKITLPGVLRYEDGIEIDQEIVICTTKGEAICLAIALMTTATMASCDHGV 360

Query:   121 VAKIKRVIMDRDTYPRKWGLGPKS 144
             VAKIKRVIM+RDTYPRKWGLGPK+
Sbjct:   361 VAKIKRVIMERDTYPRKWGLGPKA 384
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|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
UNIPROTKB|H7C2Q2 DKC1 "H/ACA ribonucleoprotein complex subunit 4" [Homo sapiens (taxid:9606)] 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|F1RZ24 DKC1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] 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|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, ., -0.70131.00.2829yesN/A
P33322CBF5_YEAST5, ., 4, ., 9, 9, ., -0.66190.98610.2939yesN/A
O43102CBF5_ASPFUNo assigned EC number0.65490.98610.2915yesN/A
O13473CBF5_KLULANo assigned EC number0.67600.98610.2995yesN/A
O44081DKC1_DROME5, ., 4, ., 9, 9, ., -0.79861.00.2834yesN/A
O14007CBF5_SCHPO5, ., 4, ., 9, 9, ., -0.67361.00.3037yesN/A
O17919DKC1_CAEEL5, ., 4, ., 9, 9, ., -0.64780.98610.3191yesN/A
Q5ZJH9DKC1_CHICK5, ., 4, ., 9, 9, ., -0.70831.00.2790yesN/A
O43100CBF5_EMENINo assigned EC number0.65490.98610.2952yesN/A
O60832DKC1_HUMAN5, ., 4, ., 9, 9, ., -0.70831.00.2801yesN/A
Q54T81DKC1_DICDI5, ., 4, ., 9, 9, ., -0.68051.00.2666yesN/A
Q9ESX5DKC1_MOUSE5, ., 4, ., 9, 9, ., -0.70131.00.2829yesN/A
Q9LD90CBF5_ARATH5, ., 4, ., 9, 9, ., -0.63881.00.2548yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

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 ?
Query144
TIGR00425322 TIGR00425, CBF5, rRNA pseudouridine synthase, puta 5e-66
PRK04270300 PRK04270, PRK04270, H/ACA RNA-protein complex comp 7e-42
pfam0147274 pfam01472, PUA, PUA domain 3e-21
smart0035976 smart00359, PUA, Putative RNA-binding Domain in Ps 5e-18
COG0130271 COG0130, TruB, Pseudouridine synthase [Translation 4e-11
PRK13795 636 PRK13795, PRK13795, hypothetical protein; Provisio 2e-09
cd02572182 cd02572, PseudoU_synth_hDyskerin, Pseudouridine sy 6e-09
COG2016161 COG2016, COG2016, Predicted RNA-binding protein (c 3e-06
PRK13794 479 PRK13794, PRK13794, hypothetical protein; Provisio 4e-06
COG5270202 COG5270, COG5270, PUA domain (predicted RNA-bindin 6e-05
TIGR03684150 TIGR03684, arCOG00985, arCOG04150 universal archae 4e-04
TIGR00451107 TIGR00451, unchar_dom_2, uncharacterized domain 2 0.003
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative Back     alignment and domain information 
 Score =  203 bits (517), Expect = 5e-66
 Identities = 73/139 (52%), Positives = 100/139 (71%), Gaps = 1/139 (0%)

Query: 1   MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
           M ELRR RSG    ED +VTLHD+ DA   + +  DES LRR+I+P+E LL   KR+++K
Sbjct: 185 MQELRRTRSGC-FGEDDMVTLHDLLDAYVFWKEDGDESYLRRIIKPMEYLLRHLKRVVVK 243

Query: 61  DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
           DSAV+A+C+GA +M+ G+ R E GIE  + +V+++ KGEAVA+ +A M+T  +A  D GV
Sbjct: 244 DSAVDAICHGADLMVRGIARLEKGIEKGDTVVVITLKGEAVAVGIALMSTKDIANADKGV 303

Query: 121 VAKIKRVIMDRDTYPRKWG 139
           VA +KRVIM+R TYPR W 
Sbjct: 304 VADVKRVIMERGTYPRMWK 322

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]. Length = 322
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>gnl|CDD|201816 pfam01472, PUA, PUA domain Back     alignment and domain information
>gnl|CDD|214635 smart00359, PUA, Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase Back     alignment and domain information
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human dyskerin like Back     alignment and domain information
>gnl|CDD|224927 COG2016, COG2016, Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|237509 PRK13794, PRK13794, hypothetical protein; Provisional Back     alignment and domain information
>gnl|CDD|227595 COG5270, COG5270, PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|234310 TIGR03684, arCOG00985, arCOG04150 universal archaeal PUA-domain protein Back     alignment and domain information
>gnl|CDD|129543 TIGR00451, unchar_dom_2, uncharacterized domain 2 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 144
TIGR00425322 CBF5 rRNA pseudouridine synthase, putative. This f 99.95
PRK04270300 H/ACA RNA-protein complex component Cbf5p; Reviewe 99.91
PRK14124308 tRNA pseudouridine synthase B; Provisional 99.76
PRK05033312 truB tRNA pseudouridine synthase B; Provisional 99.75
PRK01851303 truB tRNA pseudouridine synthase B; Provisional 99.74
PRK01550304 truB tRNA pseudouridine synthase B; Provisional 99.74
PRK04642300 truB tRNA pseudouridine synthase B; Provisional 99.74
PRK00130290 truB tRNA pseudouridine synthase B; Provisional 99.73
PRK02755295 truB tRNA pseudouridine synthase B; Provisional 99.72
PRK14123305 tRNA pseudouridine synthase B; Provisional 99.71
PRK05389305 truB tRNA pseudouridine synthase B; Provisional 99.7
PRK01528292 truB tRNA pseudouridine synthase B; Provisional 99.7
PRK03287298 truB tRNA pseudouridine synthase B; Provisional 99.67
PRK02484294 truB tRNA pseudouridine synthase B; Provisional 99.67
COG0130271 TruB Pseudouridine synthase [Translation, ribosoma 99.65
PRK14122312 tRNA pseudouridine synthase B; Provisional 99.62
cd02573277 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudou 99.59
PF0147274 PUA: PUA domain; InterPro: IPR002478 The PUA (Pseu 99.56
COG2016161 Predicted RNA-binding protein (contains PUA domain 99.55
TIGR03684150 arCOG00985 arCOG04150 universal archaeal PUA-domai 99.52
PRK14560160 putative RNA-binding protein; Provisional 99.5
TIGR00451107 unchar_dom_2 uncharacterized domain 2. This unchar 99.48
KOG2529|consensus395 99.4
PRK14846345 truB tRNA pseudouridine synthase B; Provisional 99.32
PF0915758 TruB-C_2: Pseudouridine synthase II TruB, C-termin 99.21
PRK02193279 truB tRNA pseudouridine synthase B; Provisional 99.12
KOG2523|consensus181 99.0
PRK13794 479 hypothetical protein; Provisional 98.98
smart0035977 PUA Putative RNA-binding Domain in PseudoUridine s 98.96
PRK13534639 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Pr 98.93
PRK13795 636 hypothetical protein; Provisional 98.93
COG1370155 Prefoldin, molecular chaperone implicated in de no 98.78
PRK04099273 truB tRNA pseudouridine synthase B; Provisional 98.69
PRK05429372 gamma-glutamyl kinase; Provisional 98.54
PF0914256 TruB_C: tRNA Pseudouridine synthase II, C terminal 98.51
TIGR00432540 arcsn_tRNA_tgt tRNA-guanine transglycosylase, arch 98.5
COG5270202 PUA domain (predicted RNA-binding domain) [Transla 98.39
TIGR01027363 proB glutamate 5-kinase. Bacterial ProB proteins h 98.37
KOG2522|consensus 560 98.2
PRK13402368 gamma-glutamyl kinase; Provisional 98.07
COG0263369 ProB Glutamate 5-kinase [Amino acid transport and 97.73
COG1549519 Queuine tRNA-ribosyltransferases, contain PUA doma 97.34
PRK15128 396 23S rRNA m(5)C1962 methyltransferase; Provisional 94.65
PF03657162 UPF0113: Uncharacterised protein family (UPF0113); 93.47
PF13636102 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome 92.9
KOG3492|consensus180 88.11
PRK08557 417 hypothetical protein; Provisional 85.98
cd02867312 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudou 83.54
COG3270127 Uncharacterized conserved protein [Function unknow 80.09
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative Back     alignment and domain information 
Probab=99.95  E-value=3.4e-27  Score=182.27  Aligned_cols=138  Identities=51%  Similarity=0.851  Sum_probs=116.3

Q ss_pred             CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178           1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR   80 (144)
Q Consensus         1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~   80 (144)
                      |++||||++|+|+++ +|+||++|+++...+...+++..+++.|+|++.+|.++|.+.++++++.+++||+.++.+++..
T Consensus       185 ~~~L~R~~~g~f~~~-~a~~l~~l~~~~~~~~~~~~~~~l~~~l~p~~~~l~~lP~V~Vd~~~a~~I~NG~~I~~pgv~~  263 (322)
T TIGR00425       185 MQELRRTRSGCFGED-DMVTLHDLLDAYVFWKEDGDESYLRRVIKPMEYALRHLKRVVVKDSAVDAICHGADLMVRGIAR  263 (322)
T ss_pred             EEEeEeEEECCcccc-ccccHHHHHHhhhhhhcccchhhHhhhcCCHHHHHhhCCceEeCHHHHHHHHCCCccccccccc
Confidence            789999999999999 5799999987532111211122467789999999999999999999999999999999887654


Q ss_pred             ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCccccCcC
Q psy1178          81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWG  139 (144)
Q Consensus        81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~~~~~w~  139 (144)
                      .+..+..++.|++++.+|+++|||++.++++++....+|.++++.|+|.+.|+||+.|+
T Consensus       264 ~d~~i~~gd~V~V~~~~G~~LAIGea~~s~~ei~~~~kG~vV~~~~~~~~~~~~~~~~~  322 (322)
T TIGR00425       264 LEKGIEKGDTVAVITLKGEAVAVGIALMSTKDIANADKGVVADVKRVIMERGTYPRMWK  322 (322)
T ss_pred             cccccCCCCEEEEEECCCEEEEEEEEecCHHHHhhcCCcEEEEEEEEeeCCCCCCCCcC
Confidence            43334567788898888899999999999999999899999999999999999999997

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.
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed Back     alignment and domain information
>PRK14124 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05033 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01851 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01550 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK04642 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK00130 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02755 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK14123 tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05389 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK01528 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK03287 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK02484 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK14122 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
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found [] Back     alignment and domain information
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein Back     alignment and domain information
>PRK14560 putative RNA-binding protein; Provisional Back     alignment and domain information
>TIGR00451 unchar_dom_2 uncharacterized domain 2 Back     alignment and domain information
>KOG2529|consensus Back     alignment and domain information
>PRK14846 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 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
>PRK02193 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>KOG2523|consensus Back     alignment and domain information
>PRK13794 hypothetical protein; Provisional Back     alignment and domain information
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase Back     alignment and domain information
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional Back     alignment and domain information
>PRK13795 hypothetical protein; Provisional Back     alignment and domain information
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PRK04099 truB tRNA pseudouridine synthase B; Provisional Back     alignment and domain information
>PRK05429 gamma-glutamyl kinase; Provisional Back     alignment and domain information
>PF09142 TruB_C: tRNA Pseudouridine synthase II, C terminal; InterPro: IPR015225 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
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming Back     alignment and domain information
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR01027 proB glutamate 5-kinase Back     alignment and domain information
>KOG2522|consensus Back     alignment and domain information
>PRK13402 gamma-glutamyl kinase; Provisional Back     alignment and domain information
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism] Back     alignment and domain information
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional Back     alignment and domain information
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ] Back     alignment and domain information
>PF13636 Nol1_Nop2_Fmu_2: pre-rRNA processing and ribosome biogenesis; PDB: 3M4X_A 3M6U_B 3M6V_B 3M6W_A 3M6X_A Back     alignment and domain information
>KOG3492|consensus Back     alignment and domain information
>PRK08557 hypothetical protein; Provisional Back     alignment and domain information
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4 Back     alignment and domain information
>COG3270 Uncharacterized conserved protein [Function unknown] 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 ?
Query144
3u28_A400 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex From 3e-55
3zv0_C195 Structure Of The Shq1p-Cbf5p Complex Length = 195 1e-39
2apo_A357 Crystal Structure Of The Methanococcus Jannaschii C 1e-26
2aus_C334 Crystal Structure Of The Archaeal Box HACA SRNP NOP 6e-24
3mqk_A328 Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Cont 1e-23
3hjw_A327 Structure Of A Functional Ribonucleoprotein Pseudou 1e-23
2rfk_A334 Substrate Rna Positioning In The Archaeal HACA Ribo 1e-23
3lwo_A340 Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONT 1e-23
2hvy_A346 Crystal Structure Of An HACA BOX RNP FROM PYROCOCCU 1e-23
2ey4_A333 Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Leng 1e-22
3d79_A179 Crystal Structure Of Hypothetical Protein Ph0734.1 5e-04
>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 =  210 bits (534), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 94/142 (66%), Positives = 123/142 (86%)
Query: 1   MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
           M ELRR RSG  SE D +VTLHD+ DA ++YD  +DES LR +I+PLE LLVG+KRI++K
Sbjct: 213 MQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVK 272
Query: 61  DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
           DSAVNAVCYGA++M+PG+LRYE+GIE+ +EIV+++TKGEA+A+A+AQM+T  +A+CDHGV
Sbjct: 273 DSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGV 332
Query: 121 VAKIKRVIMDRDTYPRKWGLGP 142
           VA +KR IM+RD YPR+WGLGP
Sbjct: 333 VASVKRCIMERDLYPRRWGLGP 354
>pdb|3ZV0|C Chain C, Structure Of The Shq1p-Cbf5p Complex Length = 195 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|2AUS|C Chain C, Crystal Structure Of The Archaeal Box HACA SRNP NOP10-Cbf5 Complex Length = 334 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|3HJW|A Chain A, Structure Of A Functional Ribonucleoprotein Pseudouridine Synthase Bound To A Substrate Rna Length = 327 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|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|2EY4|A Chain A, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex Length = 333 Back     alignment and structure
>pdb|3D79|A Chain A, Crystal Structure Of Hypothetical Protein Ph0734.1 From Hyperthermophilic Archaea Pyrococcus Horikoshii Ot3 Length = 179 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 ?
Query144
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 3e-62
2aus_C334 Pseudouridine synthase; isomerase, structural prot 6e-62
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 1e-59
3zv0_C195 H/ACA ribonucleoprotein complex subunit 4; cell cy 2e-46
3d79_A179 PUA domain, putative uncharacterized protein PH073 5e-25
1q7h_A153 Conserved hypothetical protein; structural genomic 2e-21
3r90_A188 Malignant T cell-amplified sequence 1; structural 4e-18
2q07_A306 Uncharacterized protein AF0587; monomer, structura 1e-06
2cx0_A187 Hypothetical protein APE0525; PUA domain, structur 2e-06
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 4e-05
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 1e-04
>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 =  193 bits (493), Expect = 3e-62
 Identities = 60/139 (43%), Positives = 86/139 (61%), Gaps = 1/139 (0%)

Query: 1   MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILK 60
           M ELRR +SG   E+D  V L D+ DA   + +  DE  LRRVI+P+E  L   K++++K
Sbjct: 217 MQELRRTKSGCFEEKD-AVYLQDLLDAYVFWKEDGDEEELRRVIKPMEYGLRHLKKVVVK 275

Query: 61  DSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGV 120
           DSAV+A+C+GA + + G+ +   GI   E +++ + KGEAVA+  A M T  +   D GV
Sbjct: 276 DSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGV 335

Query: 121 VAKIKRVIMDRDTYPRKWG 139
              ++RV MDR TYPR W 
Sbjct: 336 AVDVERVYMDRGTYPRMWK 354
>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
>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
>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
>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown function; 1.73A {Pyrococcus horikoshii} Length = 179 Back     alignment and structure
>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR structure initiative; 2.10A {Thermoplasma acidophilum dsm 1728} SCOP: b.122.1.1 d.17.6.2 Length = 153 Back     alignment and structure
>3r90_A Malignant T cell-amplified sequence 1; structural genomics consortium, surface entropy reduction, S binding protein; 1.70A {Homo sapiens} Length = 188 Back     alignment and structure
>2q07_A Uncharacterized protein AF0587; monomer, structural genomics, PSI-2, protein structure initiative; 2.04A {Archaeoglobus fulgidus dsm 4304} SCOP: b.122.1.1 c.18.1.4 d.17.6.5 Length = 306 Back     alignment and structure
>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1 d.17.6.4 PDB: 2cx1_A* 1zs7_A Length = 187 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query144
3u28_A400 H/ACA ribonucleoprotein complex subunit 4; pseudou 100.0
2apo_A357 Probable tRNA pseudouridine synthase B; protein-pr 99.95
2aus_C334 Pseudouridine synthase; isomerase, structural prot 99.95
3zv0_C195 H/ACA ribonucleoprotein complex subunit 4; cell cy 99.93
1k8w_A327 TRNA pseudouridine synthase B; protein-RNA complex 99.76
1sgv_A316 TRNA pseudouridine synthase B; hinged motion, tRNA 99.66
1r3e_A309 TRNA pseudouridine synthase B; RNA modification, p 99.63
3r90_A188 Malignant T cell-amplified sequence 1; structural 99.54
1q7h_A153 Conserved hypothetical protein; structural genomic 99.52
3d79_A179 PUA domain, putative uncharacterized protein PH073 99.48
2cx0_A187 Hypothetical protein APE0525; PUA domain, structur 99.33
1iq8_A582 Archaeosine tRNA-guanine transglycosylase; (alpha/ 99.04
2q07_A306 Uncharacterized protein AF0587; monomer, structura 98.87
2j5v_A367 Glutamate 5-kinase; proline biosynthesis, gamma gl 98.39
2p38_A166 Protein involved in ribosomal biogenesis; two alph 98.21
1sqw_A188 Saccharomyces cerevisiae NIP7P homolog; PUA, unkno 98.19
3c0k_A 396 UPF0064 protein YCCW; PUA domain, adoMet dependent 94.55
2as0_A 396 Hypothetical protein PH1915; RNA methyltransferase 94.2
4dmg_A 393 Putative uncharacterized protein TTHA1493; rRNA, m 92.44
>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=2.3e-33  Score=219.38  Aligned_cols=144  Identities=65%  Similarity=1.123  Sum_probs=122.4

Q ss_pred             CCccEeeeeecccccCceeeHHHHHHHHHHHhhcCCcccccccccccccccCcCCEEEEChhhHHhhhCCceecCCCeec
Q psy1178           1 MIELRRNRSGIQSEEDGLVTLHDIKDAMYLYDQHKDESLLRRVIRPLEGLLVGHKRIILKDSAVNAVCYGAQIMLPGVLR   80 (144)
Q Consensus         1 m~~LrRt~~g~F~~~~~~vtL~~l~~~~~~~~~~~~~~~l~~~LlP~~~aL~~lp~V~l~~~~~~~l~~G~~l~~~~~~~   80 (144)
                      |++||||++|+|+++++++||++|+++...+++..++..+++.|+|++.+|.++|+|.|+++++++++||+.++.+++..
T Consensus       213 m~~LrRt~~G~F~~~~a~vtL~~l~~~~~~~~~~~~~~~l~~~l~P~e~~l~~lp~V~L~deaa~~V~NGq~L~~pgVl~  292 (400)
T 3u28_A          213 MQELRRVRSGALSENDNMVTLHDVMDAQWVYDNTRDESYLRSIIQPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLR  292 (400)
T ss_dssp             EEEEEEEEETTEETTSSCBCHHHHHHHHHHHHHHCCCHHHHHHCEEGGGGGTTSCEEEECHHHHHHHHHHSEEEGGGEEE
T ss_pred             EEEEEEEEEcCcchhhhcCCHHHHHHhhhhhhcccchhhHhhhcCCHHHHHhhCCccccCHHHHHHHHCcCccccCcccc
Confidence            78999999999999966799999987643333334445677889999999999999999999999999999999988765


Q ss_pred             ccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCCccccCcCCCCCC
Q psy1178          81 YEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRDTYPRKWGLGPKS  144 (144)
Q Consensus        81 ~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~~~~~~w~~~~~~  144 (144)
                      ....+..++.|++++.+|+++|||++.+++++|...++|.+++++|||++.|+||..|++||++
T Consensus       293 ~~~~i~~gd~VvVvt~kGelLAIG~A~mss~em~~~~~G~vvk~~rV~m~~~~yp~~w~~~~~~  356 (400)
T 3u28_A          293 YEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVA  356 (400)
T ss_dssp             ECTTCCTTCEEEEECTTCCEEEEEEESSCHHHHHHCSSSEEEEEEEECSCTTSSCCCC------
T ss_pred             ccccCCCCCEEEEEeCCCcEEEEEEEEeCHHHHhhcCCcEEEEEEEEeecCCCCccccCcChhH
Confidence            5455677889999999999999999999999999999999999999999999999999999975
>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
>3zv0_C H/ACA ribonucleoprotein complex subunit 4; cell cycle, RNP assembly, X-linked dyskeratosis congenita; 2.80A {Saccharomyces cerevisiae} 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
>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
>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
>3r90_A Malignant T cell-amplified sequence 1; structural genomics consortium, surface entropy reduction, S binding protein; 1.70A {Homo sapiens} Back     alignment and structure
>1q7h_A Conserved hypothetical protein; structural genomics, MCSG, PSI, PR structure initiative; 2.10A {Thermoplasma acidophilum dsm 1728} SCOP: b.122.1.1 d.17.6.2 Back     alignment and structure
>3d79_A PUA domain, putative uncharacterized protein PH0734; unknown function; 1.73A {Pyrococcus horikoshii} Back     alignment and structure
>2cx0_A Hypothetical protein APE0525; PUA domain, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix} SCOP: b.122.1.1 d.17.6.4 PDB: 2cx1_A* 1zs7_A Back     alignment and structure
>1iq8_A Archaeosine tRNA-guanine transglycosylase; (alpha/beta)8 barrel, riken structural genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus horikoshii} SCOP: b.122.1.1 c.1.20.1 d.17.6.1 PDB: 1it7_A* 1it8_A* 1j2b_A Back     alignment and structure
>2q07_A Uncharacterized protein AF0587; monomer, structural genomics, PSI-2, protein structure initiative; 2.04A {Archaeoglobus fulgidus dsm 4304} SCOP: b.122.1.1 c.18.1.4 d.17.6.5 Back     alignment and structure
>2j5v_A Glutamate 5-kinase; proline biosynthesis, gamma glutamyl kinase, amino-acid biosynthesis, transferase, feedback regulation, PUA domain; HET: RGP; 2.5A {Escherichia coli} PDB: 2j5t_A* 2w21_A Back     alignment and structure
>2p38_A Protein involved in ribosomal biogenesis; two alpha/beta domains, PUA domain, biosynthetic protein; 1.80A {Pyrococcus abyssi} Back     alignment and structure
>1sqw_A Saccharomyces cerevisiae NIP7P homolog; PUA, unknown function; 1.90A {Homo sapiens} SCOP: b.122.1.1 d.17.6.3 PDB: 1t5y_A Back     alignment and structure
>3c0k_A UPF0064 protein YCCW; PUA domain, adoMet dependent methyltransferase fold; 2.00A {Escherichia coli K12} Back     alignment and structure
>2as0_A Hypothetical protein PH1915; RNA methyltransferase, structural genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: b.122.1.9 c.66.1.51 Back     alignment and structure
>4dmg_A Putative uncharacterized protein TTHA1493; rRNA, methyltransferase, S-adenosyl-methionine, 23S ribosoma transferase; HET: SAM; 1.70A {Thermus thermophilus} 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 144
d2apoa185 b.122.1.1 (A:247-331) Pseudouridine synthase II Tr 1e-28
d2ey4a184 b.122.1.1 (A:253-336) Pseudouridine synthase II Tr 4e-26
d1r3ea181 b.122.1.1 (A:238-318) Pseudouridine synthase II Tr 1e-20
d1q7ha185 b.122.1.1 (A:69-153) Hypothetical protein Ta1423, 2e-17
d1iq8a377 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine tra 1e-15
d2ey4a2245 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB 8e-13
d2q07a168 b.122.1.1 (A:460-527) Uncharacterized protein AF05 1e-12
d2apoa2230 d.265.1.2 (A:17-246) Pseudouridine synthase II Tru 4e-09
d2cx1a193 b.122.1.1 (A:91-183) Hypothetical protein APE0525, 7e-07
d1k8wa5242 d.265.1.2 (A:9-250) Pseudouridine synthase II TruB 3e-04
>d2apoa1 b.122.1.1 (A:247-331) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 85 Back     information, alignment and structure

class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: PUA domain
domain: Pseudouridine synthase II TruB, C-terminal domain
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 98.3 bits (245), Expect = 1e-28
 Identities = 35/82 (42%), Positives = 54/82 (65%)

Query: 55  KRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMA 114
           K++++KDSAV+A+C+GA + + G+ +   GI   E +++ + KGEAVA+  A M T  + 
Sbjct: 3   KKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEIL 62

Query: 115 TCDHGVVAKIKRVIMDRDTYPR 136
             D GV   ++RV MDR TYPR
Sbjct: 63  NADKGVAVDVERVYMDRGTYPR 84
>d2ey4a1 b.122.1.1 (A:253-336) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 84 Back     information, alignment and structure
>d1r3ea1 b.122.1.1 (A:238-318) Pseudouridine synthase II TruB, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 81 Back     information, alignment and structure
>d1q7ha1 b.122.1.1 (A:69-153) Hypothetical protein Ta1423, C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 85 Back     information, alignment and structure
>d1iq8a3 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine transglycosylase, C3 domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 77 Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 245 Back     information, alignment and structure
>d2q07a1 b.122.1.1 (A:460-527) Uncharacterized protein AF0587 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 68 Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 230 Back     information, alignment and structure
>d2cx1a1 b.122.1.1 (A:91-183) Hypothetical protein APE0525, C-terminal domain {Archaeon Aeropyrum pernix [TaxId: 56636]} Length = 93 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 ?
Query144
d2apoa185 Pseudouridine synthase II TruB, C-terminal domain 99.82
d2ey4a184 Pseudouridine synthase II TruB, C-terminal domain 99.79
d1r3ea181 Pseudouridine synthase II TruB, C-terminal domain 99.66
d1q7ha185 Hypothetical protein Ta1423, C-terminal domain {Ar 99.63
d1iq8a377 Archaeosine tRNA-guanine transglycosylase, C3 doma 99.55
d2cx1a193 Hypothetical protein APE0525, C-terminal domain {A 99.49
d2q07a168 Uncharacterized protein AF0587 {Archaeoglobus fulg 99.25
d1k8wa362 Pseudouridine synthase II TruB, C-terminal domain 99.22
d2ey4a2245 Pseudouridine synthase II TruB {Archaeon Pyrococcu 98.95
d2apoa2230 Pseudouridine synthase II TruB {Archaeon Methanoco 98.88
d2as0a172 Hypothetical protein PH1915, N-terminal domain {Ar 98.64
d1k8wa5242 Pseudouridine synthase II TruB {Escherichia coli [ 98.41
d1sgva157 Pseudouridine synthase II TruB, C-terminal domain 97.68
d1sqwa176 Nip7p homolog, C-terminal domain {Human (Homo sapi 97.05
d2b78a168 Hypothetical protein SMu776, N-terminal domain {St 96.48
d1wxxa164 Hypothetical protein TTHA1280, N-terminal domain { 91.13
d1eu1a1155 Dimethylsulfoxide reductase (DMSO reductase) {Rhod 82.96
>d2apoa1 b.122.1.1 (A:247-331) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
class: All beta proteins
fold: PUA domain-like
superfamily: PUA domain-like
family: PUA domain
domain: Pseudouridine synthase II TruB, C-terminal domain
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.82  E-value=3.3e-20  Score=115.57  Aligned_cols=84  Identities=42%  Similarity=0.729  Sum_probs=81.2

Q ss_pred             cCCEEEEChhhHHhhhCCceecCCCeecccCCCCCCCEEEEEcCCCCEEEEEEeecChhhHhcCCCceEEEEEEEeecCC
Q psy1178          53 GHKRIILKDSAVNAVCYGAQIMLPGVLRYEDGIEMDEEIVIVSTKGEAVALALAQMTTSTMATCDHGVVAKIKRVIMDRD  132 (144)
Q Consensus        53 ~lp~V~l~~~~~~~l~~G~~l~~~~~~~~~~~~~~~~~v~i~~~~g~~laig~~~~~~~~~~~~~~g~~v~~~rv~~~~~  132 (144)
                      |+|+|.++++++++|++|++|+++|+..++++|..|+.|.|++.+|+++|+|.+.++++++....+|.+++++|||.+.|
T Consensus         1 hlp~v~Vd~~Av~ai~~Ga~L~~pGV~~~~~~~~~Gd~V~V~~~~g~~iavG~~~~ss~ei~~~~~G~av~~~~V~~~~~   80 (85)
T d2apoa1           1 HLKKVVVKDSAVDAICHGADVYVRGIAKLSKGIGKGETVLVETLKGEAVAVGKALMNTKEILNADKGVAVDVERVYMDRG   80 (85)
T ss_dssp             TSEEEEECHHHHHHHHTTCCEEGGGEEEEETTCCTTCEEEEECTTSCEEEEEEESSCHHHHHHCSSSEEEEEEEECSCTT
T ss_pred             CCCEEEECccHHHHHHcCCCccccEEEEEcCCCcCCCEEEEEeCCCCEEEEEEEeeCHHHHhhcCCCEEEEEEEEecCCC
Confidence            78999999999999999999999999998899999999999999999999999999999999889999999999999999


Q ss_pred             cccc
Q psy1178         133 TYPR  136 (144)
Q Consensus       133 ~~~~  136 (144)
                      .||+
T Consensus        81 ~Yp~   84 (85)
T d2apoa1          81 TYPR   84 (85)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9996
>d2ey4a1 b.122.1.1 (A:253-336) Pseudouridine synthase II TruB, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1r3ea1 b.122.1.1 (A:238-318) Pseudouridine synthase II TruB, C-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1q7ha1 b.122.1.1 (A:69-153) Hypothetical protein Ta1423, C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure
>d1iq8a3 b.122.1.1 (A:506-582) Archaeosine tRNA-guanine transglycosylase, C3 domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d2cx1a1 b.122.1.1 (A:91-183) Hypothetical protein APE0525, C-terminal domain {Archaeon Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d2q07a1 b.122.1.1 (A:460-527) Uncharacterized protein AF0587 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1k8wa3 b.122.1.1 (A:251-312) Pseudouridine synthase II TruB, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ey4a2 d.265.1.2 (A:8-252) Pseudouridine synthase II TruB {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2apoa2 d.265.1.2 (A:17-246) Pseudouridine synthase II TruB {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2as0a1 b.122.1.9 (A:1-72) Hypothetical protein PH1915, N-terminal domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} 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
>d1sgva1 b.122.1.1 (A:236-292) Pseudouridine synthase II TruB, C-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1sqwa1 b.122.1.1 (A:95-170) Nip7p homolog, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2b78a1 b.122.1.9 (A:1-68) Hypothetical protein SMu776, N-terminal domain {Streptococcus mutans [TaxId: 1309]} Back     information, alignment and structure
>d1wxxa1 b.122.1.9 (A:1-64) Hypothetical protein TTHA1280, N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1eu1a1 b.52.2.2 (A:626-780) Dimethylsulfoxide reductase (DMSO reductase) {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure