Citrus Sinensis ID: 017219

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-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-----
MACSNKKLNLRVDSKQPSSMEIQSSWRNSTQVSSSSSSQIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
cccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcHHHHHHHHHHHHHcccccEEEEEEEccEEcccEEEEEEEEEccccccccccccccHHHHHHHHHHHcccccccEEccccccccccHHHHHHHHHHHcccccEEEEEEcccccccccEEEEEcccccccccccccccccccccccccccccccccccEEEcccccEEEEEcc
cccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccHHHHcccccccccccccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHHHccccHHHEEEcEccccEEEEEEEEEEcccccccccccccHHHHHHHHHccccEEEEEEcccccccEEEccccHccccHHHHHcHcHEEEEEcccccccccEEEEEcccccHHHHHHccccccccccccccccccccccccEEEccccEEEEEEcc
macsnkklnlrvdskqpssmeiqsswrnstqvssssssqIDKQFQKlsvniplpkketlsrhsflgphglrgqwlgpsaeikvhypsstdltttedislnqagqygivpikdgdpggaisTMESVLslddgrwlhpaekscppmvhearedpfqfvstkqpspppvlaqvqqasippsrvadprpgpaqdislntneyqhlhVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTliipkqestsdscqtLNEEEIFEVQdrlslfplgwihthpsqtcfmssvdlhthysYQIMLPEAVAIVmaptdtssphgifhlsdpggvsvirncqqrgfhpheepedgsplyehcshvfmnaklqfdvvdlr
macsnkklnlrvdskqpssmeiqsswrnstQVSSSSSSQIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTliipkqestsdSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
MACSNKKLNLRVDSKQPSSMEIqsswrnstqvssssssqidkqfqKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
***************************************************************FLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDG*****I*****VLSLDDGRWL*************************************************************NEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPK*******CQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQ***************LYEHCSHVFMNAKLQFDVV***
*******************************************************KETLSRHSFLGPHGLRG*****************************************************************************************************************************YQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQES*****QTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIR******F**HEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
MACSNKKLNLR*******************************QFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQ********TLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGF*********SPLYEHCSHVFMNAKLQFDVVDLR
*************************************SQIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDL********************************************************************************************************NEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
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MACSNKKLNLRVDSKQPSSMEIQSSWRNSTQVSSSSSSQIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR
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 ?
Query375 2.2.26 [Sep-21-2011]
Q5PNU3507 AMSH-like ubiquitin thioe yes no 0.938 0.694 0.704 1e-143
Q8VYB5507 AMSH-like ubiquitin thioe no no 0.888 0.656 0.511 5e-93
Q6NKP9223 AMSH-like ubiquitin thioe no no 0.466 0.784 0.628 6e-69
Q9P371435 AMSH-like protease sst2 O yes no 0.504 0.434 0.495 6e-48
Q54Q40715 Probable ubiquitin thioes yes no 0.442 0.232 0.511 1e-46
Q8R424424 STAM-binding protein OS=R yes no 0.538 0.476 0.452 1e-43
Q9CQ26424 STAM-binding protein OS=M yes no 0.453 0.400 0.514 1e-43
O95630424 STAM-binding protein OS=H yes no 0.538 0.476 0.447 4e-43
Q6TH47418 STAM-binding protein-like yes no 0.490 0.440 0.456 7e-41
Q96FJ0436 AMSH-like protease OS=Hom no no 0.44 0.378 0.482 4e-40
>sp|Q5PNU3|AMSH3_ARATH AMSH-like ubiquitin thioesterase 3 OS=Arabidopsis thaliana GN=AMSH3 PE=1 SV=2 Back     alignment and function desciption
 Score =  509 bits (1312), Expect = e-143,   Method: Compositional matrix adjust.
 Identities = 253/359 (70%), Positives = 290/359 (80%), Gaps = 7/359 (1%)

Query: 23  QSSW-RNSTQVSSSSSSQIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEI 81
           Q SW  N+   SSS+ +QID+QFQKLS +   P + TLSRHSFLGP+GL+ Q + P +EI
Sbjct: 150 QPSWTYNNNLTSSSNRTQIDQQFQKLSFDFLPPNQATLSRHSFLGPNGLKRQMVAPKSEI 209

Query: 82  KVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSC 141
           KV YPS+TD  + ++  L +AG        +GD    +ST+ SVLSLDDGRW   +E   
Sbjct: 210 KVQYPSNTDWGSADNSGLIEAGPSSSSASLNGD-SQEVSTLNSVLSLDDGRWQRHSEAVN 268

Query: 142 PPMVHEAREDPFQFVSTKQPSPPPVLAQVQQ--ASIPPSRVADPRPGPA---QDISLNTN 196
              + +A EDPFQFV  KQPSPPPVLAQV Q  A I PS+VADPRPGPA    +    +N
Sbjct: 269 SQFISDATEDPFQFVGMKQPSPPPVLAQVHQELAQICPSKVADPRPGPAIPSLEGKEGSN 328

Query: 197 EYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQ 256
            YQHLHVPV +M DFLRLA++NTE+NLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQ
Sbjct: 329 SYQHLHVPVRIMDDFLRLARSNTERNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQ 388

Query: 257 TLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDT 316
           TLNEEEIFEVQDRLSLFPLGWIHTHP+QTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTD 
Sbjct: 389 TLNEEEIFEVQDRLSLFPLGWIHTHPTQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDE 448

Query: 317 SSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR 375
           S+PHGIFHLSDP GVSVIRNCQQRGFHPHEE EDG+P+YEHCSHVF+NAKL+++V+DLR
Sbjct: 449 STPHGIFHLSDPSGVSVIRNCQQRGFHPHEESEDGNPIYEHCSHVFLNAKLKYEVLDLR 507
Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, but is not implicated in protein degradation by the 26S proteasome, deneddylation, or desumoylation. Required for intracellular trafficking (e.g. trafficking from the Golgi to the vacuole and the vacuolar trafficking of endocytosed cargo), endocytosis and vacuole biogenesis.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 4EC: .EC: 1EC: 9EC: .EC: -
>sp|Q8VYB5|AMSH1_ARATH AMSH-like ubiquitin thioesterase 1 OS=Arabidopsis thaliana GN=AMSH1 PE=2 SV=1 Back     alignment and function description
>sp|Q6NKP9|AMSH2_ARATH AMSH-like ubiquitin thioesterase 2 OS=Arabidopsis thaliana GN=AMSH2 PE=2 SV=1 Back     alignment and function description
>sp|Q9P371|SST2_SCHPO AMSH-like protease sst2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sst2 PE=1 SV=1 Back     alignment and function description
>sp|Q54Q40|D1039_DICDI Probable ubiquitin thioesterase DG1039 OS=Dictyostelium discoideum GN=DG1039 PE=3 SV=1 Back     alignment and function description
>sp|Q8R424|STABP_RAT STAM-binding protein OS=Rattus norvegicus GN=Stambp PE=2 SV=1 Back     alignment and function description
>sp|Q9CQ26|STABP_MOUSE STAM-binding protein OS=Mus musculus GN=Stambp PE=2 SV=1 Back     alignment and function description
>sp|O95630|STABP_HUMAN STAM-binding protein OS=Homo sapiens GN=STAMBP PE=1 SV=1 Back     alignment and function description
>sp|Q6TH47|STBPA_DANRE STAM-binding protein-like A OS=Danio rerio GN=stambpa PE=2 SV=3 Back     alignment and function description
>sp|Q96FJ0|STALP_HUMAN AMSH-like protease OS=Homo sapiens GN=STAMBPL1 PE=1 SV=2 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 ?
Query375
356564628 504 PREDICTED: AMSH-like ubiquitin thioleste 0.986 0.734 0.753 1e-162
356521807 513 PREDICTED: AMSH-like ubiquitin thioleste 0.936 0.684 0.784 1e-162
296083281 516 unnamed protein product [Vitis vinifera] 0.986 0.717 0.753 1e-159
224111900470 predicted protein [Populus trichocarpa] 0.88 0.702 0.8 1e-158
357478881 509 STAM-binding protein [Medicago truncatul 0.978 0.721 0.731 1e-157
449464724 507 PREDICTED: AMSH-like ubiquitin thioester 0.978 0.723 0.712 1e-149
449501513 507 PREDICTED: AMSH-like ubiquitin thioester 0.978 0.723 0.710 1e-148
297800548 507 At4g16144 [Arabidopsis lyrata subsp. lyr 0.938 0.694 0.710 1e-144
56381981 507 At4g16144 [Arabidopsis thaliana] 0.938 0.694 0.707 1e-143
240255910 507 AMSH-like ubiquitin thiolesterase 3 [Ara 0.938 0.694 0.704 1e-142
>gi|356564628|ref|XP_003550553.1| PREDICTED: AMSH-like ubiquitin thiolesterase 3-like [Glycine max] Back     alignment and taxonomy information
 Score =  578 bits (1489), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 284/377 (75%), Positives = 315/377 (83%), Gaps = 7/377 (1%)

Query: 5   NKKLNLRVDSKQPSS-MEIQSSWRNSTQVSSSSSSQIDKQFQKLSVNIPLPKKETLSRHS 63
           N  L     +KQP++    QSSW N   + S  S  IDKQFQKLSV++P P KETLSRHS
Sbjct: 127 NSSLQWPAVNKQPAAGFSSQSSW-NYDNMLSLDSWPIDKQFQKLSVSLPPPNKETLSRHS 185

Query: 64  FLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGAISTME 123
           FLGP+GLRGQWLGPSAEIKV YPSS +LT  +D S NQAG Y +V IKDGD G   STM+
Sbjct: 186 FLGPNGLRGQWLGPSAEIKVQYPSSGELTQAKDSSPNQAGLYDLVAIKDGDQGPVTSTMD 245

Query: 124 SVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPPVLAQV--QQASIPPSRVA 181
           SVLSLDDGRWL PA +SC P+V E+REDP Q ++ KQP PPP+LAQV  ++  IPPS+VA
Sbjct: 246 SVLSLDDGRWLRPAVESCSPVVTESREDPLQLLNIKQPLPPPILAQVYPERVPIPPSKVA 305

Query: 182 DPRPGPAQ---DISLNTNEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVF 238
           DPRPGPA+   D  L+   YQHLH+PV MM++FLRLA  NT KNLETCGVLAGSLK RVF
Sbjct: 306 DPRPGPAKSSHDSRLDATTYQHLHIPVKMMEEFLRLASENTRKNLETCGVLAGSLKKRVF 365

Query: 239 HITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYS 298
           HITTLIIPKQESTSDSCQTLNEEEIFEVQD LSLFPLGWIHTHPSQTCFMSSVDLHTHYS
Sbjct: 366 HITTLIIPKQESTSDSCQTLNEEEIFEVQDSLSLFPLGWIHTHPSQTCFMSSVDLHTHYS 425

Query: 299 YQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHC 358
           YQIMLPEA+AIVMAPTDT+SPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDG+P+YEHC
Sbjct: 426 YQIMLPEAIAIVMAPTDTTSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGTPIYEHC 485

Query: 359 SHVFMNAKLQFDVVDLR 375
           SHV+MNA L+FDVVDLR
Sbjct: 486 SHVYMNANLKFDVVDLR 502

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356521807|ref|XP_003529542.1| PREDICTED: AMSH-like ubiquitin thiolesterase 3-like [Glycine max] Back     alignment and taxonomy information
>gi|296083281|emb|CBI22917.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224111900|ref|XP_002316018.1| predicted protein [Populus trichocarpa] gi|222865058|gb|EEF02189.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357478881|ref|XP_003609726.1| STAM-binding protein [Medicago truncatula] gi|355510781|gb|AES91923.1| STAM-binding protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|449464724|ref|XP_004150079.1| PREDICTED: AMSH-like ubiquitin thioesterase 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449501513|ref|XP_004161388.1| PREDICTED: AMSH-like ubiquitin thioesterase 3-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297800548|ref|XP_002868158.1| At4g16144 [Arabidopsis lyrata subsp. lyrata] gi|297313994|gb|EFH44417.1| At4g16144 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|56381981|gb|AAV85709.1| At4g16144 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|240255910|ref|NP_680708.6| AMSH-like ubiquitin thiolesterase 3 [Arabidopsis thaliana] gi|302595939|sp|Q5PNU3.2|AMSH3_ARATH RecName: Full=AMSH-like ubiquitin thioesterase 3; AltName: Full=Deubiquitinating enzyme AMSH3 gi|332658301|gb|AEE83701.1| AMSH-like ubiquitin thiolesterase 3 [Arabidopsis thaliana] 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 ?
Query375
TAIR|locus:504955440507 AMSH3 "associated molecule wit 0.874 0.646 0.720 1.8e-126
TAIR|locus:2008184507 AMSH1 "AT1G48790" [Arabidopsis 0.869 0.642 0.531 2.6e-86
TAIR|locus:2019903223 AMSH2 "AT1G10600" [Arabidopsis 0.570 0.959 0.545 4.1e-65
POMBASE|SPAC19B12.10435 sst2 "human AMSH/STAMBP protei 0.741 0.639 0.405 1.8e-46
DICTYBASE|DDB_G0284037715 DDB_G0284037 "MPN/PAD-1 domain 0.602 0.316 0.425 1.9e-45
MGI|MGI:1917777424 Stambp "STAM binding protein" 0.602 0.533 0.443 8.1e-44
RGD|619963424 Stambp "Stam binding protein" 0.6 0.530 0.442 8.1e-44
UNIPROTKB|F1SLF9424 STAMBP "Uncharacterized protei 0.610 0.540 0.417 4.5e-43
UNIPROTKB|Q17QR2423 STAMBP "STAM binding protein" 0.578 0.513 0.446 5.7e-43
UNIPROTKB|O95630424 STAMBP "STAM-binding protein" 0.538 0.476 0.447 1.5e-42
TAIR|locus:504955440 AMSH3 "associated molecule with the SH3 domain of STAM 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1242 (442.3 bits), Expect = 1.8e-126, P = 1.8e-126
 Identities = 242/336 (72%), Positives = 274/336 (81%)

Query:    46 KLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQY 105
             KLS +   P + TLSRHSFLGP+GL+ Q + P +EIKV YPS+TD  + ++  L +AG  
Sbjct:   174 KLSFDFLPPNQATLSRHSFLGPNGLKRQMVAPKSEIKVQYPSNTDWGSADNSGLIEAGPS 233

Query:   106 GIVPIKDGDPGGAISTMESVLSLDDGRWLHPAEKSCPPMVHEAREDPFQFVSTKQPSPPP 165
                   +GD    +ST+ SVLSLDDGRW   +E      + +A EDPFQFV  KQPSPPP
Sbjct:   234 SSSASLNGD-SQEVSTLNSVLSLDDGRWQRHSEAVNSQFISDATEDPFQFVGMKQPSPPP 292

Query:   166 VLAQVQQ--ASIPPSRVADPRPGPAQDISLN----TNEYQHLHVPVNMMQDFLRLAQANT 219
             VLAQV Q  A I PS+VADPRPGPA   SL     +N YQHLHVPV +M DFLRLA++NT
Sbjct:   293 VLAQVHQELAQICPSKVADPRPGPAIP-SLEGKEGSNSYQHLHVPVRIMDDFLRLARSNT 351

Query:   220 EKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH 279
             E+NLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH
Sbjct:   352 ERNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH 411

Query:   280 THPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQ 339
             THP+QTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTD S+PHGIFHLSDP GVSVIRNCQQ
Sbjct:   412 THPTQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDESTPHGIFHLSDPSGVSVIRNCQQ 471

Query:   340 RGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR 375
             RGFHPHEE EDG+P+YEHCSHVF+NAKL+++V+DLR
Sbjct:   472 RGFHPHEESEDGNPIYEHCSHVFLNAKLKYEVLDLR 507
GO:0005634 "nucleus" evidence=ISM
GO:0000338 "protein deneddylation" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0006897 "endocytosis" evidence=IMP
GO:0007033 "vacuole organization" evidence=IMP
GO:0016020 "membrane" evidence=IDA
GO:0016021 "integral to membrane" evidence=IDA
GO:0016926 "protein desumoylation" evidence=IDA
GO:0019941 "modification-dependent protein catabolic process" evidence=IDA
GO:0044090 "positive regulation of vacuole organization" evidence=IMP
GO:0046907 "intracellular transport" evidence=IMP
GO:0070536 "protein K63-linked deubiquitination" evidence=IDA
GO:0071108 "protein K48-linked deubiquitination" evidence=IDA
GO:0090316 "positive regulation of intracellular protein transport" evidence=IMP
TAIR|locus:2008184 AMSH1 "AT1G48790" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2019903 AMSH2 "AT1G10600" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
POMBASE|SPAC19B12.10 sst2 "human AMSH/STAMBP protein homolog, ubiquitin specific-protease" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0284037 DDB_G0284037 "MPN/PAD-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
MGI|MGI:1917777 Stambp "STAM binding protein" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|619963 Stambp "Stam binding protein" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1SLF9 STAMBP "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q17QR2 STAMBP "STAM binding protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|O95630 STAMBP "STAM-binding protein" [Homo sapiens (taxid:9606)] 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) ?
Q5PNU3AMSH3_ARATH3, ., 4, ., 1, 9, ., -0.70470.93860.6942yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer3.4.190.691
3rd Layer3.4.17.n1LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00033104001
SubName- Full=Chromosome chr5 scaffold_64, whole genome shotgun sequence; (516 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query375
cd08066173 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family 1e-111
cd08058119 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) 9e-28
cd07767116 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domain 1e-23
pfam01398117 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro 2e-22
smart00232135 smart00232, JAB_MPN, JAB/MPN domain 1e-16
cd08069268 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: p 4e-05
COG51782365 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA p 0.001
cd08061274 cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear 0.004
>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family Back     alignment and domain information 
 Score =  321 bits (826), Expect = e-111
 Identities = 104/178 (58%), Positives = 127/178 (71%), Gaps = 5/178 (2%)

Query: 198 YQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQT 257
            + + VP ++M  FL+LA+ NT +NLETCG+L G L N  F IT LIIPKQ  TSDSCQT
Sbjct: 1   LRQVVVPADLMDKFLQLAEPNTSRNLETCGILCGKLSNNAFFITHLIIPKQSGTSDSCQT 60

Query: 258 LNEEEIFEVQDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTS 317
            NEEE+F+ QD+  L  LGWIHTHP+QTCF+SSVDLHTH SYQ+MLPEA+AIV AP    
Sbjct: 61  TNEEELFDFQDQHDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP--KY 118

Query: 318 SPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR 375
           +  GIF L+DP G+  I NC++ GFHPH +     PLYE C HV    +L+  VVDLR
Sbjct: 119 NEFGIFRLTDPPGLDEILNCKKTGFHPHPKD---PPLYEDCGHVIWKDQLKVTVVDLR 173

AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, all of which are components of ESCRT-III, suggested to be required for EGFR down-regulation. The function of AMSH-LP has not been elucidated; however, it exhibits two fundamentally distinct features from AMSH: first, there is a substitution in the critical amino acid residue in the SH3-binding motif (SBM) in the human AMSH-LP, but not in its mouse ortholog, and lacks STAM-binding ability; second, AMSH-LP lacks the ability to interact with CHMP proteins. It is therefore likely that AMSH and AMSH-LP play different roles on early endosomes. Length = 173
>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic Back     alignment and domain information
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains Back     alignment and domain information
>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease Back     alignment and domain information
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain Back     alignment and domain information
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5 Back     alignment and domain information
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification] Back     alignment and domain information
>gnl|CDD|163692 cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 375
KOG2880424 consensus SMAD6 interacting protein AMSH, contains 100.0
cd08066173 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ 100.0
cd08058119 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w 99.95
cd08069268 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal 99.94
cd08068244 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun 99.94
cd08067187 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu 99.94
smart00232135 JAB_MPN JAB/MPN domain. Domain in Jun kinase activ 99.88
cd08056252 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit 99.88
cd07767116 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al 99.87
KOG1554 347 consensus COP9 signalosome, subunit CSN5 [Posttran 99.87
cd08065266 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains wi 99.87
cd08070128 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit 99.86
PF01398114 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; Inte 99.83
KOG1560 339 consensus Translation initiation factor 3, subunit 99.83
cd08072117 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1 99.78
cd08073108 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains 99.74
KOG1555316 consensus 26S proteasome regulatory complex, subun 99.71
COG1310134 Predicted metal-dependent protease of the PAD1/JAB 99.61
cd08057157 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domai 99.58
PF14464104 Prok-JAB: Prokaryotic homologs of the JAB domain; 99.57
TIGR03735192 PRTRC_A PRTRC system protein A. A novel genetic sy 99.42
cd08062280 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains w 99.4
cd08064265 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains wi 99.39
cd08059101 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains 99.37
cd08060182 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family 99.32
PLN03246 303 26S proteasome regulatory subunit; Provisional 99.06
cd08061274 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l 99.0
cd08063 288 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains wit 99.0
TIGR02256131 ICE_VC0181 integrative and conjugative element pro 98.91
KOG17952321 consensus U5 snRNP spliceosome subunit [RNA proces 98.57
KOG1556 309 consensus 26S proteasome regulatory complex, subun 98.41
PF05021 306 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge 98.21
PF03665196 UPF0172: Uncharacterised protein family (UPF0172); 97.87
KOG2975288 consensus Translation initiation factor 3, subunit 97.55
COG51782365 PRP8 U5 snRNP spliceosome subunit [RNA processing 97.53
KOG2834 510 consensus Nuclear pore complex, rNpl4 component (s 96.84
KOG3289199 consensus Uncharacterized conserved protein encode 96.06
KOG3050 299 consensus COP9 signalosome, subunit CSN6 [Posttran 94.71
cd08071113 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 94.02
PF14220123 DUF4329: Domain of unknown function (DUF4329) 92.81
PF04002123 RadC: RadC-like JAB domain; InterPro: IPR001405 Th 90.25
PRK00024224 hypothetical protein; Reviewed 82.49
COG5100 571 NPL4 Nuclear pore protein [Nuclear structure] 82.24
TIGR00608218 radc DNA repair protein radc. This family is based 82.03
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms] Back     alignment and domain information 
Probab=100.00  E-value=9.6e-56  Score=433.08  Aligned_cols=301  Identities=46%  Similarity=0.743  Sum_probs=257.2

Q ss_pred             hHHHHhhhcccccCCCCccccccccccCCCCCCCCCCCCcccceeecCCCCCCCccccCcccccCCCCCCCCCCCCCCCC
Q 017219           39 QIDKQFQKLSVNIPLPKKETLSRHSFLGPHGLRGQWLGPSAEIKVHYPSSTDLTTTEDISLNQAGQYGIVPIKDGDPGGA  118 (375)
Q Consensus        39 ~~~~~~~~~~~~~~~p~~~tl~~h~~~gp~~~~~~~~~~~~~~~~~yps~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  118 (375)
                      -.++.+|+|..   .+.+||++.|++               ..+.||+++.++.+.+.++++|....+.+.. .++.+.+
T Consensus       122 ~~~E~~k~le~---~~~~E~e~kr~a---------------q~k~Q~l~~~~f~~~~~~~~~q~~~s~~m~s-~~~~gl~  182 (424)
T KOG2880|consen  122 NLAERFKKLEV---QREEETERKRSA---------------QTKQQQLESSQFSPLEPPSFKQLLDSGPMPS-NQSNGLP  182 (424)
T ss_pred             hHHHHHHHhhc---chhhHHHHHHHH---------------HHhhhcCCcccCCccCchHHHhhhcccCCCc-CCCCCCc
Confidence            46788999988   899999999988               7899999999999999999999998877663 3333333


Q ss_pred             -ccccccccccCCCCCccCCcCCCCCCccc-ccCCCcccccccCCCCCccccccccCCCCCCccCCCCCCCCCCCCCCCC
Q 017219          119 -ISTMESVLSLDDGRWLHPAEKSCPPMVHE-AREDPFQFVSTKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTN  196 (375)
Q Consensus       119 -~~~~~s~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  196 (375)
                       +...++.+--.+.|.....++.. ..+++ ..++-.....+++|+++++|....            ...........++
T Consensus       183 e~~~~~~~~p~~~~~~~~~s~~l~-~~~s~ep~~s~~~n~~~k~p~~~r~l~p~a------------~~n~~~~~~~~~k  249 (424)
T KOG2880|consen  183 EQPIGEPLVPSNESRSLNYSELLS-VLSSPEPSDSCTTNVTIKSPSVDRVLKPGA------------TDNSNHGESSEGK  249 (424)
T ss_pred             CCCcCCCCcccccccccCCchhhh-hccCCCccccccccccccCCCCCccccccc------------ccccccccccCCc
Confidence             45555555445555555555554 44443 455555566677777777665441            1111122456777


Q ss_pred             CceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEE
Q 017219          197 EYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLG  276 (375)
Q Consensus       197 ~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVG  276 (375)
                      .++.|+|+..++..|++.|+++++++.|+||+|+|+...+.++||.+++|+|++++++|.+++++|+|++|+.++|..||
T Consensus       250 ~lr~v~ip~~l~~~Fl~la~~NT~knlETCGiL~g~L~~n~f~IThliiPkQeatsd~C~t~neeelF~vQdq~~L~tlG  329 (424)
T KOG2880|consen  250 ILRDVHIPERLMEVFLQLAKSNTKKNLETCGILAGKLERNEFYITHLIIPKQEATSDSCNTMNEEELFEVQDQHELLTLG  329 (424)
T ss_pred             cceEEEecHHHHHHHHHHHhhcccccchHHHHhhhHhhcCcEEEEEEEeecccCCCccccccCHHHHheecccccceeee
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccCCccCCCCCCCCCccc
Q 017219          277 WIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLYE  356 (375)
Q Consensus       277 WYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~gFhph~~~~~~~~iy~  356 (375)
                      |+||||+++||+|+.|+|||++||.|+|+++||||+|..  ...|+|||++|+||++|+.|+++|||||+.  +|.|+|+
T Consensus       330 WIHTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~--~~tGiFrLt~~~Gm~~i~~C~~~GFHpH~~--~~~pl~~  405 (424)
T KOG2880|consen  330 WIHTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKS--KTTGIFRLTDPGGMEVIRGCRKKGFHPHSE--KGPPLFE  405 (424)
T ss_pred             eeecCCccchhheeccccccceeeeecchheeEEecccc--CCcceEEecCCcchHHHhhcccCCCCCCCC--CCCCcee
Confidence            999999999999999999999999999999999999985  578999999999999999999999999987  7899999


Q ss_pred             cccceEecCCCceeEeeCC
Q 017219          357 HCSHVFMNAKLQFDVVDLR  375 (375)
Q Consensus       357 ~~~~v~~~~~~~~~~~dlr  375 (375)
                      +|+||||+.|.+++|+|||
T Consensus       406 ~~~~v~~~~~~k~~v~dLR  424 (424)
T KOG2880|consen  406 HCSHVYMHHNNKLCVIDLR  424 (424)
T ss_pred             ecceeEEcCCcceeeeeCC
Confidence            9999999999999999998

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family Back     alignment and domain information
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic Back     alignment and domain information
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5 Back     alignment and domain information
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex Back     alignment and domain information
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase Back     alignment and domain information
>smart00232 JAB_MPN JAB/MPN domain Back     alignment and domain information
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8 Back     alignment and domain information
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains Back     alignment and domain information
>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h Back     alignment and domain information
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) Back     alignment and domain information
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors Back     alignment and domain information
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme Back     alignment and domain information
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains Back     alignment and domain information
>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only] Back     alignment and domain information
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic Back     alignment and domain information
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A Back     alignment and domain information
>TIGR03735 PRTRC_A PRTRC system protein A Back     alignment and domain information
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8 Back     alignment and domain information
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f Back     alignment and domain information
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic Back     alignment and domain information
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p) Back     alignment and domain information
>PLN03246 26S proteasome regulatory subunit; Provisional Back     alignment and domain information
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain Back     alignment and domain information
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6 Back     alignment and domain information
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family Back     alignment and domain information
>KOG1795 consensus U5 snRNP spliceosome subunit [RNA processing and modification] Back     alignment and domain information
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport Back     alignment and domain information
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function Back     alignment and domain information
>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification] Back     alignment and domain information
>KOG2834 consensus Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport] Back     alignment and domain information
>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only] Back     alignment and domain information
>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family Back     alignment and domain information
>PF14220 DUF4329: Domain of unknown function (DUF4329) Back     alignment and domain information
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions [] Back     alignment and domain information
>PRK00024 hypothetical protein; Reviewed Back     alignment and domain information
>COG5100 NPL4 Nuclear pore protein [Nuclear structure] Back     alignment and domain information
>TIGR00608 radc DNA repair protein radc 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 ?
Query375
3rzv_A211 The Crystal Structure Of A E280a Mutant Of The Cata 3e-43
3rzu_A187 The Crystal Structure Of The Catalytic Domain Of Am 2e-42
2znr_A178 Crystal Structure Of The Dub Domain Of Human Amsh-L 2e-40
2znv_A178 Crystal Structure Of Human Amsh-Lp Dub Domain In Co 1e-39
4b4t_V306 Near-Atomic Resolution Structural Model Of The Yeas 2e-05
>pdb|3RZV|A Chain A, The Crystal Structure Of A E280a Mutant Of The Catalytic Domain Of Amsh Length = 211 Back     alignment and structure 
Iteration: 1

 Score =  172 bits (436), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 97/219 (44%), Positives = 135/219 (61%), Gaps = 17/219 (7%)
Query: 157 STKQPSPPPVLAQVQQASIPPSRVADPRPGPAQDISLNTNEYQHLHVPVNMMQDFLRLAQ 216
           +T +P+ PPV+ +    S+ P  +++    P  D        +H+ VP  +   FL+LA 
Sbjct: 10  TTVRPAKPPVVDR----SLKPGALSNSESIPTID------GLRHVVVPGRLCPQFLQLAS 59
Query: 217 ANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLG 276
           ANT + + TCG+L G L    F IT ++IPKQ + SD C T NEEE+F +QD+  L  LG
Sbjct: 60  ANTARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLG 119
Query: 277 WIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRN 336
           WIHTHP+QT F+SSVDLHTH SYQ+MLPE+VAIV +P    +  G F L+D  G+  I +
Sbjct: 120 WIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQET--GFFKLTD-HGLEEISS 176
Query: 337 CQQRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR 375
           C+Q+GFHPH +     PL+  CSHV +  +    + DLR
Sbjct: 177 CRQKGFHPHSK---DPPLFCSCSHVTVVDR-AVTITDLR 211
>pdb|3RZU|A Chain A, The Crystal Structure Of The Catalytic Domain Of Amsh Length = 187 Back     alignment and structure
>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp Length = 178 Back     alignment and structure
>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex With Lys63-Linked Ubiquitin Dimer Length = 178 Back     alignment and structure
>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 306 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 ?
Query375
3rzv_A211 STAM-binding protein; ubiquitin hydrolase, endosom 3e-68
2znr_A178 AMSH-like protease; metal binding protein, alterna 2e-58
2og4_A254 PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN 1e-33
2p8r_A273 PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t 7e-31
3sbg_A565 PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, 1e-27
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-09
2kks_A146 Uncharacterized protein; NESG, structural genomics 2e-06
>3rzv_A STAM-binding protein; ubiquitin hydrolase, endosome-associated deubiquitinat enzyme, hydrolase; 1.67A {Homo sapiens} PDB: 3rzu_A Length = 211 Back     alignment and structure
 Score =  213 bits (543), Expect = 3e-68
 Identities = 93/217 (42%), Positives = 124/217 (57%), Gaps = 9/217 (4%)

Query: 161 PSPPPVLAQVQQASIPPSRVADPRPG--PAQDISLNTNEYQHLHVPVNMMQDFLRLAQAN 218
           P          + + PP      +PG     +     +  +H+ VP  +   FL+LA AN
Sbjct: 2   PLGSSDCHTTVRPAKPPVVDRSLKPGALSNSESIPTIDGLRHVVVPGRLCPQFLQLASAN 61

Query: 219 TEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWI 278
           T + + TCG+L G L    F IT ++IPKQ + SD C T NEEE+F +QD+  L  LGWI
Sbjct: 62  TARGVATCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWI 121

Query: 279 HTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQ 338
           HTHP+QT F+SSVDLHTH SYQ+MLPE+VAIV +P       G F L+D  G+  I +C+
Sbjct: 122 HTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSP--KFQETGFFKLTDH-GLEEISSCR 178

Query: 339 QRGFHPHEEPEDGSPLYEHCSHVFMNAKLQFDVVDLR 375
           Q+GFHPH       PL+  CSHV +       + DLR
Sbjct: 179 QKGFHPH---SKDPPLFCSCSHVTVV-DRAVTITDLR 211
>2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A Length = 178 Back     alignment and structure
>2og4_A PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN domain, protein-PR interaction, PRP8P, pseudoenzyme, spliceosome activation; 2.00A {Saccharomyces cerevisiae} Length = 254 Back     alignment and structure
>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A {Caenorhabditis elegans} PDB: 2p87_A Length = 273 Back     alignment and structure
>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain; 3.28A {Saccharomyces cerevisiae} Length = 565 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; NMR {Desulfitobacterium hafniense} Length = 146 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query375
2znr_A178 AMSH-like protease; metal binding protein, alterna 100.0
3rzv_A211 STAM-binding protein; ubiquitin hydrolase, endosom 100.0
4b4t_V306 26S proteasome regulatory subunit RPN11; hydrolase 99.95
2og4_A254 PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN 99.92
2kks_A146 Uncharacterized protein; NESG, structural genomics 99.91
2kcq_A153 MOV34/MPN/PAD-1 family; NESG, structure, structura 99.91
2p8r_A273 PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t 99.91
2o95_A187 26S proteasome non-ATPase regulatory subunit 7; PS 99.8
1oi0_A124 AF2198, hypothetical protein AF2198; proteasome, d 99.79
3sbg_A565 PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, 99.72
4e0q_A141 COP9 signalosome complex subunit 6; MPN (MPR1P and 99.64
4b4t_U 338 RPN8, 26S proteasome regulatory subunit RPN8; hydr 99.13
2qlc_A126 DNA repair protein RADC homolog; MCSG, structural 94.34
>2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A Back     alignment and structure
Probab=100.00  E-value=1.8e-47  Score=346.28  Aligned_cols=173  Identities=47%  Similarity=0.877  Sum_probs=162.3

Q ss_pred             CCceEEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccE
Q 017219          196 NEYQHLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPL  275 (375)
Q Consensus       196 ~~~~~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiV  275 (375)
                      +++++|.|+++++++|++||++++.++.|+||+|+|+..++.++|+++|+++|.++++++++.+++++++++..+++++|
T Consensus         6 ~~~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~~~~~~~~V~~v~~~pq~~t~~~~~~~~~~e~~~~~~~~~l~~v   85 (178)
T 2znr_A            6 EGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHVIVPKQSAGPDYCDMENVEELFNVQDQHDLLTL   85 (178)
T ss_dssp             CSCCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEEEETTEEEEEEEEECCEEEETTEEEECCHHHHHHHHHHHTCEEE
T ss_pred             CCcEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeEecCCCeEEEEEEeCCcCCCCCeeccCCHHHHHHHHHhCCCEEE
Confidence            46788999999999999999998734579999999999878899999999999999999999999999999889999999


Q ss_pred             EEEeCCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEeeCCCCCceeecccccCCccCCCCCCCCCcc
Q 017219          276 GWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHLSDPGGVSVIRNCQQRGFHPHEEPEDGSPLY  355 (375)
Q Consensus       276 GWYHSHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRLsdp~Gm~~~~~c~~~gFhph~~~~~~~~iy  355 (375)
                      |||||||.++|+||.+|+++|++||+++|++++||+||..+  .++||||++ +|++++++|+++|||||.+   +.+||
T Consensus        86 GwyHSHP~~~~~pS~~Dv~tq~~yq~~~~~~v~iIvsp~~~--~~~afrl~~-~g~~~~~~~~~~~f~p~~~---~~~~~  159 (178)
T 2znr_A           86 GWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHK--DTGIFRLTN-AGMLEVSACKKKGFHPHTK---EPRLF  159 (178)
T ss_dssp             EEEEECSSSCSCCCHHHHHHHHHHHHHCTTCEEEEEEGGGT--EEEEEEECH-HHHHHHHHCCCCSSCCCCC---SSCSE
T ss_pred             EEEeCCCCCCCCCCHHHHHHHHHHHhhcCCEEEEEEcCCCC--cceEEEEEC-CcEeeecccCCCCcccCCC---CCCce
Confidence            99999999999999999999999999999999999999985  489999997 6999999999999999984   57999


Q ss_pred             ccccceEecCCCceeEeeCC
Q 017219          356 EHCSHVFMNAKLQFDVVDLR  375 (375)
Q Consensus       356 ~~~~~v~~~~~~~~~~~dlr  375 (375)
                      ++|+||++++++ |+|+|||
T Consensus       160 ~~~~~~~~~~~~-~~~~~~r  178 (178)
T 2znr_A          160 SICKHVLVKDIK-IIVLDLR  178 (178)
T ss_dssp             EECSSEEEECCC-CEEEECC
T ss_pred             EEeceEEEeCCe-eEEEecC
Confidence            999999999999 9999999
>3rzv_A STAM-binding protein; ubiquitin hydrolase, endosome-associated deubiquitinat enzyme, hydrolase; 1.67A {Homo sapiens} PDB: 3rzu_A Back     alignment and structure
>4b4t_V 26S proteasome regulatory subunit RPN11; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>2og4_A PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN domain, protein-PR interaction, PRP8P, pseudoenzyme, spliceosome activation; 2.00A {Saccharomyces cerevisiae} Back     alignment and structure
>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; NMR {Desulfitobacterium hafniense} Back     alignment and structure
>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855} Back     alignment and structure
>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A {Caenorhabditis elegans} PDB: 2p87_A Back     alignment and structure
>2o95_A 26S proteasome non-ATPase regulatory subunit 7; PSMD7, MOV34, JAB1/MPN, metal-free dimer, UN function; HET: SO4 12P ETE PG4 PGE; 1.95A {Homo sapiens} PDB: 2o96_A Back     alignment and structure
>1oi0_A AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} SCOP: c.97.3.1 PDB: 1r5x_A Back     alignment and structure
>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain; 3.28A {Saccharomyces cerevisiae} Back     alignment and structure
>4e0q_A COP9 signalosome complex subunit 6; MPN (MPR1P and PAD1P N-terminal) domain, unknown function; 2.50A {Drosophila melanogaster} Back     alignment and structure
>4b4t_U RPN8, 26S proteasome regulatory subunit RPN8; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>2qlc_A DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, structure initiative; HET: DNA; 2.30A {Chlorobium tepidum tls} 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 375
d1oi0a_121 c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeo 5e-08
>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 121 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: JAB1/MPN domain
family: JAB1/MPN domain
domain: Hypothetical protein AF2198
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 48.8 bits (116), Expect = 5e-08
 Identities = 24/119 (20%), Positives = 43/119 (36%), Gaps = 18/119 (15%)

Query: 201 LHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNE 260
           + +   +++  L  A++      E   +L+G        +  LI     S S S      
Sbjct: 4   MKISRGLLKTILEAAKSAHPD--EFIALLSG----SKDVMDELIFLPFVSGSVS------ 51

Query: 261 EEIFEV-QDRLSLFPLGWIHTHPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSS 318
             +  +    + +   G +H+HPS +C  S  DL           +   IV  P D +S
Sbjct: 52  -AVIHLDMLPIGMKVFGTVHSHPSPSCRPSEEDLSLFT----RFGKYHIIVCYPYDENS 105

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query375
d1oi0a_121 Hypothetical protein AF2198 {Archaeon Archaeoglobu 99.8
>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: JAB1/MPN domain
family: JAB1/MPN domain
domain: Hypothetical protein AF2198
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.80  E-value=7.2e-20  Score=154.17  Aligned_cols=109  Identities=19%  Similarity=0.203  Sum_probs=84.6

Q ss_pred             EEEECHHHHHHHHHHHHhcCCCCcceEEEeeeeeCCCeEEEEEEEecCCCCCCCcccccCHHHHHHHHhhCCCccEEEEe
Q 017219          200 HLHVPVNMMQDFLRLAQANTEKNLETCGVLAGSLKNRVFHITTLIIPKQESTSDSCQTLNEEEIFEVQDRLSLFPLGWIH  279 (375)
Q Consensus       200 ~V~Ip~~ll~kILkHA~s~t~~P~EvCGLLlG~~~~~~l~VT~lfpppq~~ts~s~~~~DpeEif~~q~~rgLeiVGWYH  279 (375)
                      +|.|++++++.|++||++++  |+|+||+|+|+..    .|+.+++.++...+...  ..+    ..+...++.+|||||
T Consensus         3 ~l~I~~~~l~~i~~hA~~~~--P~E~cGlL~G~~~----~i~~~~~~~n~~~~~~~--~~~----~~~~~~~~~ivgi~H   70 (121)
T d1oi0a_           3 SMKISRGLLKTILEAAKSAH--PDEFIALLSGSKD----VMDELIFLPFVSGSVSA--VIH----LDMLPIGMKVFGTVH   70 (121)
T ss_dssp             SCEECHHHHHHHHHHHHHHT--TSCCEEEEEESTT----EECEEEECCCCC-------------------CCCEEEEEEE
T ss_pred             eEEECHHHHHHHHHHHHhcC--CceeEEEEEecCC----cEEEEEEcCCCCCCccc--ccc----cchhhcCCeEEEEEE
Confidence            37899999999999999999  9999999999754    57788888886543321  111    114568999999999


Q ss_pred             CCCCCCCCCCHHHHHHHHHHhhcCCCeEEEEEcCCCCCCceeEEEe
Q 017219          280 THPSQTCFMSSVDLHTHYSYQIMLPEAVAIVMAPTDTSSPHGIFHL  325 (375)
Q Consensus       280 SHP~~~afPSstDL~tq~sYQ~~~PeaVaLIvSP~~ts~~lrAFRL  325 (375)
                      |||..+++||.+|++++.     .++.++||+++-.+...++||+.
T Consensus        71 SHP~~~a~PS~~D~~~~~-----~~g~~~~Ivs~p~~~~~~~~~~~  111 (121)
T d1oi0a_          71 SHPSPSCRPSEEDLSLFT-----RFGKYHIIVCYPYDENSWKCYNR  111 (121)
T ss_dssp             EESSSCCSCCHHHHHHHH-----HSCSEEEEEETTCCTTCEEEEET
T ss_pred             ecCCCCCCcCHHHHHhhh-----ccCCEEEEEeCCCCCCCEEEEeC
Confidence            999999999999998643     57889999998777677899974