Psyllid ID: psy1724

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-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470---

MFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLELDGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPASAHKEFQFGFNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPPVGYTEPEKVKEKEEDNMIDPVDLMPEPSGFVAFHGTGNRLDGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPASAHKE

ccccccccccccEEEEEEEccccccccccccccEEEEcHHHHHHHHHccccccEEEEEEccccccEEEEEEEEEEEccccEEEcHHHHHHcccccccccccccEEEEEEccccccccccccccccEEEEEccccccccEEEEEEEEEccccEEccccccccccHHHHHcccccccccccEEEEEEcccccccccccccccccccccccccccEEEEEEEEEcccccccccccccEEEccHHHHHHHHHccccccEEEEEEccccccEEEEEEEEEEccccEEEccHHHHHccccccccEEEEEEEEccccEEEEEEEccccccccccccEEEcccccccEEEccccEEEEEEccEEEEEEEEEEEcccEEEEEcccEEEEEccccccccccccccccccccccccccccccccccEEEEEEEEccccccccccccccccccccccccccccccccccEEEEcccccccccccc

ccccccccccEEEEEEEEEEccccccHHHccccEEEccHHHHHHHHHccccccEEEEEEccccccccccEEEEEEcccccEEccHHHHHcccccccccccccccEEEEEccccccHcccccHHHHHHHHHHHHHHcccccEEEEEEcccEEEEEEEEcccccccccccccccccccccccccccccccccccHHcccccccccccccccccEEEEEEEEEEccccccccHccccEEEccHHHHHHHHHccccccEEEEEEcccccccccccEEEEEcccccEEcHHHHHHHcccccccEEEEEEccccccEEEEEccccccHcccccHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEEcccccEEEEEEccEEEccccccccccccccccccccHccHccccccccccccccccccEccccccccccccccccccccccccccccccccccEEEEEccccccccccc

mfpdiprpfnrsykcfsvsmfpgneredverggkiimppsaleQLTRLNICYPMLFkltnqkmgrithSGVLEFVadegkvylpywcfsvsmfpgneredverggkiimppsaleQLTRLNICYPMLFkltnqkmgrithsgvleldgkrkkkdtvetggtptkreyqrgiphydyepntlvflrnikpasahkefqfgfnmfpdiprpfnrsykcfsvsmfpgneredverggkiimppsaleQLTRLNICYPMLFkltnqkmgrithSGVLEFVadegkvylpYWMMRNLLLdegelvniesvslpvatfskfqpqtcdflditnpKAVLENCLRNfacltsgdmiaiNYNSKIYELCVLetkpgnavtiiecdmnvdfappvgytepekvkekeednmidpvdlmpepsgfvafhgtgnrldgkrkkkdtvetggtptkreyqrgiphydyepntlVFLRnikpasahke

mfpdiprpfnrsykcfsvsmFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKltnqkmgrITHSgvleldgkrkkkdtvetggtptkreyqrgiphYDYEPNTLVFLRNIKPASAHKEFQFGFNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPPVGYTEPEKVKEKEEDNMIDPVDLMPEPSGFVAFHgtgnrldgkrkkkdtvetggtptkreyqrgiphydyepntlVFLRNIkpasahke

************YKCFSVSMF************KIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPGNE***VERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVL***********************QRGIPHYDYEPNTLVFLRNIKPASAHKEFQFGFNMFPDIPRPFNRSYKCFSVSMFPG********GGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPPVGY************************************************************GIPHYDYEPNTLVFLRNI********

*****PRPFNRSYKCFSVSMF*********RGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLELDGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPASAHKEFQFGFNMFPDIPRPFNRSYKCFSVSM*************KIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAP*********************************************************************DYEPNTLVFL***********

*F**IPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLELDGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPASAHKEFQFGFNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPPVGYTE********************************************************QRGIPHYDYEPNTLVFLRNIK*******

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		473	2.2.26 [Sep-21-2011]
Q9VTF9		316	Ubiquitin fusion degradat	yes	N/A	0.572	0.857	0.621	4e-94
Q92890		307	Ubiquitin fusion degradat	yes	N/A	0.562	0.866	0.637	3e-90
Q9ES53		307	Ubiquitin fusion degradat	yes	N/A	0.562	0.866	0.637	6e-90
P70362		307	Ubiquitin fusion degradat	yes	N/A	0.562	0.866	0.637	7e-90
P53044		361	Ubiquitin fusion degradat	yes	N/A	0.391	0.512	0.507	1e-53
O42915		342	Ubiquitin fusion degradat	yes	N/A	0.467	0.646	0.425	2e-53
Q55BK0		330	Ubiquitin fusion degradat	yes	N/A	0.384	0.551	0.535	1e-52
Q19584		342	Ubiquitin fusion degradat	yes	N/A	0.490	0.678	0.417	6e-49

>sp\|Q9VTF9\|UFD1_DROME Ubiquitin fusion degradation protein 1 homolog OS=Drosophila melanogaster GN=Ufd1-like PE=2 SV=1	Back alignment and function desciption

 Score =  345 bits (886), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 177/285 (62%), Positives = 209/285 (73%), Gaps = 14/285 (4%)

Query: 196 FQF-GFNM-FPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICY 253
           F F GFNM FP+  R F+ +YKCFSVSM PGNER DVE+GGKIIMPPSAL+ LTRLN+ Y
Sbjct: 2   FHFSGFNMMFPE-GRNFHANYKCFSVSMLPGNERTDVEKGGKIIMPPSALDTLTRLNVEY 60

Query: 254 PMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFS 313
           PMLFKLTN K  R +H+GVLEFVADEGK YLP+WMM NLLL EG+++NIESVSLPVATFS
Sbjct: 61  PMLFKLTNVKKSRSSHAGVLEFVADEGKCYLPHWMMENLLLGEGDILNIESVSLPVATFS 120

Query: 314 KFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTII 373
           KFQP + DFLDITNPKAVLEN LRNFACLT GD+IAI YN K+YELCVLETKPGNAV+II
Sbjct: 121 KFQPHSTDFLDITNPKAVLENALRNFACLTRGDVIAIKYNKKVYELCVLETKPGNAVSII 180

Query: 374 ECDMNVDFAPPVGYTEPEKVKEKEEDNMIDPVDLMPEPSGFV---------AFHGTGNRL 424
           ECDMNV+F  PVGY +  + +            +  E +G            F G+G RL
Sbjct: 181 ECDMNVEFEAPVGYKDHSETQASGSGQQGAAGTVGGEIAGATNAILEEVVETFKGSGVRL 240

Query: 425 DGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPAS 469
           DGK+KK+  +ET     K+   RG+P YD++   + F RNI+P S
Sbjct: 241 DGKKKKESQLET--PVVKKVLARGVPDYDFQFGLIRFDRNIRPIS 283

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway.
Drosophila melanogaster (taxid: 7227)

>sp\|Q92890\|UFD1_HUMAN Ubiquitin fusion degradation protein 1 homolog OS=Homo sapiens GN=UFD1L PE=1 SV=3	Back alignment and function description

>sp\|Q9ES53\|UFD1_RAT Ubiquitin fusion degradation protein 1 homolog OS=Rattus norvegicus GN=Ufd1l PE=1 SV=1	Back alignment and function description

>sp\|P70362\|UFD1_MOUSE Ubiquitin fusion degradation protein 1 homolog OS=Mus musculus GN=Ufd1l PE=1 SV=2	Back alignment and function description

>sp\|P53044\|UFD1_YEAST Ubiquitin fusion degradation protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=UFD1 PE=1 SV=1	Back alignment and function description

>sp\|O42915\|UFD1_SCHPO Ubiquitin fusion degradation protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ufd1 PE=2 SV=4	Back alignment and function description

>sp\|Q55BK0\|UFD1_DICDI Ubiquitin fusion degradation protein 1 homolog OS=Dictyostelium discoideum GN=ufd1 PE=3 SV=1	Back alignment and function description

>sp\|Q19584\|UFD1_CAEEL Ubiquitin fusion degradation protein 1 homolog OS=Caenorhabditis elegans GN=ufd-1 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
Query		473
345479998		294	PREDICTED: ubiquitin fusion degradation	0.572	0.921	0.750	1e-116
383861689		296	PREDICTED: ubiquitin fusion degradation	0.570	0.912	0.738	1e-114
332374826		298	unknown [Dendroctonus ponderosae]	0.564	0.895	0.727	1e-112
307212287		417	Ubiquitin fusion degradation protein 1-l	0.577	0.654	0.759	1e-112
242013341		316	ubiquitin fusion degradaton protein, put	0.583	0.873	0.703	1e-111
239788276		317	ACYPI006611 [Acyrthosiphon pisum]	0.581	0.867	0.700	1e-110
326320041		300	ubiquitin fusion degradation protein 1 h	0.581	0.916	0.700	1e-110
307178215		287	Ubiquitin fusion degradation protein 1-l	0.577	0.951	0.744	1e-110
157120560		303	ubiquitin fusion degradaton protein [Aed	0.587	0.917	0.692	1e-110
157120562		301	ubiquitin fusion degradaton protein [Aed	0.581	0.913	0.692	1e-109

>gi\|345479998\|ref\|XP_001605370.2\| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Nasonia vitripennis]	Back alignment and taxonomy information

 Score =  424 bits (1090), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 205/273 (75%), Positives = 233/273 (85%), Gaps = 2/273 (0%)

Query: 200 FNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKL 259
           F +FP+IPRPFN  YKCFSVSM PGNER+DVERGGKIIMPPSAL+ LTRLNI YPMLFKL
Sbjct: 2   FRLFPEIPRPFNTQYKCFSVSMLPGNERQDVERGGKIIMPPSALDTLTRLNIVYPMLFKL 61

Query: 260 TNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQT 319
           TN+K  RITH GVLEFVADEGKVYLPYWMM NLLL EGE++N+E VSLPVAT+++FQPQ+
Sbjct: 62  TNKKTNRITHCGVLEFVADEGKVYLPYWMMHNLLLQEGEILNVECVSLPVATYARFQPQS 121

Query: 320 CDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNV 379
            DFLDITNPKAVLEN LRNFACLT+GD+IAI YN++IYE+CVLETKPG+AVTIIECDMNV
Sbjct: 122 EDFLDITNPKAVLENGLRNFACLTTGDVIAIKYNARIYEMCVLETKPGSAVTIIECDMNV 181

Query: 380 DFAPPVGYTEPEKVKEKEEDNMIDPVDLMPEPSGFVAFHGTGNRLDGKRKKKDTVETGGT 439
           +FAPPVGY EPEK   KEEDN +DPVDLMPEP+GFVAF G GNRLDGK K+K++  T   
Sbjct: 182 EFAPPVGYKEPEKPVSKEEDN-VDPVDLMPEPTGFVAFKGQGNRLDGK-KRKESAPTETA 239

Query: 440 PTKREYQRGIPHYDYEPNTLVFLRNIKPASAHK 472
             K  Y RGIP YDY+  TL FLRN+KP +  +
Sbjct: 240 SDKPVYVRGIPDYDYKIGTLKFLRNVKPVNVKE 272

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|383861689\|ref\|XP_003706317.1\| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Megachile rotundata]	Back alignment and taxonomy information

>gi\|332374826\|gb\|AEE62554.1\| unknown [Dendroctonus ponderosae]	Back alignment and taxonomy information

>gi\|307212287\|gb\|EFN88095.1\| Ubiquitin fusion degradation protein 1-like protein [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|242013341\|ref\|XP_002427368.1\| ubiquitin fusion degradaton protein, putative [Pediculus humanus corporis] gi\|212511737\|gb\|EEB14630.1\| ubiquitin fusion degradaton protein, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

>gi\|239788276\|dbj\|BAH70826.1\| ACYPI006611 [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|326320041\|ref\|NP_001191887.1\| ubiquitin fusion degradation protein 1 homolog [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|307178215\|gb\|EFN67000.1\| Ubiquitin fusion degradation protein 1-like protein [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|157120560\|ref\|XP_001653664.1\| ubiquitin fusion degradaton protein [Aedes aegypti] gi\|108874904\|gb\|EAT39129.1\| AAEL009042-PA [Aedes aegypti]	Back alignment and taxonomy information

>gi\|157120562\|ref\|XP_001653665.1\| ubiquitin fusion degradaton protein [Aedes aegypti] gi\|108874905\|gb\|EAT39130.1\| AAEL009042-PB [Aedes aegypti]	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
Query		473
FB\|FBgn0036136		316	Ufd1-like "Ubiquitin fusion-de	0.572	0.857	0.621	2.6e-86
UNIPROTKB\|F1NVD8		307	UFD1L "Uncharacterized protein	0.564	0.869	0.639	2.6e-86
UNIPROTKB\|J9NYF2		307	UFD1L "Uncharacterized protein	0.562	0.866	0.637	1.4e-85
UNIPROTKB\|Q92890		307	UFD1L "Ubiquitin fusion degrad	0.562	0.866	0.637	1.4e-85
RGD\|619822		307	Ufd1l "ubiquitin fusion degrad	0.562	0.866	0.637	1.4e-85
MGI\|MGI:109353		307	Ufd1l "ubiquitin fusion degrad	0.562	0.866	0.637	1.4e-85
UNIPROTKB\|F1RK61		307	UFD1L "Uncharacterized protein	0.562	0.866	0.637	2.4e-85
ZFIN\|ZDB-GENE-040718-150		308	ufd1l "ubiquitin fusion degrad	0.560	0.860	0.620	1.2e-83
UNIPROTKB\|F1PAI5		310	UFD1L "Uncharacterized protein	0.562	0.858	0.628	3.1e-83
UNIPROTKB\|A6NJ11		296	UFD1L "Ubiquitin fusion degrad	0.539	0.861	0.602	3.4e-77

FB\|FBgn0036136 Ufd1-like "Ubiquitin fusion-degradation 1-like" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 863 (308.9 bits), Expect = 2.6e-86, P = 2.6e-86
 Identities = 177/285 (62%), Positives = 209/285 (73%)

Query:   196 FQF-GFNM-FPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICY 253
             F F GFNM FP+  R F+ +YKCFSVSM PGNER DVE+GGKIIMPPSAL+ LTRLN+ Y
Sbjct:     2 FHFSGFNMMFPE-GRNFHANYKCFSVSMLPGNERTDVEKGGKIIMPPSALDTLTRLNVEY 60

Query:   254 PMLFKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFS 313
             PMLFKLTN K  R +H+GVLEFVADEGK YLP+WMM NLLL EG+++NIESVSLPVATFS
Sbjct:    61 PMLFKLTNVKKSRSSHAGVLEFVADEGKCYLPHWMMENLLLGEGDILNIESVSLPVATFS 120

Query:   314 KFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTII 373
             KFQP + DFLDITNPKAVLEN LRNFACLT GD+IAI YN K+YELCVLETKPGNAV+II
Sbjct:   121 KFQPHSTDFLDITNPKAVLENALRNFACLTRGDVIAIKYNKKVYELCVLETKPGNAVSII 180

Query:   374 ECDMNVDFAPPVGYTEPEKVKEKEEDNMIDPVDLMPEPSGFV---------AFHGTGNRL 424
             ECDMNV+F  PVGY +  + +            +  E +G            F G+G RL
Sbjct:   181 ECDMNVEFEAPVGYKDHSETQASGSGQQGAAGTVGGEIAGATNAILEEVVETFKGSGVRL 240

Query:   425 DGKRKKKDTVETGGTPTKREYQRGIPHYDYEPNTLVFLRNIKPAS 469
             DGK+KK+  +ET     K+   RG+P YD++   + F RNI+P S
Sbjct:   241 DGKKKKESQLET--PVVKKVLARGVPDYDFQFGLIRFDRNIRPIS 283

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IMP;NAS

GO:0006508 "proteolysis" evidence=IMP

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IMP

GO:0000502 "proteasome complex" evidence=NAS

UNIPROTKB\|F1NVD8 UFD1L "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|J9NYF2 UFD1L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q92890 UFD1L "Ubiquitin fusion degradation protein 1 homolog" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

RGD\|619822 Ufd1l "ubiquitin fusion degradation 1 like (yeast)" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:109353 Ufd1l "ubiquitin fusion degradation 1 like" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RK61 UFD1L "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040718-150 ufd1l "ubiquitin fusion degradation 1-like" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PAI5 UFD1L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|A6NJ11 UFD1L "Ubiquitin fusion degradation protein 1 homolog" [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)
Q9ES53	UFD1_RAT	No assigned EC number	0.6379	0.5623	0.8664	yes	N/A
Q92890	UFD1_HUMAN	No assigned EC number	0.6379	0.5623	0.8664	yes	N/A
P70362	UFD1_MOUSE	No assigned EC number	0.6379	0.5623	0.8664	yes	N/A
Q9VTF9	UFD1_DROME	No assigned EC number	0.6210	0.5729	0.8575	yes	N/A
P53044	UFD1_YEAST	No assigned EC number	0.5077	0.3911	0.5124	yes	N/A
Q55BK0	UFD1_DICDI	No assigned EC number	0.5355	0.3847	0.5515	yes	N/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
Query		473
pfam03152		176	pfam03152, UFD1, Ubiquitin fusion degradation prot	1e-104
COG5140		331	COG5140, UFD1, Ubiquitin fusion-degradation protei	1e-70
pfam03152		176	pfam03152, UFD1, Ubiquitin fusion degradation prot	8e-39
PLN03086		567	PLN03086, PLN03086, PRLI-interacting factor K; Pro	6e-28
COG5140		331	COG5140, UFD1, Ubiquitin fusion-degradation protei	7e-28
pfam03152		176	pfam03152, UFD1, Ubiquitin fusion degradation prot	3e-26
COG5140		331	COG5140, UFD1, Ubiquitin fusion-degradation protei	2e-16
PLN03086		567	PLN03086, PLN03086, PRLI-interacting factor K; Pro	4e-04

>gnl\|CDD\|217391 pfam03152, UFD1, Ubiquitin fusion degradation protein UFD1	Back alignment and domain information

 Score =  307 bits (790), Expect = e-104
 Identities = 116/176 (65%), Positives = 142/176 (80%)

Query: 209 PFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRIT 268
            F ++Y+C+ VS  PGNERED+E GGKII+PPSAL++L+RLNI YPMLF+L N    ++T
Sbjct: 1   RFEQTYRCYPVSFLPGNEREDIEYGGKIILPPSALDRLSRLNIEYPMLFELQNPANKKVT 60

Query: 269 HSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNP 328
           H GVLEF+A+EG +YLPYWMM+NL L+EG+LV I S SLP  TF K QPQ+ DFLDI+NP
Sbjct: 61  HCGVLEFIAEEGTIYLPYWMMQNLGLEEGDLVQITSASLPKGTFVKLQPQSTDFLDISNP 120

Query: 329 KAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVDFAPP 384
           KAVLEN LRNF+ LT GD I INYN KIYE+ +LE KP NA++IIE D+ VDFAPP
Sbjct: 121 KAVLENALRNFSTLTKGDTIVINYNDKIYEIDILEVKPANAISIIETDLEVDFAPP 176

Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation. Length = 176

>gnl\|CDD\|227469 COG5140, UFD1, Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|217391 pfam03152, UFD1, Ubiquitin fusion degradation protein UFD1	Back alignment and domain information

>gnl\|CDD\|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional	Back alignment and domain information

>gnl\|CDD\|227469 COG5140, UFD1, Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|217391 pfam03152, UFD1, Ubiquitin fusion degradation protein UFD1	Back alignment and domain information

>gnl\|CDD\|227469 COG5140, UFD1, Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		473
KOG1816\|consensus		308		100.0
COG5140		331	UFD1 Ubiquitin fusion-degradation protein [Posttra	100.0
PF03152		176	UFD1: Ubiquitin fusion degradation protein UFD1; I	100.0
KOG1816\|consensus		308		100.0
PLN03086		567	PRLI-interacting factor K; Provisional	100.0
PF03152		176	UFD1: Ubiquitin fusion degradation protein UFD1; I	100.0
COG5140		331	UFD1 Ubiquitin fusion-degradation protein [Posttra	100.0
PLN03086		567	PRLI-interacting factor K; Provisional	99.98
KOG0735\|consensus		952		95.76
PF02933		64	CDC48_2: Cell division protein 48 (CDC48), domain	95.71
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.15
PF09262		80	PEX-1N: Peroxisome biogenesis factor 1, N-terminal	88.11

>KOG1816\|consensus	Back alignment and domain information

Probab=100.00  E-value=3.9e-91  Score=685.83  Aligned_cols=270  Identities=56%  Similarity=0.953  Sum_probs=237.3

Q ss_pred             cCCCCCCCCCCccceEEeeeeccCCCCCCCCCCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCC
Q psy1724         200 FNMFPDIPRPFNRSYKCFSVSMFPGNEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADE  279 (473)
Q Consensus       200 ~~~~~~~~~~f~~~yrcyp~s~~~~~~r~~~~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~E  279 (473)
                      |+.|.+....|+++|||||++|+++++++++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+|||
T Consensus         4 f~~~~~~g~~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeE   83 (308)
T KOG1816|consen    4 FDGFGPRGFQFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEE   83 (308)
T ss_pred             ccccCcCCcceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecC
Confidence            44444334679999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEE
Q psy1724         280 GKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYEL  359 (473)
Q Consensus       280 G~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l  359 (473)
                      |.||||+|||++|+|+|||+|+|++++||+||||||||||.|||||+|||||||++||||+|||+||+|+|+||++.|+|
T Consensus        84 G~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i  163 (308)
T KOG1816|consen   84 GRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLENALRNYACLTTGDVILINYNEKTYEL  163 (308)
T ss_pred             ceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHHHHhhccccccCCEEEEecCCeEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCCeEEEEccceEEEecCCCCCCCCCccccccccC--CCCCCC-CCCC----CCccceeeeeeeecCCccCCCC
Q psy1724         360 CVLETKPGNAVTIIECDMNVDFAPPVGYTEPEKVKEKEEDN--MIDPVD-LMPE----PSGFVAFHGTGNRLDGKRKKKD  432 (473)
Q Consensus       360 ~V~e~kP~~aVsIIdTDleVDf~pP~~y~ep~~~~~~~~~~--~~~~~~-~~~~----~~~~~~F~G~G~rLdGK~~~~~  432 (473)
                      +|+|+||++|||||||||+|||+||+||+||+++.++....  +.+... .+..    +.++++|+|+|+|||||+.. .
T Consensus       164 ~V~e~kPa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK~~~-~  242 (308)
T KOG1816|consen  164 KVVETKPANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGKKKV-E  242 (308)
T ss_pred             EEEEecCCceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccccccccceeeeccccceecccccc-c
Confidence            99999999999999999999999999999999885443221  111111 2211    67899999999999999876 3


Q ss_pred             CcccCCCCccc-cccCCCCCCCCCCCeEEEeecccCCCcC
Q psy1724         433 TVETGGTPTKR-EYQRGIPHYDYEPNTLVFLRNIKPASAH  471 (473)
Q Consensus       433 ~~~~~~~~~~~-~~~~~~p~~~~~~g~l~f~~~~~p~~~~  471 (473)
                      ++.. .++... ...+++|++|++.|+|+|+||..|.++.
T Consensus       243 e~~~-~pv~~~~~~~~~~~~~d~~~G~l~F~~~~~~~~~~  281 (308)
T KOG1816|consen  243 EVSK-HPVKNGDLIQRGVPNHDFKLGKLVFGRNVDPLKKE  281 (308)
T ss_pred             ccCC-CcccCcccccCCCCccccCCceEEEecCCCccccc
Confidence            3222 344333 4789999999999999999996665443

>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway	Back alignment and domain information

>KOG1816\|consensus	Back alignment and domain information

>PLN03086 PRLI-interacting factor K; Provisional	Back alignment and domain information

>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway	Back alignment and domain information

>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PLN03086 PRLI-interacting factor K; Provisional	Back alignment and domain information

>KOG0735\|consensus	Back alignment and domain information

>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	Back alignment and domain information

>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain	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
Query		473
2yuj_A		190	Solution Structure Of Human Ubiquitin Fusion Degrad		7e-74
1zc1_A		208	Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct		1e-53

>pdb|2YUJ|A Chain A, Solution Structure Of Human Ubiquitin Fusion Degradation Protein 1 Homolog Ufd1 Length = 190

Back alignment and structure

Iteration: 1

Score = 274 bits (701), Expect = 7e-74, Method: Compositional matrix adjust. Identities = 137/181 (75%), Positives = 155/181 (85%), Gaps = 5/181 (2%) Query: 206 IPRPF-NR---SYKCFSVSMFPG-NEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLT 260 IPR F NR Y+CFSVSM G N+R DVE+GGKIIMPPSAL+QL+RLNI YPMLFKLT Sbjct: 8 IPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLT 67 Query: 261 NQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTC 320 N+ R+TH GVLEFVADEG YLP+WMM+NLLL+EG LV +ESV+L VAT+SKFQPQ+ Sbjct: 68 NKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSP 127 Query: 321 DFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVD 380 DFLDITNPKAVLEN LRNFACLT+GD+IAINYN KIYEL V+ETKP AV+IIECDMNVD Sbjct: 128 DFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVD 187 Query: 381 F 381 F Sbjct: 188 F 188

PyMOL of 2yuj

>pdb|1ZC1|A Chain A, Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct Ubiquitin Interaction Sites Length = 208

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
Query		473
1zc1_A		208	Ubiquitin fusion degradation protein 1; UFD1, doub	3e-86
1zc1_A		208	Ubiquitin fusion degradation protein 1; UFD1, doub	2e-31
1zc1_A		208	Ubiquitin fusion degradation protein 1; UFD1, doub	4e-19
2yuj_A		190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	3e-83
2yuj_A		190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	2e-30
2yuj_A		190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	1e-19
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
3tiw_A		187	Transitional endoplasmic reticulum ATPase; beta-ba	1e-07

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae} Length = 208	Back alignment and structure

 Score =  262 bits (671), Expect = 3e-86
 Identities = 99/199 (49%), Positives = 137/199 (68%), Gaps = 4/199 (2%)

Query: 198 FGFNMFPDIPRPFNRSYKCFSVSMFPGNE-REDVERGGKIIMPPSALEQLTRLNICYPML 256
            G N F ++P+ F   ++C+ ++M      ++D   GGKI +PPSAL +L+ LNI YPML
Sbjct: 9   GGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPML 68

Query: 257 FKLTNQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQ 316
           FKLT  + GR+TH GVLEF+A+EG+VYLP WMM  L +  G L+ I S  +P+  F K +
Sbjct: 69  FKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLE 128

Query: 317 PQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKP---GNAVTII 373
           PQ+ DFLDI++PKAVLEN LRNF+ LT  D+I I+YN K +++ +LE KP     ++ +I
Sbjct: 129 PQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVI 188

Query: 374 ECDMNVDFAPPVGYTEPEK 392
           E D+  DFAPPVGY EP+ 
Sbjct: 189 ETDLVTDFAPPVGYVEPDY 207

PyMOL of 1zc1

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae} Length = 208	Back alignment and structure

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae} Length = 208	Back alignment and structure

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 190	Back alignment and structure

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 190	Back alignment and structure

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 190	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

>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

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A Length = 187	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		473
1zc1_A		208	Ubiquitin fusion degradation protein 1; UFD1, doub	100.0
2yuj_A		190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	100.0
2yuj_A		190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	100.0
1zc1_A		208	Ubiquitin fusion degradation protein 1; UFD1, doub	100.0
3qwz_A		211	Transitional endoplasmic reticulum ATPase; UBX, P9	99.33
1cz4_A		185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	99.33
3tiw_A		187	Transitional endoplasmic reticulum ATPase; beta-ba	99.32
1wlf_A		179	PEX1, peroxisome biogenesis factor 1; N-terminal d	98.9
3cf2_A		806	TER ATPase, transitional endoplasmic reticulum ATP	97.51
2jv2_A		83	Putative uncharacterized protein PH1500; AAA ATPas	96.94
1ypw_A		806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.91
3hu3_A		489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.19
3qwz_A		211	Transitional endoplasmic reticulum ATPase; UBX, P9	94.62
3tiw_A		187	Transitional endoplasmic reticulum ATPase; beta-ba	94.54
1cz4_A		185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	93.69
1yfb_A		59	Transition state regulatory protein ABRB; , homodi	88.27
2glw_A		92	PHS018, 92AA long hypothetical protein; RIFT barre	86.46
1cr5_A		189	SEC18P (residues 22 - 210); double-PSI beta barrel	83.25
1qcs_A		211	N-ethylmaleimide sensitive factor (NSF-N); double-	80.26

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae}	Back alignment and structure

Probab=100.00  E-value=7.6e-77  Score=565.86  Aligned_cols=192  Identities=51%  Similarity=0.967  Sum_probs=186.8

Q ss_pred             CCCCCCCCCccceEEeeeeccCCC-CCCCCCCCCeEeeCHHHHHHHHhCCCCCceeEEEEeCCCCceEEEEEEeeeeCCC
Q psy1724         202 MFPDIPRPFNRSYKCFSVSMFPGN-EREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGVLEFVADEG  280 (473)
Q Consensus       202 ~~~~~~~~f~~~yrcyp~s~~~~~-~r~~~~~GdKIiLPpSaL~~L~~~~i~~Pm~F~L~n~~~~r~th~GVLEFsA~EG  280 (473)
                      .|++.+++|+++|||||+||++++ +|+++++||||+||||||++|++++++|||+|+|+|..++++||||||||+|+||
T Consensus        13 ~~~~~~~~f~~~~rc~~~~~~p~~~~r~~~~~GdKIiLP~SaL~~L~~~~i~~Pm~F~l~n~~~~~~th~GVlEF~A~EG   92 (208)
T 1zc1_A           13 GFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEG   92 (208)
T ss_dssp             TCCCCCEEEEEEEEEEEGGGSCTTTSCHHHHHSSEEEECHHHHHHHHHTTCCSSCCEEEECTTTCCEEEEEEEEECCSSC
T ss_pred             cCCcccccccceEEEEEEEeccCcccccccCCCCeEECCHHHHHHHHHCCCCcCEEEEEEeCCCCCEEEEEEEEEEcCCC
Confidence            455567899999999999999998 9999999999999999999999999999999999999999999999999999999


Q ss_pred             cEEcCHHHHhhcCCCCCCeEEEEEeecCCceEEEEEeCccCcCCCCCcHHHHHHhcccceecccCCEEEEEECCEEEEEE
Q psy1724         281 KVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELC  360 (473)
Q Consensus       281 ~v~LP~WMm~~L~l~egd~V~I~~v~LPkGtfvkLqP~s~~FldIsnpKavLE~~LRnystLT~GD~I~I~yn~~~Y~l~  360 (473)
                      +||||+|||++|++++||.|+|++++||||||||||||+++|++|+|||||||++||||+|||+||+|.|+||++.|+|+
T Consensus        93 ~v~lP~wmm~~L~l~~gd~V~i~~~~LPkgt~vklqP~~~~Fldi~npKavLE~~LRnfstLT~Gd~I~i~~~~~~y~l~  172 (208)
T 1zc1_A           93 RVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIK  172 (208)
T ss_dssp             EEEECHHHHHHHTCCTTCEEEEEEEECCCCSEEEEECCHHHHHTSSCHHHHHHHHHHHCSCEESSSEEEEEETTEEEEEE
T ss_pred             eEEcCHHHHHhcCCCCCCEEEEEEeEcCCCCEEEEeECccccccccCHHHHHHHHhhcCccccCCCEEEEEeCCEEEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEecCCC---eEEEEccceEEEecCCCCCCCCCcc
Q psy1724         361 VLETKPGN---AVTIIECDMNVDFAPPVGYTEPEKV  393 (473)
Q Consensus       361 V~e~kP~~---aVsIIdTDleVDf~pP~~y~ep~~~  393 (473)
                      |+|++|++   |||||||||+|||+||+||+||+++
T Consensus       173 V~e~kP~~~~~aV~IidTDleVDf~~p~~y~ep~~~  208 (208)
T 1zc1_A          173 ILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYK  208 (208)
T ss_dssp             EEEEECSSTTCEECCSSSCSEEEECCCCCCCCCCCC
T ss_pred             EEEEcCCCCCceEEEEeCceEEEecCCCCCcCCCCC
Confidence            99999997   9999999999999999999999863

PyMOL of 1zc1

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B	Back alignment and structure

>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate recognition DOM hydrolase; NMR {Thermoplasma acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A	Back alignment and structure

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A	Back alignment and structure

>1wlf_A PEX1, peroxisome biogenesis factor 1; N-terminal domain, protein transport; 2.05A {Mus musculus} SCOP: b.52.2.3 d.31.1.1	Back alignment and structure

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*	Back alignment and structure

>2jv2_A Putative uncharacterized protein PH1500; AAA ATPase NC-domain-like, unknown function; NMR {Pyrococcus horikoshii}	Back alignment and structure

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*	Back alignment and structure

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B	Back alignment and structure

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A	Back alignment and structure

>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate recognition DOM hydrolase; NMR {Thermoplasma acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A	Back alignment and structure

>1yfb_A Transition state regulatory protein ABRB; , homodimer, bioinformatics, swapped-hairpin barrel, transcription; NMR {Bacillus subtilis} SCOP: b.129.1.3 PDB: 1ysf_A 2k1n_A* 1z0r_A 2ro4_A 2fy9_A 2ro3_A	Back alignment and structure

>2glw_A PHS018, 92AA long hypothetical protein; RIFT barrel, bioinformatics, transcription; NMR {Pyrococcus horikoshii}	Back alignment and structure

>1cr5_A SEC18P (residues 22 - 210); double-PSI beta barrel, vesicle fusion, endocytosis/exocytosis complex; 2.30A {Saccharomyces cerevisiae} SCOP: b.52.2.3 d.31.1.1	Back alignment and structure

>1qcs_A N-ethylmaleimide sensitive factor (NSF-N); double-PSI beta barrel alpha beta roll, fusion protein; 1.90A {Cricetulus griseus} SCOP: b.52.2.3 d.31.1.1 PDB: 1qdn_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		473
d1e32a3		94	Membrane fusion atpase p97 domain 2, P97-Nc {Mouse	95.95
d1cz5a2		94	C-terminal domain of VAT-N, VAT-Nc {Archaeon Therm	92.13
d1wlfa1		80	Peroxisome biogenesis factor 1 (PEX-1), domain 2 {	89.48
d1e32a1		86	Membrane fusion ATPase p97 N-terminal domain , P97	87.06

>d1e32a3 d.31.1.1 (A:107-200) Membrane fusion atpase p97 domain 2, P97-Nc {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Cdc48 domain 2-like
superfamily: Cdc48 domain 2-like
family: Cdc48 domain 2-like
domain: Membrane fusion atpase p97 domain 2, P97-Nc
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.95  E-value=0.0092  Score=48.67  Aligned_cols=72  Identities=19%  Similarity=0.219  Sum_probs=53.1

Q ss_pred             ecCCceEEEEEeCccCcCCCC-C-cHHHHHHhcc-cceecccCCEEEEEECCEEEEEEEEEecCCCeEEEEccceE
Q psy1724         306 SLPVATFSKFQPQTCDFLDIT-N-PKAVLENCLR-NFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMN  378 (473)
Q Consensus       306 ~LPkGtfvkLqP~s~~FldIs-n-pKavLE~~LR-nystLT~GD~I~I~yn~~~Y~l~V~e~kP~~aVsIIdTDle  378 (473)
                      ++|-|+.|.+-|-+..--.++ | .+.+|.-.+. +|--+++||++.|....+.-+|+|++++|++. |||-.|=.
T Consensus         1 di~~~krV~vlP~~DTieglsgnlf~~ylkPYf~~~yrPv~~gD~f~v~g~~r~VEFKVv~~dp~~~-~iV~~~T~   75 (94)
T d1e32a3           1 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPY-CIVAPDTV   75 (94)
T ss_dssp             TCCBCSCEEEEEBGGGTTTCBSCHHHHTHHHHHTTSCEEEETTCEEEEEETTEEEEEEEEEESSSSE-EEECTTCC
T ss_pred             CCCcccEEEEEecccccCCCCccHHHHHHhHHHhhcCccccCCCEEEEccCCeeEEEEEEeecCCCc-eEEcCCCE
Confidence            368889999999764433333 1 2344555554 58899999999999999999999999999984 55544433

PyMOL of d1e32a3

>d1cz5a2 d.31.1.1 (A:92-185) C-terminal domain of VAT-N, VAT-Nc {Archaeon Thermoplasma acidophilum [TaxId: 2303]}	Back information, alignment and structure

>d1wlfa1 d.31.1.1 (A:100-179) Peroxisome biogenesis factor 1 (PEX-1), domain 2 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1e32a1 b.52.2.3 (A:21-106) Membrane fusion ATPase p97 N-terminal domain , P97-Nn {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure