Psyllid ID: psy14660

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-----

MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKKKDEKKEKK

cccEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHcccccccEEEEEEcccEEEEEcccccHHHHHHHHccccccccccHHHHHHHHHHHHHHcccccccEEEEEEEcccccccHHHHHHHHHHHHHcccEEEEEEEcccccHHHHHHHHHHHHccccccccEEEEccccccHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccHHHHHHHHcccccHHHHcccHHHHHHHHHcccccccccHHHHHHHHHHHccccccccHHHccc

ccEEEEEEEEEccHHcccccccccHHHHHHHHHHHHHHHHHcccccccEEEEEEccccEEEEEccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccEEEEEEEcccccccHHHHHHHHHHHHHcccEEEEEEcccccccHHHHHHHHHHHccccccccEEEEccccccHHHHHHcccEEEccccccccccccccccccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHcHHccccccccccccccHHHHHHHcccccccccccccHccccHHHHHHHHHHHHHccccccHHHHHHcccccccccccccccccHHHHHccHHHHHHHHHcccccccccHHHHHHHHHHHHccccccccccccc

MVLESTmicvdnsdfmrngdflptRLQAQQDAVNLVChsktrsnpennvgLLAMADSVEVLATLTSDVGRILSKLhqvqpngninfMTGIRIAHLALKHrqgknhkmRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTlngkdgsgshmVTVAVgphlsdalisspiiqgedgaggapgssyefgvdpnedpELALALRVSMEEQRARQESEARRAaegasgadtsassavpkptaeakdapgdmataahpvggqpdfatMTEEEQIAFAMQMSmqdtqepaassskapasaaaseeakaepmdtdemVNDAAFLQSVLenlpgvdpqsAEVRHALsssaekpakkkdekkekk

mvlestmicvdnsdfmRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLhqvqpngniNFMTGIRIAHLALKHRQGKNHKMRIIAfvgspvdleeRELTKLAkrlkkekvnvdivsfgeevvnTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEArraaegasgadtsassavpKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRhalsssaekpakkkdekkekk

MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMeeqrarqesearraaegasgadtsassaVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQepaassskapasaaaseeakaepMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHalsssaekpakkkdekkekk

******MICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHS********NVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTL***********************************************************************************************************************************************************************************************************************

*VLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLH*VQPNGNINFMTGIRIAHLALKHR*GKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALI*********************GVDPNEDPELALA**********************************************************************AFA******************************************AFLQSVLENLPGVDPQSAE***********************

MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVS*****************************************GDMATAAHPVGGQPDFATMTEEEQIAFAMQM*******************************TDEMVNDAAFLQSVLENLPGVDPQSA************************

MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQ*AR*E*************************************************T*T*EEQIAF**********************************DTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSS****************

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MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPxxxxxxxxxxxxxxxxxxxxxVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGGAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAAEGASGADTSASSAVPKPTAEAKDAPGDMATAAHPVGGQPDFATMTEEEQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHALSSSAEKPAKKKDEKKEKK

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		375	2.2.26 [Sep-21-2011]
P55036		377	26S proteasome non-ATPase	yes	N/A	0.957	0.952	0.642	1e-120
Q58DA0		382	26S proteasome non-ATPase	yes	N/A	0.957	0.939	0.639	1e-119
P55035		396	26S proteasome non-ATPase	yes	N/A	0.930	0.881	0.604	1e-119
O35226		376	26S proteasome non-ATPase	yes	N/A	0.962	0.960	0.645	1e-118
A2A3N6		862	Putative PIP5K1A and PSMD	no	N/A	0.928	0.403	0.604	1e-104
O17453		420	26S proteasome non-ATPase	N/A	N/A	0.952	0.85	0.455	3e-93
P55034		386	26S proteasome non-ATPase	yes	N/A	0.946	0.919	0.423	2e-73
Q553E0		349	26S proteasome non-ATPase	yes	N/A	0.877	0.942	0.405	8e-58
O94444		243	26S proteasome regulatory	yes	N/A	0.618	0.954	0.481	3e-55
P38886		268	26S proteasome regulatory	yes	N/A	0.594	0.832	0.466	5e-50

>sp\|P55036\|PSMD4_HUMAN 26S proteasome non-ATPase regulatory subunit 4 OS=Homo sapiens GN=PSMD4 PE=1 SV=1	Back alignment and function desciption

 Score =  431 bits (1107), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 235/366 (64%), Positives = 279/366 (76%), Gaps = 7/366 (1%)

Query: 1   MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEV 60
           MVLESTM+CVDNS++MRNGDFLPTRLQAQQDAVN+VCHSKTRSNPENNVGL+ +A+  EV
Sbjct: 1   MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV 60

Query: 61  LATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLE 120
           L TLT D GRILSKLH VQP G I F TGIR+AHLALKHRQGKNHKMRIIAFVGSPV+  
Sbjct: 61  LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN 120

Query: 121 ERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLS 180
           E++L KLAKRLKKEKVNVDI++FGEE VNTE L  F++TLNGKDG+GSH+VTV  GP L+
Sbjct: 121 EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA 180

Query: 181 DALISSPIIQGEDGAG-GAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAAE 239
           DALISSPI+ GE GA  G   S +EFGVDP+ DPELALALRVSMEEQR RQE EARRAA 
Sbjct: 181 DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA 240

Query: 240 GASGADTSASSAVPKPTAEAKDAPGDMATAAHPVG--GQPDFATMTEEEQIAFAMQMSMQ 297
            ++     A++     T ++ DA   M  +    G  G PD ++MTEEEQIA+AMQMS+Q
Sbjct: 241 ASAAEAGIATTG----TEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQ 296

Query: 298 DTQEPAASSSKAPASAAASEEAKAEPMDTDEMVNDAAFLQSVLENLPGVDPQSAEVRHAL 357
             +   A S+   AS+A      A+  D  +++ D  FLQSVLENLPGVDP +  +R+A+
Sbjct: 297 GAEFGQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAM 356

Query: 358 SSSAEK 363
            S A +
Sbjct: 357 GSLASQ 362

Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion.
Homo sapiens (taxid: 9606)

>sp\|Q58DA0\|PSMD4_BOVIN 26S proteasome non-ATPase regulatory subunit 4 OS=Bos taurus GN=PSMD4 PE=2 SV=1	Back alignment and function description

>sp\|P55035\|PSMD4_DROME 26S proteasome non-ATPase regulatory subunit 4 OS=Drosophila melanogaster GN=Pros54 PE=1 SV=2	Back alignment and function description

>sp\|O35226\|PSMD4_MOUSE 26S proteasome non-ATPase regulatory subunit 4 OS=Mus musculus GN=Psmd4 PE=1 SV=1	Back alignment and function description

>sp\|A2A3N6\|PIPSL_HUMAN Putative PIP5K1A and PSMD4-like protein OS=Homo sapiens GN=PIPSL PE=5 SV=1	Back alignment and function description

>sp\|O17453\|PSMD4_SCHMA 26S proteasome non-ATPase regulatory subunit 4 OS=Schistosoma mansoni PE=2 SV=2	Back alignment and function description

>sp\|P55034\|PSMD4_ARATH 26S proteasome non-ATPase regulatory subunit 4 OS=Arabidopsis thaliana GN=MBP1 PE=1 SV=1	Back alignment and function description

>sp\|Q553E0\|PSMD4_DICDI 26S proteasome non-ATPase regulatory subunit 4 OS=Dictyostelium discoideum GN=psmD4 PE=2 SV=1	Back alignment and function description

>sp\|O94444\|RPN10_SCHPO 26S proteasome regulatory subunit rpn10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpn10 PE=1 SV=1	Back alignment and function description

>sp\|P38886\|RPN10_YEAST 26S proteasome regulatory subunit RPN10 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPN10 PE=1 SV=3	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		375
307182568		414	26S proteasome non-ATPase regulatory sub	0.917	0.830	0.661	1e-136
332027690		389	26S proteasome non-ATPase regulatory sub	0.917	0.884	0.658	1e-135
66524917		399	PREDICTED: 26S proteasome non-ATPase reg	0.904	0.849	0.665	1e-133
380016206		401	PREDICTED: 26S proteasome non-ATPase reg	0.904	0.845	0.665	1e-133
340725510		388	PREDICTED: 26S proteasome non-ATPase reg	0.904	0.873	0.661	1e-133
383866255		410	PREDICTED: 26S proteasome non-ATPase reg	0.917	0.839	0.667	1e-132
189241794		375	PREDICTED: similar to GA20484-PA isoform	0.922	0.922	0.715	1e-131
307202133		386	26S proteasome non-ATPase regulatory sub	0.917	0.891	0.653	1e-131
156554405		383	PREDICTED: 26S proteasome non-ATPase reg	0.92	0.900	0.662	1e-130
91091988		381	PREDICTED: similar to GA20484-PA isoform	0.922	0.908	0.709	1e-130

>gi\|307182568\|gb\|EFN69761.1\| 26S proteasome non-ATPase regulatory subunit 4 [Camponotus floridanus]	Back alignment and taxonomy information

 Score =  490 bits (1262), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 250/378 (66%), Positives = 284/378 (75%), Gaps = 34/378 (8%)

Query: 1   MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEV 60
           MVLESTMICVDNSD+MRNGDF+PTRLQAQQDAVNLVCHSKTRSNPENNVGL+ +A+ VEV
Sbjct: 36  MVLESTMICVDNSDYMRNGDFVPTRLQAQQDAVNLVCHSKTRSNPENNVGLITLAN-VEV 94

Query: 61  LATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLE 120
           LATLTSDVGRILSKLHQVQPNG +  +TGIRIAHLALKHRQGKNHKMRI+AF+GSP+D++
Sbjct: 95  LATLTSDVGRILSKLHQVQPNGKLCLITGIRIAHLALKHRQGKNHKMRIVAFIGSPIDID 154

Query: 121 ERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLS 180
           E+EL KLAKRLKKEKVNVD++SFGEE +N E+L  F++ LNGKDG+GSH+VTV  GPHLS
Sbjct: 155 EKELVKLAKRLKKEKVNVDVISFGEESINNEVLTAFVNALNGKDGTGSHLVTVPPGPHLS 214

Query: 181 DALISSPIIQGEDGAG--GAPGSSYEFGVDPNEDPELALALRVSMEEQRARQESEARRAA 238
           DALISSPIIQGEDG G  G   +++EFGVDPNEDPELALALRVSMEEQR RQE EARRA 
Sbjct: 215 DALISSPIIQGEDGMGAAGMGSAAFEFGVDPNEDPELALALRVSMEEQRQRQEDEARRAQ 274

Query: 239 EGASGADTSASSAVPKPTAE-------------AKDAPGDMATAAHPVGGQPDFATMTEE 285
              +  +    +    P  E             A+D+       A   G  PDF  MTEE
Sbjct: 275 ANETATNKQPETIKEAPNEEAMLKRALAMSLEGAEDSTAATDDTAPCRGNVPDFTNMTEE 334

Query: 286 EQIAFAMQMSMQDTQEPAASSSKAPASAAASEEAKAEPMDTDE----MVNDAAFLQSVLE 341
           EQIAFAMQMSMQD QE               E  K E MD +E    +++D AFLQSVLE
Sbjct: 335 EQIAFAMQMSMQDQQE--------------LESQKEEAMDVEEDYAAVMSDPAFLQSVLE 380

Query: 342 NLPGVDPQSAEVRHALSS 359
           NLPGVDPQS  VR A+ S
Sbjct: 381 NLPGVDPQSEAVRQAVGS 398

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|332027690\|gb\|EGI67758.1\| 26S proteasome non-ATPase regulatory subunit 4 [Acromyrmex echinatior]	Back alignment and taxonomy information

>gi\|66524917\|ref\|XP_393112.2\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4 [Apis mellifera]	Back alignment and taxonomy information

>gi\|380016206\|ref\|XP_003692079.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4-like [Apis florea]	Back alignment and taxonomy information

>gi\|340725510\|ref\|XP_003401112.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4-like [Bombus terrestris] gi\|350403747\|ref\|XP_003486889.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|383866255\|ref\|XP_003708586.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4-like [Megachile rotundata]	Back alignment and taxonomy information

>gi\|189241794\|ref\|XP_976078.2\| PREDICTED: similar to GA20484-PA isoform 2 [Tribolium castaneum] gi\|270001159\|gb\|EEZ97606.1\| hypothetical protein TcasGA2_TC011476 [Tribolium castaneum]	Back alignment and taxonomy information

>gi\|307202133\|gb\|EFN81633.1\| 26S proteasome non-ATPase regulatory subunit 4 [Harpegnathos saltator]	Back alignment and taxonomy information

>gi\|156554405\|ref\|XP_001604762.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 4-like [Nasonia vitripennis]	Back alignment and taxonomy information

>gi\|91091988\|ref\|XP_967302.1\| PREDICTED: similar to GA20484-PA isoform 1 [Tribolium castaneum]	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		375
MGI\|MGI:1201670		376	Psmd4 "proteasome (prosome, ma	0.930	0.928	0.607	5.3e-104
UNIPROTKB\|Q58DA0		382	PSMD4 "26S proteasome non-ATPa	0.936	0.918	0.592	6.7e-104
UNIPROTKB\|P55036		377	PSMD4 "26S proteasome non-ATPa	0.936	0.931	0.592	6.7e-104
UNIPROTKB\|Q5VWC4		380	PSMD4 "26S proteasome non-ATPa	0.944	0.931	0.589	8.6e-104
UNIPROTKB\|Q32YV9		377	PSMD4 "Uncharacterized protein	0.936	0.931	0.592	8.6e-104
RGD\|621109		377	Psmd4 "proteasome (prosome, ma	0.936	0.931	0.594	1.4e-103
UNIPROTKB\|F1PRW0		377	PSMD4 "Uncharacterized protein	0.936	0.931	0.589	2.3e-103
UNIPROTKB\|O88321		380	Psmd4 "Proteasome (Prosome, ma	0.944	0.931	0.589	2.3e-103
FB\|FBgn0015283		396	Rpn10 "Regulatory particle non	0.594	0.563	0.728	2e-102
ZFIN\|ZDB-GENE-050417-96		372	psmd4b "proteasome (prosome, m	0.922	0.930	0.589	1.4e-101

MGI\|MGI:1201670 Psmd4 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 4" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

 Score = 1030 (367.6 bits), Expect = 5.3e-104, P = 5.3e-104
 Identities = 217/357 (60%), Positives = 247/357 (69%)

Query:     1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEV 60
             MVLESTM+CVDNS++MRNGDFLPTRLQAQQDAVN+VCHSKTRSNPENNVGL+ +A+  EV
Sbjct:     1 MVLESTMVCVDNSEYMRNGDFLPTRLQAQQDAVNIVCHSKTRSNPENNVGLITLANDCEV 60

Query:    61 LATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLE 120
             L TLT D GRILSKLH VQP G I F TGIR+AHLALKHRQGKNHKMRIIAFVGSPV+  
Sbjct:    61 LTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDN 120

Query:   121 ERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHLS 180
             E++L KLAKRLKKEKVNVDI++FGEE VNTE L  F++TLNGKDG+GSH+VTV  GP L+
Sbjct:   121 EKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLA 180

Query:   181 DALISSPIIQGEDGAG-GAPGSSYEFGVDPNEDPELALALRVSMXXXXXXXXXXXXXXXX 239
             DALISSPI+ GE GA  G   S +EFGVDP+ DPELALALRVSM                
Sbjct:   181 DALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAA 240

Query:   240 XXXXXXXXXXXXVPKPTAEAKDAPGDMATAAHPVG--GQPDFATMTEEEQIAFAMQMSMQ 297
                          P  T ++ DA   M       G  G PD ++MTEEEQIA+AMQMS+Q
Sbjct:   241 ASAAEAGIAT---PG-TEDSDDALLKMTINQQEFGRPGLPDLSSMTEEEQIAYAMQMSLQ 296

Query:   298 DTQXXXXXXXXXXXXXXXXXXXXXXXMDTDEMVNDAAFLQSVLENLPGVDPQSAEVR 354
              T+                        D D M  D  FLQSVLENLPGVDP +A +R
Sbjct:   297 GTEFSQESADMDASSAMDTSDPVKEEDDYDVM-QDPEFLQSVLENLPGVDPNNAAIR 352

GO:0000502 "proteasome complex" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISO

GO:0022624 "proteasome accessory complex" evidence=IDA

UNIPROTKB\|Q58DA0 PSMD4 "26S proteasome non-ATPase regulatory subunit 4" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|P55036 PSMD4 "26S proteasome non-ATPase regulatory subunit 4" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5VWC4 PSMD4 "26S proteasome non-ATPase regulatory subunit 4" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q32YV9 PSMD4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

RGD\|621109 Psmd4 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 4" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PRW0 PSMD4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|O88321 Psmd4 "Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 4, isoform CRA_a" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

FB\|FBgn0015283 Rpn10 "Regulatory particle non-ATPase 10" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-050417-96 psmd4b "proteasome (prosome, macropain) 26S subunit, non-ATPase, 4b" [Danio rerio (taxid:7955)]	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)
O94444	RPN10_SCHPO	No assigned EC number	0.4813	0.6186	0.9547	yes	N/A
Q553E0	PSMD4_DICDI	No assigned EC number	0.4055	0.8773	0.9426	yes	N/A
P55035	PSMD4_DROME	No assigned EC number	0.6041	0.9306	0.8813	yes	N/A
P55034	PSMD4_ARATH	No assigned EC number	0.4235	0.9466	0.9196	yes	N/A
P55036	PSMD4_HUMAN	No assigned EC number	0.6420	0.9573	0.9522	yes	N/A
Q58DA0	PSMD4_BOVIN	No assigned EC number	0.6393	0.9573	0.9397	yes	N/A
O35226	PSMD4_MOUSE	No assigned EC number	0.6451	0.9626	0.9601	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		375
cd01452		187	cd01452, VWA_26S_proteasome_subunit, 26S proteasom	1e-106
COG5148		243	COG5148, RPN10, 26S proteasome regulatory complex,	8e-66
smart00327		175	smart00327, VWA, von Willebrand factor (vWF) type	7e-13
pfam13519		172	pfam13519, VWA_2, von Willebrand factor type A dom	3e-11
cd00198		161	cd00198, vWFA, Von Willebrand factor type A (vWA)	3e-10
cd01453		183	cd01453, vWA_transcription_factor_IIH_type, Transc	1e-06
pfam04056		193	pfam04056, Ssl1, Ssl1-like	8e-05
COG5151		421	COG5151, SSL1, RNA polymerase II transcription ini	6e-04
PRK05035		695	PRK05035, PRK05035, electron transport complex pro	0.002

>gnl\|CDD\|238729 cd01452, VWA_26S_proteasome_subunit, 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins	Back alignment and domain information

 Score =  310 bits (795), Expect = e-106
 Identities = 127/189 (67%), Positives = 154/189 (81%), Gaps = 4/189 (2%)

Query: 1   MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMA-DSVE 59
           MVLE+TMIC+DNS++MRNGD+ PTR QAQ DAVNL+C +KTRSNPENNVGL+ MA +S E
Sbjct: 1   MVLEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPE 60

Query: 60  VLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDL 119
           VL TLT+D G+ILSKLH VQP G  NF+TGI+IA LALKHRQ KN K RI+AFVGSP++ 
Sbjct: 61  VLVTLTNDQGKILSKLHDVQPKGKANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEE 120

Query: 120 EERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPHL 179
           +E++L KLAKRLKK  V+VDI++FGE   NTE L  FI  +NGKD  GSH+V+V  G +L
Sbjct: 121 DEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNGKD--GSHLVSVPPGENL 178

Query: 180 -SDALISSP 187
            SDAL+SSP
Sbjct: 179 LSDALLSSP 187

It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association. Length = 187

>gnl\|CDD\|227477 COG5148, RPN10, 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|214621 smart00327, VWA, von Willebrand factor (vWF) type A domain	Back alignment and domain information

>gnl\|CDD\|222192 pfam13519, VWA_2, von Willebrand factor type A domain	Back alignment and domain information

>gnl\|CDD\|238119 cd00198, vWFA, Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>gnl\|CDD\|238730 cd01453, vWA_transcription_factor_IIH_type, Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme	Back alignment and domain information

>gnl\|CDD\|190848 pfam04056, Ssl1, Ssl1-like	Back alignment and domain information

>gnl\|CDD\|227480 COG5151, SSL1, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|235334 PRK05035, PRK05035, electron transport complex protein RnfC; 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		375
KOG2884\|consensus		259		100.0
COG5148		243	RPN10 26S proteasome regulatory complex, subunit R	100.0
cd01452		187	VWA_26S_proteasome_subunit 26S proteasome plays a	100.0
PF04056		193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	100.0
cd01453		183	vWA_transcription_factor_IIH_type Transcription fa	99.97
KOG2807\|consensus		378		99.93
COG5151		421	SSL1 RNA polymerase II transcription initiation/nu	99.86
PRK13685		326	hypothetical protein; Provisional	99.84
PF13519		172	VWA_2: von Willebrand factor type A domain; PDB: 3	99.8
cd01467		180	vWA_BatA_type VWA BatA type: Von Willebrand factor	99.75
cd01465		170	vWA_subgroup VWA subgroup: Von Willebrand factor t	99.74
cd01458		218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	99.7
cd01451		178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	99.69
cd01472		164	vWA_collagen von Willebrand factor (vWF) type A do	99.69
cd01466		155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	99.65
cd01480		186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	99.65
cd01482		164	vWA_collagen_alphaI-XII-like Collagen: The extrace	99.64
cd01470		198	vWA_complement_factors Complement factors B and C2	99.62
TIGR03436		296	acidobact_VWFA VWFA-related Acidobacterial domain.	99.61
cd01456		206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	99.61
smart00327		177	VWA von Willebrand factor (vWF) type A domain. VWA	99.61
cd01469		177	vWA_integrins_alpha_subunit Integrins are a class	99.61
cd01471		186	vWA_micronemal_protein Micronemal proteins: The To	99.61
cd01463		190	vWA_VGCC_like VWA Voltage gated Calcium channel li	99.61
cd01477		193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	99.6
cd00198		161	vWFA Von Willebrand factor type A (vWA) domain was	99.58
cd01461		171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	99.58
cd01450		161	vWFA_subfamily_ECM Von Willebrand factor type A (v	99.57
cd01474		185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	99.56
cd01475		224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	99.56
cd01473		192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	99.55
PRK13406		584	bchD magnesium chelatase subunit D; Provisional	99.53
cd01460		266	vWA_midasin VWA_Midasin: Midasin is a member of th	99.5
cd01464		176	vWA_subfamily VWA subfamily: Von Willebrand factor	99.49
TIGR00868		863	hCaCC calcium-activated chloride channel protein 1	99.49
cd01455		191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	99.48
cd01476		163	VWA_integrin_invertebrates VWA_integrin (invertebr	99.47
cd01454		174	vWA_norD_type norD type: Denitrifying bacteria con	99.47
PF00092		178	VWA: von Willebrand factor type A domain; InterPro	99.4
TIGR02031		589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.4
cd01462		152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	99.39
PTZ00441		576	sporozoite surface protein 2 (SSP2); Provisional	99.37
cd01457		199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	99.36
TIGR02442		633	Cob-chelat-sub cobaltochelatase subunit. A number	99.36
cd01481		165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	99.34
PF13768		155	VWA_3: von Willebrand factor type A domain	99.26
COG1240		261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	99.26
TIGR03788		596	marine_srt_targ marine proteobacterial sortase tar	99.21
PF03731		224	Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; Inte	98.73
TIGR00578		584	ku70 ATP-dependent DNA helicase ii, 70 kDa subunit	98.65
PF10138		200	vWA-TerF-like: vWA found in TerF C terminus ; Inte	98.49
TIGR00627		279	tfb4 transcription factor tfb4. This family is bas	98.49
PRK10997		487	yieM hypothetical protein; Provisional	98.44
COG4245		207	TerY Uncharacterized protein encoded in toxicity p	98.39
cd01479		244	Sec24-like Sec24-like: Protein and membrane traffi	98.35
cd01468		239	trunk_domain trunk domain. COPII-coated vesicles c	98.29
PF04811		243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	98.28
cd01478		267	Sec23-like Sec23-like: Protein and membrane traffi	98.14
PF03850		276	Tfb4: Transcription factor Tfb4; InterPro: IPR0046	97.99
COG2425		437	Uncharacterized protein containing a von Willebran	97.98
PF05762		222	VWA_CoxE: VWA domain containing CoxE-like protein;	97.81
PLN00162		761	transport protein sec23; Provisional	97.63
PTZ00395		1560	Sec24-related protein; Provisional	97.13
smart00187		423	INB Integrin beta subunits (N-terminal portion of	97.1
COG2304		399	Uncharacterized protein containing a von Willebran	97.03
COG4867		652	Uncharacterized protein with a von Willebrand fact	96.87
cd01459		254	vWA_copine_like VWA Copine: Copines are phospholip	96.69
PF11265		226	Med25_VWA: Mediator complex subunit 25 von Willebr	96.64
KOG2487\|consensus		314		96.52
KOG1984\|consensus		1007		96.48
KOG2353\|consensus		1104		96.47
PF06707		205	DUF1194: Protein of unknown function (DUF1194); In	96.34
COG1721		416	Uncharacterized conserved protein (some members co	96.08
PF02809		18	UIM: Ubiquitin interaction motif; InterPro: IPR003	95.51
KOG2326\|consensus		669		95.48
COG5242		296	TFB4 RNA polymerase II transcription initiation/nu	95.12
PF02809		18	UIM: Ubiquitin interaction motif; InterPro: IPR003	94.64
smart00726		26	UIM Ubiquitin-interacting motif. Present in protea	94.41
TIGR01651		600	CobT cobaltochelatase, CobT subunit. This model de	94.29
PF11775		219	CobT_C: Cobalamin biosynthesis protein CobT VWA do	94.01
PF07002		146	Copine: Copine; InterPro: IPR010734 This represent	93.29
KOG1327\|consensus		529		93.24
PF03853		169	YjeF_N: YjeF-related protein N-terminus; InterPro:	92.71
smart00726		26	UIM Ubiquitin-interacting motif. Present in protea	92.08
PF09967		126	DUF2201: VWA-like domain (DUF2201); InterPro: IPR0	91.94
PF11443		534	DUF2828: Domain of unknown function (DUF2828); Int	91.26
COG5028		861	Vesicle coat complex COPII, subunit SEC24/subunit	89.82
COG4548		637	NorD Nitric oxide reductase activation protein [In	88.52
PF00362		426	Integrin_beta: Integrin, beta chain; InterPro: IPR	86.43
KOG1986\|consensus		745		86.06
KOG2327\|consensus		602		85.83
PLN03049		462	pyridoxine (pyridoxamine) 5'-phosphate oxidase; Pr	83.06
cd03811		353	GT1_WabH_like This family is most closely related	82.37
COG0062		203	Uncharacterized conserved protein [Function unknow	82.28
cd03794		394	GT1_wbuB_like This family is most closely related	81.87
cd03814		364	GT1_like_2 This family is most closely related to	81.49
KOG2941\|consensus		444		80.88
cd05844		367	GT1_like_7 Glycosyltransferases catalyze the trans	80.6
KOG1985\|consensus		887		80.54

>KOG2884\|consensus	Back alignment and domain information

Probab=100.00  E-value=1.6e-86  Score=614.61  Aligned_cols=239  Identities=69%  Similarity=1.065  Sum_probs=228.6

Q ss_pred             CCcceEEEEEeCCccccCCCCCCCHHHHHHHHHHHHHHhhccCCCCCcEEEEEecC-ceeEEecCCCCHHHHHHhhcccC
Q psy14660          1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMAD-SVEVLATLTSDVGRILSKLHQVQ   79 (375)
Q Consensus         1 m~lEaivI~lDnSesMrngD~~PsRL~Aq~~Av~~~v~~k~~~NPe~~VGLVt~ag-~a~vl~pLT~D~~~Il~~L~~l~   79 (375)
                      ||||+||||||||+|||||||.||||+||+++|+++|+.|+++||||+||||++++ .+.||+|||+|.++|+++||.+.
T Consensus         1 MvlEatmi~iDNse~mrNgDy~PtRf~aQ~daVn~v~~~K~~snpEntvGiitla~a~~~vLsT~T~d~gkils~lh~i~   80 (259)
T KOG2884|consen    1 MVLEATMICIDNSEYMRNGDYLPTRFQAQKDAVNLVCQAKLRSNPENTVGIITLANASVQVLSTLTSDRGKILSKLHGIQ   80 (259)
T ss_pred             CCcceEEEEEeChHHhhcCCCChHHHHHHHHHHHHHHHhhhcCCcccceeeEeccCCCceeeeeccccchHHHHHhcCCC
Confidence            99999999999999999999999999999999999999999999999999999999 69999999999999999999999


Q ss_pred             CCCCccHHHHHHHHHHHhhccCCCCCccEEEEEEcCCCCCChHHHHHHHHHHHhCCcEEEEEEecCCcchHHHHHHHHHh
Q psy14660         80 PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFIST  159 (375)
Q Consensus        80 ~~G~~~l~~gI~vA~laLKhr~~k~~~~RIIvfvgSp~~~d~~~l~~lakkLKk~~I~VdiIgfG~e~~n~~kL~~fi~~  159 (375)
                      ++|+++|.+||++|+++||||++|++++|||+|+|||+.+++++|+++||+|||++|.||||.||+...|+++|.+||++
T Consensus        81 ~~g~~~~~~~i~iA~lalkhRqnk~~~~riVvFvGSpi~e~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida  160 (259)
T KOG2884|consen   81 PHGKANFMTGIQIAQLALKHRQNKNQKQRIVVFVGSPIEESEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDA  160 (259)
T ss_pred             cCCcccHHHHHHHHHHHHHhhcCCCcceEEEEEecCcchhhHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999998899999999999


Q ss_pred             hCCCCCCCeeEEEecCCCchhhHhhhCCcccCCCCCCC----CCCCCCccCCCCCCCHHHHHHHHhcHHHHHHHHHHHHH
Q psy14660        160 LNGKDGSGSHMVTVAVGPHLSDALISSPIIQGEDGAGG----APGSSYEFGVDPNEDPELALALRVSMEEQRARQESEAR  235 (375)
Q Consensus       160 vn~~~~~~Sh~v~vp~g~~Lsd~l~sspi~~~~~~~~~----~~~~~~~fgvdp~~DPELa~Alr~Sleee~~rq~~~~~  235 (375)
                      +|++ +++||||+||||+.|+|+|++|||+.||+|+++    +.|..|+|||||++|||||||||+||||||+|||++++
T Consensus       161 ~N~~-~~gshlv~Vppg~~L~d~l~ssPii~ge~g~a~~~~~a~g~~f~fgvdp~~DPELAlALRlSMEEer~rQe~aa~  239 (259)
T KOG2884|consen  161 LNGK-GDGSHLVSVPPGPLLSDALLSSPIIQGEDGGAAAGLGANGMDFEFGVDPEDDPELALALRLSMEEERARQERAAQ  239 (259)
T ss_pred             hcCC-CCCceEEEeCCCccHHHHhhcCceeccCcccccccccccccccccCCCcccCHHHHHHHHhhHHHHHHHHHHHhh
Confidence            9997 679999999999999999999999999976643    33457999999999999999999999999999998877


Q ss_pred             HHhcc
Q psy14660        236 RAAEG  240 (375)
Q Consensus       236 ~~~~~  240 (375)
                      +++.+
T Consensus       240 ~~a~~  244 (259)
T KOG2884|consen  240 KAAAE  244 (259)
T ss_pred             hcccc
Confidence            65543

>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins	Back alignment and domain information

>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex	Back alignment and domain information

>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme	Back alignment and domain information

>KOG2807\|consensus	Back alignment and domain information

>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PRK13685 hypothetical protein; Provisional	Back alignment and domain information

>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A	Back alignment and domain information

>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01458 vWA_ku Ku70/Ku80 N-terminal domain	Back alignment and domain information

>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto)	Back alignment and domain information

>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins	Back alignment and domain information

>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions	Back alignment and domain information

>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions	Back alignment and domain information

>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation	Back alignment and domain information

>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain	Back alignment and domain information

>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>smart00327 VWA von Willebrand factor (vWF) type A domain	Back alignment and domain information

>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration	Back alignment and domain information

>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell	Back alignment and domain information

>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta	Back alignment and domain information

>cd01477 vWA_F09G8-8_type VWA F09G8	Back alignment and domain information

>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin)	Back alignment and domain information

>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax	Back alignment and domain information

>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity	Back alignment and domain information

>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology	Back alignment and domain information

>PRK13406 bchD magnesium chelatase subunit D; Provisional	Back alignment and domain information

>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family	Back alignment and domain information

>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>TIGR00868 hCaCC calcium-activated chloride channel protein 1	Back alignment and domain information

>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions	Back alignment and domain information

>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases	Back alignment and domain information

>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma	Back alignment and domain information

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D	Back alignment and domain information

>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional	Back alignment and domain information

>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	Back alignment and domain information

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit	Back alignment and domain information

>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions	Back alignment and domain information

>PF13768 VWA_3: von Willebrand factor type A domain	Back alignment and domain information

>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]	Back alignment and domain information

>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein	Back alignment and domain information

>PF03731 Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; InterPro: IPR005161 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway	Back alignment and domain information

>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70)	Back alignment and domain information

>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts	Back alignment and domain information

>TIGR00627 tfb4 transcription factor tfb4	Back alignment and domain information

>PRK10997 yieM hypothetical protein; Provisional	Back alignment and domain information

>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]	Back alignment and domain information

>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles	Back alignment and domain information

>cd01468 trunk_domain trunk domain	Back alignment and domain information

>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []	Back alignment and domain information

>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles	Back alignment and domain information

>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair	Back alignment and domain information

>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown	Back alignment and domain information

>PLN00162 transport protein sec23; Provisional	Back alignment and domain information

>PTZ00395 Sec24-related protein; Provisional	Back alignment and domain information

>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region)	Back alignment and domain information

>COG2304 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]	Back alignment and domain information

>cd01459 vWA_copine_like VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium	Back alignment and domain information

>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells	Back alignment and domain information

>KOG2487\|consensus	Back alignment and domain information

>KOG1984\|consensus	Back alignment and domain information

>KOG2353\|consensus	Back alignment and domain information

>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length	Back alignment and domain information

>COG1721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]	Back alignment and domain information

>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]	Back alignment and domain information

>KOG2326\|consensus	Back alignment and domain information

>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]	Back alignment and domain information

>smart00726 UIM Ubiquitin-interacting motif	Back alignment and domain information

>TIGR01651 CobT cobaltochelatase, CobT subunit	Back alignment and domain information

>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain	Back alignment and domain information

>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines	Back alignment and domain information

>KOG1327\|consensus	Back alignment and domain information

>PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes	Back alignment and domain information

>smart00726 UIM Ubiquitin-interacting motif	Back alignment and domain information

>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function	Back alignment and domain information

>PF11443 DUF2828: Domain of unknown function (DUF2828); InterPro: IPR024553 This uncharacterised domain is found in eukaryotic, bacterial and viral proteins	Back alignment and domain information

>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]	Back alignment and domain information

>COG4548 NorD Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]	Back alignment and domain information

>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]	Back alignment and domain information

>KOG1986\|consensus	Back alignment and domain information

>KOG2327\|consensus	Back alignment and domain information

>PLN03049 pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional	Back alignment and domain information

>cd03811 GT1_WabH_like This family is most closely related to the GT1 family of glycosyltransferases	Back alignment and domain information

>COG0062 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>cd03794 GT1_wbuB_like This family is most closely related to the GT1 family of glycosyltransferases	Back alignment and domain information

>cd03814 GT1_like_2 This family is most closely related to the GT1 family of glycosyltransferases	Back alignment and domain information

>KOG2941\|consensus	Back alignment and domain information

>cd05844 GT1_like_7 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds	Back alignment and domain information

>KOG1985\|consensus	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		375
4b4t_W		268	Near-Atomic Resolution Structural Model Of The Yeas		4e-51
2x5n_A		192	Crystal Structure Of The Sprpn10 Vwa Domain Length		1e-42
1yx4_A		132	Structure Of S5a Bound To Monoubiquitin Provides A		2e-10
2kde_A		111	Nmr Structure Of Major S5a (196-306):k48 Linked Diu		2e-10

>pdb|4B4T|W Chain W, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 268

Back alignment and structure

Iteration: 1

Score = 198 bits (504), Expect = 4e-51, Method: Compositional matrix adjust. Identities = 110/236 (46%), Positives = 150/236 (63%), Gaps = 13/236 (5%) Query: 1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADS-VE 59 MVLE+T++ +DNS++ RNGDF TR +AQ D+V + +K SNPEN VGL++ A + Sbjct: 1 MVLEATVLVIDNSEYSRNGDFPRTRFEAQIDSVEFIFQAKRNSNPENTVGLISGAGANPR 60 Query: 60 VLATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDL 119 VL+T T++ G+IL+ LH Q G ++ T ++IA L LKHRQ K RI+AFV SP+ Sbjct: 61 VLSTFTAEFGKILAGLHDTQIEGKLHMATALQIAQLTLKHRQNKVQHQRIVAFVCSPISD 120 Query: 120 EERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPH- 178 EL +LAK LKK V VDI++FGE NTELL+ FI+ +N SH++TV GP Sbjct: 121 SRDELIRLAKTLKKNNVAVDIINFGEIEQNTELLDEFIAAVNNPQEETSHLLTVTPGPRL 180 Query: 179 LSDALISSPIIQGEDGA-----------GGAPGSSYEFGVDPNEDPELALALRVSM 223 L + + SSPII E + A G+ +FGVDP+ DPELA+ALR+SM Sbjct: 181 LYENIASSPIILEEGSSGMGAFGGSGGDSDANGTFMDFGVDPSMDPELAMALRLSM 236

PyMOL of 4b4t

>pdb|2X5N|A Chain A, Crystal Structure Of The Sprpn10 Vwa Domain Length = 192

Back alignment and structure

>pdb|1YX4|A Chain A, Structure Of S5a Bound To Monoubiquitin Provides A Model For Polyubiquitin Recognition Length = 132

Back alignment and structure

>pdb|2KDE|A Chain A, Nmr Structure Of Major S5a (196-306):k48 Linked Diubiquitin Species Length = 111

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		375
2x5n_A		192	SPRPN10, 26S proteasome regulatory subunit RPN10;	2e-69
1yx4_A		132	26S proteasome non-ATPase regulatory subunit 4; po	6e-21
3ibs_A		218	Conserved hypothetical protein BATB; structural ge	1e-05
1shu_X		182	Anthrax toxin receptor 2; alpha/beta rossmann fold	1e-04
1p9c_A		45	26S proteasome non-ATPase regulatory subunit 4; al	3e-04

>2x5n_A SPRPN10, 26S proteasome regulatory subunit RPN10; nuclear protein, nucleus, ubiquitin; 1.30A {Schizosaccharomyces pombe} Length = 192	Back alignment and structure

 Score =  215 bits (548), Expect = 2e-69
 Identities = 90/194 (46%), Positives = 125/194 (64%), Gaps = 5/194 (2%)

Query: 2   VLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADS-VEV 60
           VLE+TMI +DNS++M NGD++PTR +AQ+D V+++ + K   NPEN  GL+ + D+  +V
Sbjct: 1   VLEATMILIDNSEWMINGDYIPTRFEAQKDTVHMIFNQKINDNPENMCGLMTIGDNSPQV 60

Query: 61  LATLTSDVGRILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLE 120
           L+TLT D G+ LS +H +   GN  F  GI+IA LALKHR+ K  + RI+AFVGSP+  +
Sbjct: 61  LSTLTRDYGKFLSAMHDLPVRGNAKFGDGIQIAQLALKHRENKIQRQRIVAFVGSPIVED 120

Query: 121 ERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFISTLNGKDGSGSHMVTVAVGPH-L 179
           E+ L +LAKR+KK  V +DI+  GE   N   L  FI   N  D    H+V++   P  L
Sbjct: 121 EKNLIRLAKRMKKNNVAIDIIHIGEL-QNESALQHFIDAANSSD--SCHLVSIPPSPQLL 177

Query: 180 SDALISSPIIQGED 193
           SD +  SPI QG  
Sbjct: 178 SDLVNQSPIGQGVV 191

PyMOL of 2x5n

>1yx4_A 26S proteasome non-ATPase regulatory subunit 4; polyubiquitin, UIM, hydrolase; NMR {Homo sapiens} PDB: 1yx5_A 1yx6_A 2kde_A 2kdf_A Length = 132	Back alignment and structure

>3ibs_A Conserved hypothetical protein BATB; structural genomics, protein structure, midwest center for S genomics, MCSG, PSI-2; HET: MSE; 2.10A {Bacteroides thetaiotaomicron} Length = 218	Back alignment and structure

>1shu_X Anthrax toxin receptor 2; alpha/beta rossmann fold, membrane protein; 1.50A {Homo sapiens} SCOP: c.62.1.1 PDB: 1tzn_a 1sht_X 1t6b_Y* Length = 182	Back alignment and structure

>1p9c_A 26S proteasome non-ATPase regulatory subunit 4; alpha helix, hairpin loop, ligand binding protein; NMR {Homo sapiens} SCOP: j.105.1.1 PDB: 1p9d_S 1uel_B Length = 45	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		375
4b4t_W		268	RPN10, 26S proteasome regulatory subunit RPN10; hy	100.0
2x5n_A		192	SPRPN10, 26S proteasome regulatory subunit RPN10;	100.0
1yx4_A		132	26S proteasome non-ATPase regulatory subunit 4; po	99.96
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	99.86
3ibs_A		218	Conserved hypothetical protein BATB; structural ge	99.84
1atz_A		189	VON willebrand factor; collagen-binding, hemostasi	99.71
1ijb_A		202	VON willebrand factor; dinucleotide-binding fold,	99.71
1shu_X		182	Anthrax toxin receptor 2; alpha/beta rossmann fold	99.69
2xgg_A		178	Microneme protein 2; A/I domain, cell adhesion, hy	99.69
1q0p_A		223	Complement factor B; VON willebrand factor, MAC-1,	99.69
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	99.67
4hqf_A		281	Thrombospondin-related anonymous protein, trap; ma	99.66
4hqo_A		266	Sporozoite surface protein 2; malaria, gliding mot	99.66
2b2x_A		223	Integrin alpha-1; computational design, antibody-a	99.65
1v7p_C		200	Integrin alpha-2; snake venom, C-type lectin, anta	99.65
3n2n_F		185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	99.65
1pt6_A		213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	99.63
1mf7_A		194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	99.63
1n3y_A		198	Integrin alpha-X; alpha/beta rossmann fold, cell a	99.63
4fx5_A		464	VON willebrand factor type A; structural genomics,	99.63
2odp_A		509	Complement C2; C3/C5 convertase, complement serin	99.56
1rrk_A		497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	99.56
2x31_A		189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	99.55
3hrz_D		741	Complement factor B; serine protease, glycosilated	99.47
3zqk_A		199	VON willebrand factor; blood clotting, adamts-13,	99.43
1mjn_A		179	Integrin alpha-L; rossmann fold, immune system; 1.	99.35
3k6s_A		1095	Integrin alpha-X; cell receptor, adhesion molecule	99.24
1yvr_A		538	RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein,	98.99
2ww8_A		893	RRGA, cell WALL surface anchor family protein; IGG	98.89
2nvo_A		535	RO sixty-related protein, RSR; alpha helical repea	98.69
3rag_A		242	Uncharacterized protein; structural genomics, PSI-	98.6
2nut_A		769	Protein transport protein SEC23A; human copii SEC2	98.44
1pcx_A		810	Protein transport protein SEC24; 2.50A {Saccharomy	98.19
2iue_A		212	Pactolus I-domain; membrane protein, CD, ITC, limb	98.13
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	98.07
1m2o_A		768	SEC23, protein transport protein SEC23, SEC23P; zi	97.94
3fcs_B		690	Integrin beta-3; beta propeller, rossmann fold, EG	97.79
1p9c_A		45	26S proteasome non-ATPase regulatory subunit 4; al	97.7
3eh1_A		751	Protein transport protein SEC24B; copii coat prote	97.58
3eh2_A		766	Protein transport protein SEC24C; copii-coat prote	97.56
3k6s_B		687	Integrin beta-2; cell receptor, adhesion molecule,	97.53
3efo_B		770	SEC24 related gene family, member D; copii, coat p	97.5
3vi3_B		454	Integrin beta-1; beta propeller fold, rossman fold	97.2
3t3p_B		472	Integrin beta-3; integrin, cell adhesion, blood cl	97.04
3v4v_B		503	Integrin beta-7; cell adhesion, madcam-1, membrane	96.75
3rag_A		242	Uncharacterized protein; structural genomics, PSI-	96.51
2klz_A		52	Ataxin-3; UIM, ubiquitin-binding, hydrolase, neuro	92.6
3a1q_C		45	Ubiquitin interaction motif-containing protein 1;	91.92
2rr9_C		46	Putative uncharacterized protein UIMC1; Lys63-link	91.7
1q0v_A		81	Hydrophilic protein; has cysteine rich putative zi	83.21
3qhp_A		166	Type 1 capsular polysaccharide biosynthesis prote	82.84

>4b4t_W RPN10, 26S proteasome regulatory subunit RPN10; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

Probab=100.00  E-value=6.9e-77  Score=571.01  Aligned_cols=239  Identities=49%  Similarity=0.756  Sum_probs=189.0

Q ss_pred             CCcceEEEEEeCCccccCCCCCCCHHHHHHHHHHHHHHhhccCCCCCcEEEEEecCc-eeEEecCCCCHHHHHHhhcccC
Q psy14660          1 MVLESTMICVDNSDFMRNGDFLPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADS-VEVLATLTSDVGRILSKLHQVQ   79 (375)
Q Consensus         1 m~lEaivI~lDnSesMrngD~~PsRL~Aq~~Av~~~v~~k~~~NPe~~VGLVt~ag~-a~vl~pLT~D~~~Il~~L~~l~   79 (375)
                      |||||||||||+|.||+|+||.||||+++++|++.|++.|+++||+++||||+|+|. +.|++|||+|+++|+.+||.++
T Consensus         1 m~lEAtViviD~S~SM~~~D~~PsRl~a~k~Av~~li~~~~~~nPed~VGLVtfag~~~~vl~plT~D~~~il~aL~~l~   80 (268)
T 4b4t_W            1 MVLEATVLVIDNSEYSRNGDFPRTRFEAQIDSVEFIFQAKRNSNPENTVGLISGAGANPRVLSTFTAEFGKILAGLHDTQ   80 (268)
T ss_dssp             CCCEEEEEEECCSSTTSSTTSSSCHHHHHHHHHHHHHHHHHHHCTTCEEEEEECCTTSCEEEEEEESCHHHHHHHHTTCC
T ss_pred             CCceeEEEEEECCHHHhCCCCCCcHHHHHHHHHHHHHHHHhhCCCcceEEEEEecCCcceeccCCcchHHHHHHHhhhcC
Confidence            999999999999999999999999999999999999999999999999999999995 7899999999999999999999


Q ss_pred             CCCCccHHHHHHHHHHHhhccCCCCCccEEEEEEcCCCCCChHHHHHHHHHHHhCCcEEEEEEecCCcchHHHHHHHHHh
Q psy14660         80 PNGNINFMTGIRIAHLALKHRQGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTELLNTFIST  159 (375)
Q Consensus        80 ~~G~~~l~~gI~vA~laLKhr~~k~~~~RIIvfvgSp~~~d~~~l~~lakkLKk~~I~VdiIgfG~e~~n~~kL~~fi~~  159 (375)
                      ++|.+++.+||++|+++||||+++++++|||||++|+.+++++++.+++|++||+||+|+|||||+..+|.++|++|+++
T Consensus        81 ~~G~T~l~~gL~~A~~aLk~~~~k~~~~rIIlf~ds~~~~~~~~l~~lak~lkk~gI~v~vIgFG~~~~n~~kLe~l~~~  160 (268)
T 4b4t_W           81 IEGKLHMATALQIAQLTLKHRQNKVQHQRIVAFVCSPISDSRDELIRLAKTLKKNNVAVDIINFGEIEQNTELLDEFIAA  160 (268)
T ss_dssp             CCSCCCHHHHHHHHHHHHHTCSCTTSEEEEEEEECSCCSSCHHHHHHHHHHHHHHTEEEEEEEESSCCSSCCHHHHHHHH
T ss_pred             cCCCCChHHHHHHHHHHHHhcccCCCceEEEEEECCCCCCCHHHHHHHHHHHHHcCCEEEEEEeCCCccchHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCCCeeEEEecCCCc-hhhHhhhCCcccCCCCCCC-----------CCCCCCccCCCCCCCHHHHHHHHhcHHHHH
Q psy14660        160 LNGKDGSGSHMVTVAVGPH-LSDALISSPIIQGEDGAGG-----------APGSSYEFGVDPNEDPELALALRVSMEEQR  227 (375)
Q Consensus       160 vn~~~~~~Sh~v~vp~g~~-Lsd~l~sspi~~~~~~~~~-----------~~~~~~~fgvdp~~DPELa~Alr~Sleee~  227 (375)
                      +|++.+++||||+||||++ |||.|++|||+.|++++++           ++|++|||||||++||||||||||||||||
T Consensus       161 ~Ng~~~~~s~~v~v~~g~~~lsd~l~~s~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~dpela~alr~s~eee~  240 (268)
T 4b4t_W          161 VNNPQEETSHLLTVTPGPRLLYENIASSPIILEEGSSGMGAFGGSGGDSDANGTFMDFGVDPSMDPELAMALRLSMEEEQ  240 (268)
T ss_dssp             HCSSTTTSCEEEEECCCSSCHHHHHHTSTTSCCCCC--------------------------------------------
T ss_pred             hcCCCCCceeEEEeCCCCccHHHHHhcCCccccCCccccccccccccccccCCcccccCCCCCCCHHHHHHHHHhHHHHH
Confidence            9998778999999999986 9999999999999864321           234568999999999999999999999999


Q ss_pred             HHHHHHHHHHhc
Q psy14660        228 ARQESEARRAAE  239 (375)
Q Consensus       228 ~rq~~~~~~~~~  239 (375)
                      +|||++++++..
T Consensus       241 ~rq~~~~~~~~~  252 (268)
T 4b4t_W          241 QRQERLRQQQQQ  252 (268)
T ss_dssp             ------------
T ss_pred             HHHHHHhhcccc
Confidence            999999887654

PyMOL of 4b4t

>2x5n_A SPRPN10, 26S proteasome regulatory subunit RPN10; nuclear protein, nucleus, ubiquitin; 1.30A {Schizosaccharomyces pombe}	Back alignment and structure

>1yx4_A 26S proteasome non-ATPase regulatory subunit 4; polyubiquitin, UIM, hydrolase; NMR {Homo sapiens} PDB: 1yx5_A 1yx6_A 2kde_A 2kdf_A	Back alignment and structure

>1jey_B KU80; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.2 c.62.1.4 PDB: 1jeq_B*	Back alignment and structure

>3ibs_A Conserved hypothetical protein BATB; structural genomics, protein structure, midwest center for S genomics, MCSG, PSI-2; HET: MSE; 2.10A {Bacteroides thetaiotaomicron}	Back alignment and structure

>1atz_A VON willebrand factor; collagen-binding, hemostasis, dinucleotide binding fold; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 4dmu_B 2adf_A 1fe8_A 1ao3_A	Back alignment and structure

>1ijb_A VON willebrand factor; dinucleotide-binding fold, blood clotting; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 1ijk_A 1auq_A 1u0n_A 3hxo_A 1uex_C 3hxq_A 1sq0_A 1m10_A 1fns_A 1oak_A 1u0o_C	Back alignment and structure

>1shu_X Anthrax toxin receptor 2; alpha/beta rossmann fold, membrane protein; 1.50A {Homo sapiens} SCOP: c.62.1.1 PDB: 1tzn_a 1sht_X 1t6b_Y*	Back alignment and structure

>2xgg_A Microneme protein 2; A/I domain, cell adhesion, hydrolase; 2.05A {Toxoplasma gondii}	Back alignment and structure

>1q0p_A Complement factor B; VON willebrand factor, MAC-1, I domain, A domain, hydrolase; 1.80A {Homo sapiens} SCOP: c.62.1.1	Back alignment and structure

>1jey_A KU70; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.1 c.62.1.3 PDB: 1jeq_A* 3rzx_B	Back alignment and structure

>4hqf_A Thrombospondin-related anonymous protein, trap; malaria, parasite motility, I domain, TSR domain, receptor O sporozoite, vaccine target; 2.20A {Plasmodium falciparum} PDB: 4hqk_A 2bbx_A	Back alignment and structure

>4hqo_A Sporozoite surface protein 2; malaria, gliding motility, VWA domain, TSR domain, extensibl ribbon, receptor on sporozoite, vaccine target; HET: FUC BGC; 2.19A {Plasmodium vivax} PDB: 4hql_A* 4hqn_A*	Back alignment and structure

>2b2x_A Integrin alpha-1; computational design, antibody-antigen complex, immune syste; 2.20A {Rattus norvegicus} SCOP: c.62.1.1	Back alignment and structure

>1v7p_C Integrin alpha-2; snake venom, C-type lectin, antagonist, cell adhes glycoprotein, toxin-cell adhesion complex; HET: NAG; 1.90A {Homo sapiens} SCOP: c.62.1.1 PDB: 1aox_A 1dzi_A	Back alignment and structure

>3n2n_F Anthrax toxin receptor 1; rossmann fold; 1.80A {Homo sapiens} SCOP: c.62.1.1	Back alignment and structure

>1pt6_A Integrin alpha-1; cell adhesion; 1.87A {Homo sapiens} SCOP: c.62.1.1 PDB: 4a0q_A 1qcy_A 1qc5_A 1qc5_B 1ck4_A 1mhp_A	Back alignment and structure

>1mf7_A Integrin alpha M; cell adhesion; 1.25A {Homo sapiens} SCOP: c.62.1.1 PDB: 1na5_A 1jlm_A 1ido_A 1m1u_A 3q3g_G 1n9z_A 1bhq_1 1bho_1 1idn_1 3qa3_G	Back alignment and structure

>1n3y_A Integrin alpha-X; alpha/beta rossmann fold, cell adhesion; 1.65A {Homo sapiens} SCOP: c.62.1.1	Back alignment and structure

>4fx5_A VON willebrand factor type A; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, blood clotting; HET: MSE; 1.73A {Catenulispora acidiphila}	Back alignment and structure

>2odp_A Complement C2; C3/C5 convertase, complement serin protease, human complement system, glycoprotein, SP, VWFA,; HET: NAG; 1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A*	Back alignment and structure

>1rrk_A Complement factor B; BB, hydrolase; 2.00A {Homo sapiens} SCOP: b.47.1.2 c.62.1.1 PDB: 1rs0_A* 1rtk_A* 2win_I* 1dle_A	Back alignment and structure

>2x31_A Magnesium-chelatase 60 kDa subunit; ligase, bacteriochlorophyll biosynthesis, photosynthesis; 7.50A {Rhodobacter capsulatus}	Back alignment and structure

>3hrz_D Complement factor B; serine protease, glycosilated, multi-domain, complement SYST convertase, complement alternate pathway; HET: NAG P6G; 2.20A {Homo sapiens} PDB: 2xwj_I* 3hs0_D* 2ok5_A* 2xwb_F*	Back alignment and structure

>3zqk_A VON willebrand factor; blood clotting, adamts-13, force sensor, VON willebrand DISE domain, haemostasis; HET: NAG; 1.70A {Homo sapiens} PDB: 3ppv_A 3ppx_A 3ppw_A 3ppy_A 3gxb_A*	Back alignment and structure

>1mjn_A Integrin alpha-L; rossmann fold, immune system; 1.30A {Homo sapiens} SCOP: c.62.1.1 PDB: 3hi6_A 1mq8_B* 3eoa_I 3eob_I 1rd4_A* 1lfa_A 1zon_A 1zoo_A 1zop_A 1dgq_A 1xdd_A* 1xdg_A* 1xuo_A* 3e2m_A* 3bqn_B* 1cqp_A* 3bqm_B* 2ica_A* 2o7n_A* 3m6f_A* ...	Back alignment and structure

>3k6s_A Integrin alpha-X; cell receptor, adhesion molecule, cell adhesion, pyrrolidone carboxylic acid; HET: NAG MAN; 3.50A {Homo sapiens} PDB: 3k71_A* 3k72_A*	Back alignment and structure

>1yvr_A RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein, 60 kDa; heat repeat, VON willebrand factor A, rossmann fold, midas motif', RNA binding protein; 1.95A {Xenopus laevis} SCOP: a.118.25.1 c.62.1.5 PDB: 1yvp_A 2i91_A	Back alignment and structure

>2ww8_A RRGA, cell WALL surface anchor family protein; IGG, pilus, CNA_B, adhesin, integrin, cell adhesion; HET: EPE; 1.90A {Streptococcus pneumoniae}	Back alignment and structure

>2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON willebrand factor A domain, beta- RNA binding protein; 1.89A {Deinococcus radiodurans}	Back alignment and structure

>3rag_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tructural genomics; 1.80A {Alicyclobacillus acidocaldarius subsp}	Back alignment and structure

>2nut_A Protein transport protein SEC23A; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_A 3egd_A 3eg9_A 3egx_A 3efo_A	Back alignment and structure

>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1pd0_A 1pd1_A	Back alignment and structure

>2iue_A Pactolus I-domain; membrane protein, CD, ITC, limbs, midas, admidas, membrane, integrin, titration, rossman fold, cell adhesion, transmembrane; NMR {Mus musculus}	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1	Back alignment and structure

>1m2o_A SEC23, protein transport protein SEC23, SEC23P; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1m2v_A 2qtv_A*	Back alignment and structure

>3fcs_B Integrin beta-3; beta propeller, rossmann fold, EGF domain, cell adhesion, DI mutation, glycoprotein, HOST-virus interaction, M phosphoprotein; HET: NAG MAN; 2.55A {Homo sapiens} PDB: 4g1e_B* 3ije_B* 4g1m_B* 1jv2_B* 1l5g_B* 1m1x_B* 1u8c_B*	Back alignment and structure

>1p9c_A 26S proteasome non-ATPase regulatory subunit 4; alpha helix, hairpin loop, ligand binding protein; NMR {Homo sapiens} SCOP: j.105.1.1 PDB: 1p9d_S 1uel_B	Back alignment and structure

>3eh1_A Protein transport protein SEC24B; copii coat protein, vesicle transport, transport signal sequence, cytoplasm, endoplasmic reticulum; 1.80A {Homo sapiens} PDB: 2nut_B 2nup_B 3egd_B 3egx_B	Back alignment and structure

>3eh2_A Protein transport protein SEC24C; copii-coat protein, vesicle transport, cytoplasm, endoplasmic reticulum, ER-golgi transport, golgi apparatus; 2.35A {Homo sapiens}	Back alignment and structure

>3k6s_B Integrin beta-2; cell receptor, adhesion molecule, cell adhesion, pyrrolidone carboxylic acid; HET: NAG MAN; 3.50A {Homo sapiens} PDB: 3k71_B* 3k72_B*	Back alignment and structure

>3efo_B SEC24 related gene family, member D; copii, coat protein, transport signal, disease mutation, endoplasmic reticulum, ER-golgi transport, golgi apparatus, membrane; 2.70A {Homo sapiens} PDB: 3eg9_B	Back alignment and structure

>3vi3_B Integrin beta-1; beta propeller fold, rossman fold, beta sandwich, fibronecti receptor, cell adhesion-immune system complex; HET: NAG BMA MAN; 2.90A {Homo sapiens} PDB: 3vi4_B*	Back alignment and structure

>3t3p_B Integrin beta-3; integrin, cell adhesion, blood clotting, fibrinogen, platele; HET: NAG BMA MAN; 2.20A {Homo sapiens} PDB: 3t3m_B* 3nig_B* 3nif_B* 3nid_B* 2vdr_B* 2vc2_B* 2vdk_B* 2vdm_B* 2vdn_B* 2vdl_B* 2vdp_B* 2vdq_B* 2vdo_B* 3fcu_B* 1txv_B* 1ty3_B* 1ty5_B* 1ty6_B* 1ty7_B* 1tye_B*	Back alignment and structure

>3v4v_B Integrin beta-7; cell adhesion, madcam-1, membrane; HET: NAG BMA MAN 0DU; 3.10A {Homo sapiens} PDB: 3v4p_B*	Back alignment and structure

>3rag_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tructural genomics; 1.80A {Alicyclobacillus acidocaldarius subsp}	Back alignment and structure

>2klz_A Ataxin-3; UIM, ubiquitin-binding, hydrolase, neurodegenerati nucleus, phosphoprotein, spinocerebellar ataxia, transcript transcription regulation; NMR {Homo sapiens}	Back alignment and structure

>3a1q_C Ubiquitin interaction motif-containing protein 1; protein complex, cytoplasm, nucleus, phosphoprotein, UBL conjugation, transcription regulation; 2.20A {Mus musculus}	Back alignment and structure

>2rr9_C Putative uncharacterized protein UIMC1; Lys63-linked diubiquitin, ubiquitin-interacting motif, ubiqu RAP80, DNA repair, nuclear protein; NMR {Homo sapiens}	Back alignment and structure

>1q0v_A Hydrophilic protein; has cysteine rich putative zinc finger esential for function;...; stable, non-interacting alpha-helices; NMR {Saccharomyces cerevisiae} SCOP: j.105.1.1 PDB: 1q0w_A	Back alignment and structure

>3qhp_A Type 1 capsular polysaccharide biosynthesis prote (CAPJ); rossmann fold, glycosyltransferase, transferase; 1.50A {Helicobacter pylori}	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
d1jeyb2		236	c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain	2e-17
d1jeya2		220	c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain	8e-05
d1yvra2		174	c.62.1.5 (A:364-537) 60-kda SS-A/Ro ribonucleoprot	0.003

>d1jeyb2 c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 236	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku80 subunit N-terminal domain
domain: Ku80 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.5 bits (192), Expect = 2e-17
 Identities = 17/167 (10%), Positives = 45/167 (26%), Gaps = 19/167 (11%)

Query: 4   ESTMICVDNSDFMRNGDF-LPTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSVEVLA 62
            + ++C+D    M N    + +  +  +  + +    +  +  ++ + L+          
Sbjct: 3   AAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNP 62

Query: 63  TLTSDVG------------------RILSKLHQVQPNGNINFMTGIRIAHLALKHRQGKN 104
               D                     I SK+       +      + +  +  +    K 
Sbjct: 63  LSGGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKF 122

Query: 105 HKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFGEEVVNTE 151
            K  I  F        + +L  +   LKK  +++             
Sbjct: 123 EKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDG 169

PyMOL of d1jeyb2

>d1jeya2 c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 220	Back information, alignment and structure

>d1yvra2 c.62.1.5 (A:364-537) 60-kda SS-A/Ro ribonucleoprotein, RoRNP {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 174	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		375
d1jeyb2		236	Ku80 subunit N-terminal domain {Human (Homo sapien	99.81
d1jeya2		220	Ku70 subunit N-terminal domain {Human (Homo sapien	99.7
d1shux_		181	Capillary morphogenesis protein 2 domain {Human (H	99.62
d1atza_		184	von Willebrand factor A3 domain, vWA3 {Human (Homo	99.55
d1ijba_		202	von Willebrand factor A1 domain, vWA1 {Human (Homo	99.51
d1n3ya_		189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	99.48
d1q0pa_		209	Complement factor B domain {Human (Homo sapiens) [	99.47
d1pt6a_		192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	99.46
d1v7pc_		193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	99.45
d1mf7a_		194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	99.38
d1mjna_		179	Integrin CD11a/CD18 (Leukocyte function associated	99.07
d1yvra2		174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	99.01
d1tyeb2		248	Integrin beta A domain {Human (Homo sapiens) [TaxI	98.75
d1pd0a3		252	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	98.6
d2qtva3		271	Sec23 {Baker's yeast (Saccharomyces cerevisiae) [T	98.35
d1jzta_		243	Hypothetical protein YNL200c (YNU0_YEAST) {Baker's	88.16
d2ax3a2		211	Hypothetical protein TM0922, N-terminal domain {Th	83.96
d1e5da1		152	Rubredoxin oxygen:oxidoreductase (ROO), C-terminal	80.93

>d1jeyb2 c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku80 subunit N-terminal domain
domain: Ku80 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.2e-19  Score=160.16  Aligned_cols=144  Identities=13%  Similarity=0.162  Sum_probs=117.3

Q ss_pred             ceEEEEEeCCccccCCCCC-CCHHHHHHHHHHHHHHhhccCCCCCcEEEEEecCce--------------eEEecCCCCH
Q psy14660          4 ESTMICVDNSDFMRNGDFL-PTRLQAQQDAVNLVCHSKTRSNPENNVGLLAMADSV--------------EVLATLTSDV   68 (375)
Q Consensus         4 EaivI~lDnSesMrngD~~-PsRL~Aq~~Av~~~v~~k~~~NPe~~VGLVt~ag~a--------------~vl~pLT~D~   68 (375)
                      |+||||||+|.||...|.. ||||+++++++..|++.++..+|.++||||.|++.+              .++.+++...
T Consensus         3 ~aiv~~lD~S~SM~~~~~~~~srl~~ak~~~~~~v~~~~~~~~~d~vglV~f~~~~t~~~~~~~~~~~~i~~~~~~~~~~   82 (236)
T d1jeyb2           3 AAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPD   82 (236)
T ss_dssp             EEEEEEEECCGGGGCCBTTBCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCTTTCSTTEEEEEEEECCC
T ss_pred             ceEEEEEECChhhccCCCCCCCHHHHHHHHHHHHHHHHhcCCCCCeEEEEEEcCCCcccccccccccceEEEEeccccch
Confidence            7999999999999988764 899999999999999999999999999999999764              4666666666


Q ss_pred             HHHHHhhcccC--CCCCccHHHHHHHHHHHhhcc--CCCCCccEEEEEEcCCCCCChHHHHHHHHHHHhCCcEEEEEEec
Q psy14660         69 GRILSKLHQVQ--PNGNINFMTGIRIAHLALKHR--QGKNHKMRIIAFVGSPVDLEERELTKLAKRLKKEKVNVDIVSFG  144 (375)
Q Consensus        69 ~~Il~~L~~l~--~~G~~~l~~gI~vA~laLKhr--~~k~~~~RIIvfvgSp~~~d~~~l~~lakkLKk~~I~VdiIgfG  144 (375)
                      ..++..+....  ..+.+++..+|..|...+.++  ..+..+++||+|+++..+.+...+..+++.|++.||+|++||+|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~al~~a~~~~~~~~~~~~~~~r~IiL~TDG~~~~~~~~~~~~a~~l~~~~I~i~~ig~g  162 (236)
T d1jeyb2          83 FDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPF  162 (236)
T ss_dssp             HHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHHSSSSCCSEEEEEEECCCCSCCCCTTHHHHHHHHHHTTEEEEEEESS
T ss_pred             hhHHHHHhhhccccccccchhHHHHHHHHHHHHhhhcccccccEEEEEecCCCCcChHHHHHHHHHHHHcCCEEEEEecC
Confidence            66666666553  335689999999999777654  33445567888876655556677889999999999999999999


Q ss_pred             CCc
Q psy14660        145 EEV  147 (375)
Q Consensus       145 ~e~  147 (375)
                      ...
T Consensus       163 ~~~  165 (236)
T d1jeyb2         163 SLG  165 (236)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            764

PyMOL of d1jeyb2

>d1jeya2 c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1shux_ c.62.1.1 (X:) Capillary morphogenesis protein 2 domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1atza_ c.62.1.1 (A:) von Willebrand factor A3 domain, vWA3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ijba_ c.62.1.1 (A:) von Willebrand factor A1 domain, vWA1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1n3ya_ c.62.1.1 (A:) Integrin alpha-x beta2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1q0pa_ c.62.1.1 (A:) Complement factor B domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1pt6a_ c.62.1.1 (A:) Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v7pc_ c.62.1.1 (C:) Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1mf7a_ c.62.1.1 (A:) Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1mjna_ c.62.1.1 (A:) Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1yvra2 c.62.1.5 (A:364-537) 60-kda SS-A/Ro ribonucleoprotein, RoRNP {African clawed frog (Xenopus laevis) [TaxId: 8355]}	Back information, alignment and structure

>d1tyeb2 c.62.1.1 (B:107-354) Integrin beta A domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1pd0a3 c.62.1.2 (A:301-552) Sec24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2qtva3 c.62.1.2 (A:120-390) Sec23 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1jzta_ c.104.1.1 (A:) Hypothetical protein YNL200c (YNU0_YEAST) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2ax3a2 c.104.1.1 (A:1-211) Hypothetical protein TM0922, N-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1e5da1 c.23.5.1 (A:251-402) Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure