Citrus Sinensis ID: 032009

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-------15
MATSSSTQLENRPEEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIHIGEHPKVEDQ
cccccccccccccccHHHHHHcccccEEEEcccccccccccccccccccccccccccccccccEEEEcccccccccccccHHHHHHHHHcccEEEEEccccEEEEccccccccccccccHHHHHHHHHHHHHccccccccccccccccc
cccHHHHHHcccccccHHHHHHcHHccEccccccccccEEcccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHccccEEEEEcccEEEEEcccHHccHHHHHHHHHHHHHHHHHHcccccccccccccccccc
matssstqlenrpeeedemmfgaesgwvepltsCDHLVASLssdlahiptpdtpcnrcqhpsenwlclcckevlcsrFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDaylnaqvipqlrpVYETAYIlkfgeappihigehpkvedq
matssstqlenrpeeEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGeappihigehpkvedq
MATSSSTQLENRPEEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIHIGEHPKVEDQ
************************SGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIH**********
*********************GAESGWVEPLTSCDHLVASL**********DTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKF*****************
*****************EMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIHIGEHPKVEDQ
*************EEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIHIGE*******
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MATSSSTQLENRPEEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPPIHIGEHPKVEDQ
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 ?
Query149 2.2.26 [Sep-21-2011]
Q9UBN71215 Histone deacetylase 6 OS= yes no 0.758 0.093 0.404 6e-18
Q20296955 Histone deacetylase 6 OS= yes no 0.818 0.127 0.396 3e-17
Q9Z2V51149 Histone deacetylase 6 OS= yes no 0.711 0.092 0.409 2e-15
Q54QE6 512 NAD-dependent deacetylase yes no 0.409 0.119 0.475 2e-13
Q9H0E7 712 Ubiquitin carboxyl-termin no no 0.677 0.141 0.300 2e-08
Q7ZUM8 695 Ubiquitin carboxyl-termin no no 0.516 0.110 0.358 2e-08
D2HBJ8 711 Ubiquitin carboxyl-termin no no 0.389 0.081 0.379 9e-08
Q5XGZ2 690 Ubiquitin carboxyl-termin N/A no 0.516 0.111 0.333 1e-07
Q0V9G5 652 Ubiquitin carboxyl-termin no no 0.516 0.118 0.333 1e-07
Q6NTR6 690 Ubiquitin carboxyl-termin N/A no 0.516 0.111 0.333 1e-07
>sp|Q9UBN7|HDAC6_HUMAN Histone deacetylase 6 OS=Homo sapiens GN=HDAC6 PE=1 SV=2 Back     alignment and function desciption
 Score = 89.7 bits (221), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 49/121 (40%), Positives = 67/121 (55%), Gaps = 8/121 (6%)

Query: 17   DEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCS 76
            D+ +F A    V PL  C HLVA      A +     PC  C    ENW+CL C +V C 
Sbjct: 1100 DQAIFYA----VTPLPWCPHLVAVCPIPAAGLDVTQ-PCGDCGTIQENWVCLSCYQVYCG 1154

Query: 77   RFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAP 136
            R++N HMLQH+  + H + LSY DLS WC+ C AY++ Q +  ++ +   A+  KFGE  
Sbjct: 1155 RYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNI---AHQNKFGEDM 1211

Query: 137  P 137
            P
Sbjct: 1212 P 1212
In addition to its protein deacetylase activity, plays a key role in the degradation of misfolded proteins: when misfolded proteins are too abundant to be degraded by the chaperone refolding system and the ubiquitin-proteasome, mediates the transport of misfolded proteins to a cytoplasmic juxtanuclear structure called aggresome. Probably acts as an adapter that recognizes polyubiquitinated misfolded proteins and target them to the aggresome, facilitating their clearance by autophagy.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 5EC: .EC: 1EC: .EC: 9EC: 8
>sp|Q20296|HDA6_CAEEL Histone deacetylase 6 OS=Caenorhabditis elegans GN=hda-6 PE=2 SV=2 Back     alignment and function description
>sp|Q9Z2V5|HDAC6_MOUSE Histone deacetylase 6 OS=Mus musculus GN=Hdac6 PE=1 SV=3 Back     alignment and function description
>sp|Q54QE6|SIR2A_DICDI NAD-dependent deacetylase sir2A OS=Dictyostelium discoideum GN=sir2A PE=2 SV=1 Back     alignment and function description
>sp|Q9H0E7|UBP44_HUMAN Ubiquitin carboxyl-terminal hydrolase 44 OS=Homo sapiens GN=USP44 PE=1 SV=2 Back     alignment and function description
>sp|Q7ZUM8|UBP44_DANRE Ubiquitin carboxyl-terminal hydrolase 44 OS=Danio rerio GN=usp44 PE=2 SV=1 Back     alignment and function description
>sp|D2HBJ8|UBP44_AILME Ubiquitin carboxyl-terminal hydrolase 44 OS=Ailuropoda melanoleuca GN=USP44 PE=3 SV=1 Back     alignment and function description
>sp|Q5XGZ2|UP44B_XENLA Ubiquitin carboxyl-terminal hydrolase 44-B OS=Xenopus laevis GN=usp44-b PE=2 SV=1 Back     alignment and function description
>sp|Q0V9G5|UBP44_XENTR Ubiquitin carboxyl-terminal hydrolase 44 OS=Xenopus tropicalis GN=usp44 PE=2 SV=1 Back     alignment and function description
>sp|Q6NTR6|UP44A_XENLA Ubiquitin carboxyl-terminal hydrolase 44-A OS=Xenopus laevis GN=usp44-a 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 ?
Query149
225428959154 PREDICTED: histone deacetylase 6-like [V 0.912 0.883 0.759 4e-55
296083068153 unnamed protein product [Vitis vinifera] 0.906 0.882 0.773 6e-55
255573133159 histone deacetylase hda2, putative [Rici 0.859 0.805 0.801 1e-54
224105697160 predicted protein [Populus trichocarpa] 0.912 0.85 0.751 4e-54
357480677140 Histone deacetylase [Medicago truncatula 0.919 0.978 0.717 6e-52
449469124146 PREDICTED: histone deacetylase 6-like [C 0.919 0.938 0.702 4e-51
238479248146 Regulator of Vps4 activity in the MVB pa 0.832 0.849 0.688 3e-46
51971481146 unnamed protein product [Arabidopsis tha 0.832 0.849 0.688 3e-46
26984073140 hypothetical protein [Arabidopsis thalia 0.832 0.885 0.68 2e-45
357150533188 PREDICTED: histone deacetylase 6-like [B 0.865 0.686 0.591 1e-42
>gi|225428959|ref|XP_002263779.1| PREDICTED: histone deacetylase 6-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 104/137 (75%), Positives = 118/137 (86%), Gaps = 1/137 (0%)

Query: 2   ATSSSTQLENRPEEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHP 61
           A+SSST L     E++E ++GAESGWVE  TSCDHL ASLSSDL HIPTP+TPCNRC +P
Sbjct: 5   ASSSSTALVEVLIEDEEFLYGAESGWVEARTSCDHL-ASLSSDLVHIPTPETPCNRCHNP 63

Query: 62  SENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLR 121
           SENWLCLCCKEVLCSRFVNKHML+HY + NH +ALSYSDLS+WCF+CDAYL+AQ I QL 
Sbjct: 64  SENWLCLCCKEVLCSRFVNKHMLEHYQKVNHCLALSYSDLSIWCFSCDAYLDAQAILQLH 123

Query: 122 PVYETAYILKFGEAPPI 138
           PVYETAYILKFG+APP 
Sbjct: 124 PVYETAYILKFGQAPPF 140

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|296083068|emb|CBI22472.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255573133|ref|XP_002527496.1| histone deacetylase hda2, putative [Ricinus communis] gi|223533136|gb|EEF34894.1| histone deacetylase hda2, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224105697|ref|XP_002313903.1| predicted protein [Populus trichocarpa] gi|118483848|gb|ABK93815.1| unknown [Populus trichocarpa] gi|222850311|gb|EEE87858.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357480677|ref|XP_003610624.1| Histone deacetylase [Medicago truncatula] gi|355511959|gb|AES93582.1| Histone deacetylase [Medicago truncatula] gi|388516653|gb|AFK46388.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|449469124|ref|XP_004152271.1| PREDICTED: histone deacetylase 6-like [Cucumis sativus] gi|449484341|ref|XP_004156856.1| PREDICTED: histone deacetylase 6-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|238479248|ref|NP_001154518.1| Regulator of Vps4 activity in the MVB pathway protein [Arabidopsis thaliana] gi|330251244|gb|AEC06338.1| Regulator of Vps4 activity in the MVB pathway protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|51971481|dbj|BAD44405.1| unnamed protein product [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|26984073|gb|AAN85200.1| hypothetical protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|357150533|ref|XP_003575491.1| PREDICTED: histone deacetylase 6-like [Brachypodium distachyon] 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 ?
Query149
UNIPROTKB|G8JYB7138 hda-6 "Protein HDA-6, isoform 0.885 0.956 0.382 1e-20
UNIPROTKB|Q20296955 hda-6 "Histone deacetylase 6" 0.885 0.138 0.382 1.9e-19
WB|WBGene00018319957 hda-6 [Caenorhabditis elegans 0.885 0.137 0.382 1.9e-19
UNIPROTKB|A7LPD8957 hda-6 "Protein HDA-6, isoform 0.885 0.137 0.382 1.9e-19
ZFIN|ZDB-GENE-030131-32321081 hdac6 "histone deacetylase 6" 0.711 0.098 0.410 3e-19
UNIPROTKB|I3LEZ71130 HDAC6 "Uncharacterized protein 0.818 0.107 0.376 6.6e-19
UNIPROTKB|Q9UBN71215 HDAC6 "Histone deacetylase 6" 0.711 0.087 0.418 2.5e-18
UNIPROTKB|B4DZH61229 HDAC6 "Histone deacetylase 6" 0.711 0.086 0.418 2.5e-18
UNIPROTKB|F1MQP31128 HDAC6 "Uncharacterized protein 0.771 0.101 0.406 4.7e-18
UNIPROTKB|F1PN111157 HDAC6 "Uncharacterized protein 0.711 0.091 0.4 1.3e-17
UNIPROTKB|G8JYB7 hda-6 "Protein HDA-6, isoform d" [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 52/136 (38%), Positives = 73/136 (53%)

Query:     2 ATSSSTQLENRPEEEDEMMFGAESGWVEPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHP 61
             ++S S+    RP    E+M    +  V PL +C HL        A I    T C+ CQ  
Sbjct:     6 SSSGSSSSSTRPSHNLEIMDSGPAHAVVPLATCPHLKEVKPLPPAKI-NARTACSECQIG 64

Query:    62 SENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLR 121
             +E W CL C +  C RFVN+H + H+L ++H +ALS +DLSVWC+ CD+Y++    P L 
Sbjct:    65 AEVWTCLTCYKYNCGRFVNEHAMMHHLSSSHPMALSMADLSVWCYPCDSYVHN---PALI 121

Query:   122 PVYETAYILKFGEAPP 137
                  A+  KFGE  P
Sbjct:   122 GAKSAAHESKFGETMP 137
GO:0006476 "protein deacetylation" evidence=ISS
UNIPROTKB|Q20296 hda-6 "Histone deacetylase 6" [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
WB|WBGene00018319 hda-6 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
UNIPROTKB|A7LPD8 hda-6 "Protein HDA-6, isoform c" [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-3232 hdac6 "histone deacetylase 6" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|I3LEZ7 HDAC6 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q9UBN7 HDAC6 "Histone deacetylase 6" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|B4DZH6 HDAC6 "Histone deacetylase 6" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1MQP3 HDAC6 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|F1PN11 HDAC6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query149
pfam0214863 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolas 4e-17
COG5207 749 COG5207, UBP14, Isopeptidase T [Posttranslational 4e-09
smart0029050 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal H 5e-09
>gnl|CDD|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein Back     alignment and domain information 
 Score = 70.5 bits (173), Expect = 4e-17
 Identities = 26/58 (44%), Positives = 33/58 (56%)

Query: 55  CNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTCDAYL 112
           C+ C      WLCL C  V C R+ N H L+HY ET H +A+S     VWC+ CD Y+
Sbjct: 1   CSECGSTENLWLCLTCGHVGCGRYSNGHALKHYEETGHPLAVSLETGRVWCYACDDYV 58

Length = 63
>gnl|CDD|227532 COG5207, UBP14, Isopeptidase T [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>gnl|CDD|197632 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 149
KOG0944 763 consensus Ubiquitin-specific protease UBP14 [Postt 99.92
PF0214863 zf-UBP: Zn-finger in ubiquitin-hydrolases and othe 99.89
COG5207 749 UBP14 Isopeptidase T [Posttranslational modificati 99.85
KOG0804 493 consensus Cytoplasmic Zn-finger protein BRAP2 (BRC 99.73
cd02669 440 Peptidase_C19M A subfamily of Peptidase C19. Pepti 99.63
smart0029050 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like 99.55
KOG1873 877 consensus Ubiquitin-specific protease [Posttransla 99.51
KOG2026 442 consensus Spindle pole body protein - Sad1p [Cytos 96.2
COG5207 749 UBP14 Isopeptidase T [Posttranslational modificati 95.48
KOG0944 763 consensus Ubiquitin-specific protease UBP14 [Postt 94.61
KOG1867 492 consensus Ubiquitin-specific protease [Posttransla 94.54
PF09416152 UPF1_Zn_bind: RNA helicase (UPF2 interacting domai 93.32
PRK1489059 putative Zn-ribbon RNA-binding protein; Provisiona 87.01
COG288861 Predicted Zn-ribbon RNA-binding protein with a fun 84.11
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information 
Probab=99.92  E-value=1.9e-25  Score=201.21  Aligned_cols=109  Identities=30%  Similarity=0.608  Sum_probs=93.7

Q ss_pred             hhcCccccccCCCC-CcccccccccC--CCCCCCCCCCCCCCCCCCCceeccccCeeeecCC------CChhHHHHhhhc
Q 032009           20 MFGAESGWVEPLTS-CDHLVASLSSD--LAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRF------VNKHMLQHYLET   90 (149)
Q Consensus        20 ~~~~~~~w~~~~~~-CpHl~~~l~~~--~~~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~------~~~Ha~~H~~~t   90 (149)
                      .+..+.+|+.++.. +.|. ..+.|.  .+++++..|+|..|....|||+||+||.|||||.      +|+||+.||++|
T Consensus       145 ~k~~~~aWd~Evr~v~k~~-~nl~q~dng~~~~~~gwkCs~CDL~~NLWlcLtcG~v~CGR~qfg~~GgNgHA~~HYr~t  223 (763)
T KOG0944|consen  145 RKDRVNAWDNEVRTVSKHA-NNLSQIDNGKRIPPSGWKCSKCDLTENLWLCLTCGSVGCGRKQFGGSGGNGHALSHYRET  223 (763)
T ss_pred             hhhhhhhhhhheeeccCCC-CChhhcccCcccCCCcceecccCcccceEEEeccCceeecceeecCCCCCcchHHhhhhc
Confidence            34467899999855 5555 567664  3577789999999999999999999999999993      599999999999


Q ss_pred             CCeeEEECCCC-----cEEEcCCCceecccccCCchhhhHHHHHHhhCCCCC
Q 032009           91 NHSVALSYSDL-----SVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP  137 (149)
Q Consensus        91 ~H~l~v~l~t~-----~vwCY~Cd~~V~~~~~~~L~~~~~~~hl~kfg~~~~  137 (149)
                      +|||+|+|+|+     +||||.||+   ..++|+|     +.||.+|||++.
T Consensus       224 ghPLaVKLgsIs~dg~DvycY~cDd---~v~dPnl-----~~hl~hfGId~~  267 (763)
T KOG0944|consen  224 GHPLAVKLGSISPDGADVYCYDCDD---EVRDPNL-----ESHLSHFGIDMA  267 (763)
T ss_pred             CCceEEEecccCCCccceeeecccc---cccCccH-----HHHHHhcCccHH
Confidence            99999999986     899999994   5577899     899999999984

>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule Back     alignment and domain information
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only] Back     alignment and domain information
>cd02669 Peptidase_C19M A subfamily of Peptidase C19 Back     alignment and domain information
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger Back     alignment and domain information
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton] Back     alignment and domain information
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation Back     alignment and domain information
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional Back     alignment and domain information
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis] 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 ?
Query149
3c5k_A109 Crystal Structure Of Human Hdac6 Zinc Finger Domain 1e-17
3gv4_A107 Crystal Structure Of Human Hdac6 Zinc Finger Domain 1e-17
2i50_A126 Solution Structure Of Ubp-M Znf-Ubp Domain Length = 8e-04
>pdb|3C5K|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain Length = 109 Back     alignment and structure 
Iteration: 1

 Score = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/109 (43%), Positives = 59/109 (54%), Gaps = 4/109 (3%)
Query: 29  EPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYL 88
            PL  C HLVA      A +     PC  C    ENW+CL C +V C R++N HMLQH+ 
Sbjct: 2   SPLPWCPHLVAVCPIPAAGLDV-TQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHG 60
Query: 89  ETNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137
            + H + LSY DLS WC+ C AY++ Q    L  V   A+  KFGE  P
Sbjct: 61  NSGHPLVLSYIDLSAWCYYCQAYVHHQA---LLDVKNIAHQNKFGEDMP 106
>pdb|3GV4|A Chain A, Crystal Structure Of Human Hdac6 Zinc Finger Domain And Ubiquitin C-Terminal Peptide Rlrgg Length = 107 Back     alignment and structure
>pdb|2I50|A Chain A, Solution Structure Of Ubp-M Znf-Ubp Domain Length = 126 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 ?
Query149
3c5k_A109 HD6, histone deacetylase 6; HDAC6, zinc finger, ac 8e-24
2uzg_A97 Ubiquitin carboxyl-terminal hydrolase 33; UBL conj 1e-17
2i50_A126 Ubiquitin carboxyl-terminal hydrolase 16; alpha/be 2e-16
2g45_A129 Ubiquitin carboxyl-terminal hydrolase 5; zinc fing 4e-15
2ida_A102 Hypothetical protein; zinc binding protein, struct 5e-14
3ihp_A 854 Ubiquitin carboxyl-terminal hydrolase 5; hydrolase 7e-09
3mhs_A 476 Ubiquitin carboxyl-terminal hydrolase 8; multi-pro 2e-08
>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A Length = 109 Back     alignment and structure
 Score = 88.2 bits (218), Expect = 8e-24
 Identities = 45/108 (41%), Positives = 58/108 (53%), Gaps = 4/108 (3%)

Query: 30  PLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLE 89
           PL  C HLV ++    A       PC  C    ENW+CL C +V C R++N HMLQH+  
Sbjct: 3   PLPWCPHLV-AVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGN 61

Query: 90  TNHSVALSYSDLSVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP 137
           + H + LSY DLS WC+ C AY++      L  V   A+  KFGE  P
Sbjct: 62  SGHPLVLSYIDLSAWCYYCQAYVHH---QALLDVKNIAHQNKFGEDMP 106
>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens} Length = 126 Back     alignment and structure
>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A Length = 129 Back     alignment and structure
>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5 Length = 102 Back     alignment and structure
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Length = 854 Back     alignment and structure
>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 3m99_A Length = 476 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query149
3c5k_A109 HD6, histone deacetylase 6; HDAC6, zinc finger, ac 100.0
2g45_A129 Ubiquitin carboxyl-terminal hydrolase 5; zinc fing 99.98
2uzg_A97 Ubiquitin carboxyl-terminal hydrolase 33; UBL conj 99.93
2ida_A102 Hypothetical protein; zinc binding protein, struct 99.93
2i50_A126 Ubiquitin carboxyl-terminal hydrolase 16; alpha/be 99.92
3ihp_A 854 Ubiquitin carboxyl-terminal hydrolase 5; hydrolase 99.91
3mhs_A 476 Ubiquitin carboxyl-terminal hydrolase 8; multi-pro 99.78
3ihp_A 854 Ubiquitin carboxyl-terminal hydrolase 5; hydrolase 97.14
1wg2_A64 Zinc finger (AN1-like) family protein; riken struc 83.64
1wfh_A64 Zinc finger (AN1-like) family protein; ZF-AN1 doma 82.72
1wfp_A74 Zinc finger (AN1-like) family protein; ZF-AN1 doma 81.41
2xzl_A 802 ATP-dependent helicase NAM7; hydrolase-RNA complex 81.3
>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A Back     alignment and structure
Probab=100.00  E-value=5.9e-34  Score=207.11  Aligned_cols=108  Identities=42%  Similarity=0.779  Sum_probs=94.3

Q ss_pred             cCCCCCcccccccccCCCCCCCCCCCCCCCCCCCCceeccccCeeeecCCCChhHHHHhhhcCCeeEEECCCCcEEEcCC
Q 032009           29 EPLTSCDHLVASLSSDLAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRFVNKHMLQHYLETNHSVALSYSDLSVWCFTC  108 (149)
Q Consensus        29 ~~~~~CpHl~~~l~~~~~~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~~~~Ha~~H~~~t~H~l~v~l~t~~vwCY~C  108 (149)
                      ++...|||+ .++.+.........+.|.+|+...++|+||+||++||||+.++||++||++++|+++|++++++||||.|
T Consensus         2 ~~~~~C~Hl-~~l~~~~~~~~~~~~~C~~C~~~~~~W~CL~CG~vgCgr~~~~HA~~H~~~t~H~~~~~l~~~~vwCy~c   80 (109)
T 3c5k_A            2 SPLPWCPHL-VAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYC   80 (109)
T ss_dssp             CCBSCCTTG-GGCCCCCTTCCCTTCCCTTTCCCSSEEEETTTCCEEECTTTTCHHHHHHHHHCCCEEEETTTCCEEETTT
T ss_pred             CCCCCCcCc-ccccccCCCCCCcCCcCccccCCCCeeeeeecCccccCCCcChHHHHHhcccCCCEEEECCCCCEEECCC
Confidence            466899999 6776643223335788999999999999999999999999999999999999999999999999999999


Q ss_pred             CceecccccCCchhhhHHHHHHhhCCCCCCCC
Q 032009          109 DAYLNAQVIPQLRPVYETAYILKFGEAPPIHI  140 (149)
Q Consensus       109 d~~V~~~~~~~L~~~~~~~hl~kfg~~~~~~~  140 (149)
                      |+||+++   .|.+...++|++||||++++.+
T Consensus        81 d~~V~~~---~L~d~~~~~hl~~fg~~~~~~~  109 (109)
T 3c5k_A           81 QAYVHHQ---ALLDVKNIAHQNKFGEDMPHPH  109 (109)
T ss_dssp             TEEBCCG---GGHHHHHHHHHHHHCSCCSSCC
T ss_pred             CCEEecc---cccChHHHHHHHHhCCCCCCCC
Confidence            9999874   4667778999999999999853
>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A Back     alignment and structure
>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5 Back     alignment and structure
>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens} Back     alignment and structure
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Back     alignment and structure
>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 4fjc_A 4fk5_A 4fip_A 3m99_A Back     alignment and structure
>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Back     alignment and structure
>1wg2_A Zinc finger (AN1-like) family protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.80.1.1 Back     alignment and structure
>1wfh_A Zinc finger (AN1-like) family protein; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: g.80.1.1 Back     alignment and structure
>1wfp_A Zinc finger (AN1-like) family protein; ZF-AN1 domain, zinc binding, structural genomics, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: g.80.1.1 Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} 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 149
d2uzga195 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hy 1e-16
d2g45a1113 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal h 4e-15
d2idaa1102 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {R 6e-13
>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]} Length = 95 Back     information, alignment and structure

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 33, UBP33
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 68.1 bits (166), Expect = 1e-16
 Identities = 22/84 (26%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 32  TSCDHLVASLSSDLAHIPTPDT-PCNRCQHPSEN-WLCLC--CKEVLCSRFVNKHMLQHY 87
             C HL +        +       C  C+    N W CL   C  V C      H   H 
Sbjct: 2   NHCPHLDSVGEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIHS 61

Query: 88  LETNHSVALSYSDLSVWCFTCDAY 111
            ET H + ++ + L VWC+ C   
Sbjct: 62  QETKHYLTVNLTTLRVWCYACSKE 85
>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]} Length = 113 Back     information, alignment and structure
>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]} Length = 102 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 ?
Query149
d2g45a1113 Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Hum 99.97
d2uzga195 Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {H 99.92
d2idaa1102 Hypothetical protein RPA1320 {Rhodopseudomonas pal 99.9
>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 5, UBP5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.7e-31  Score=192.50  Aligned_cols=97  Identities=28%  Similarity=0.467  Sum_probs=85.6

Q ss_pred             CCCcccccccccC--CCCCCCCCCCCCCCCCCCCceeccccCeeeecCC------CChhHHHHhhhcCCeeEEECCCC--
Q 032009           32 TSCDHLVASLSSD--LAHIPTPDTPCNRCQHPSENWLCLCCKEVLCSRF------VNKHMLQHYLETNHSVALSYSDL--  101 (149)
Q Consensus        32 ~~CpHl~~~l~~~--~~~i~~~~~~C~~C~~~~~lW~CL~Cg~vgCgr~------~~~Ha~~H~~~t~H~l~v~l~t~--  101 (149)
                      ..|+|+ ..|.|.  .+.+++..++|.+|+...++|+||+||++||||+      +++||++||++++||++|+|+|+  
T Consensus         3 ~~~~h~-~~l~q~~~~~~~~p~~~~C~~C~~~~~lWlCL~CG~vgCgR~~~~~~~~~~HA~~H~~~t~H~l~v~l~t~~~   81 (113)
T d2g45a1           3 QVSKHA-FSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITP   81 (113)
T ss_dssp             EECTTT-TTCCCCSSCCCCCCCBCCCSSSSCCSSEEEETTTCCEEECCBCTTSCBCCSHHHHHHHHHCCCEEEETTCCBT
T ss_pred             ccChhh-cchhhccCCccCCCCCCcccCCCCcCCEEEEecCCCCccCcccccCCCCChHHHHHHHhcCCCEEEEecCCCC
Confidence            468999 678764  3567778899999999999999999999999996      48999999999999999999875  


Q ss_pred             ---cEEEcCCCceecccccCCchhhhHHHHHHhhCCCCC
Q 032009          102 ---SVWCFTCDAYLNAQVIPQLRPVYETAYILKFGEAPP  137 (149)
Q Consensus       102 ---~vwCY~Cd~~V~~~~~~~L~~~~~~~hl~kfg~~~~  137 (149)
                         +||||.||+||.+   |+|     +.||+||||++.
T Consensus        82 ~~~~vwCY~cd~~V~d---p~l-----~~hl~~fgi~~~  112 (113)
T d2g45a1          82 DGADVYSYDEDDMVLD---PSL-----AEHLSHFGIDML  112 (113)
T ss_dssp             TBCCEEETTTTEEEEC---TTH-----HHHHHTTTCCTT
T ss_pred             CCceEEEecCCCEEEC---hhH-----HHHHHHhCcccc
Confidence               6999999999965   667     899999999985
>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]} Back     information, alignment and structure