Citrus Sinensis ID: 006975

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-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620---

MELDPDDVFRDDDEESDNEFYQEHEATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYDEEGDVKVSEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK

cccccccccccccccccHHHHcccccccEEEEEEEEcccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccEEEEEEEEcccccccccccccEEEEEEEEcccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcccccccccEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccccccccHHcccccccccccccccccHHHHHHHHHHHHHHHHcccccEEEEEEEcccEEEEEEEEEEccccccccEEEEcccccccccEEEEEEEcccccccccccccccccccEEEEEcHHHHHHHHccccccEEEEEEEccccccccEEccccEEEEccccccccHHHHHHHHHHHHHHcccEEEEEEccccccEEEEEEEEHHHcccccccccccEEEEEccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHcc

cccccccccccccccccccHcccccccccEEEEEEEccHHHccccccccccccccHHHHHHHHHHHHHHHHEEEccccEEEEEEEEccccccccccccEEEEEEEEEEccccccHHHHHHHHHHHHHHHHcHHHHcccccccccccHHHHHHHHHHHHHcccccccccEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccccHHHHHHHHcccccHHHcccccccHHHHHHHHHHHHHccccccEEEEEEEEEcccEEEEEEEEEEEEcccccccEEEccccccEEEEEEEEEEccccccccHHcEEEEEccccEEEEcHHHHHHHHHcccccEEEEEEccHHHccHHccccccEEEEccccccccHHHHHHHHHHHHHHcccEEEEEEEcccccEEEEEEccccccccccccccccEEEEEcccHHHHcccccccccccccccccHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccccccccccccccccHHHccHHHHHHHHHHHHHHHccccccHcccHHHHHHHcccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHcc

meldpddvfrdddeesdnefYQEHEATKEYVVYLVDaspkmfsttcpaedqtdetHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRkkknlqdlnAVFVFNVaereqldrptaRFIKEFDHIEESFEKEIgsqygivsgsrENSLYNALWVAQGllrkgssktaDKRILLFtneddpfgsikgaakndmTRTTMQRAKDAQdlgisiellplsppdeefkvsHFYADMIglegddlalfmpsagqklEDMKDQLRKRMFSKRIVKRISFIIANGlsielntyalirptvpgaitwldsvtnhplktersficadtgalmqepakrfqpykgeniKFSVQELSEIKrvstghlrlhgfkplsylkdyhnlrpstfvfpsdkevvgstCIFIALHRSMLRLNRFAVAfygnpsnprLVALVAQDEIVraggqveppgmhmiylpysddirpveelhsdtdavprasdDEVKKAAALMKRidlkdfsvcqfanpslQRHYAVLQALAleeddmpeikdetvpdeegmarpgvVKAVEEFKlsvygdnydeegdvkvSEASRKRKAATENAAKecanydwadladkgklkEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK

meldpddvfrdddeesdnefyqeheatkEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFnvaereqldrptARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLlrkgssktaDKRILLftneddpfgsikgaakndmtRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPStfvfpsdkevVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAggqveppgmHMIYLPYSDDIRPVEELhsdtdavprasdDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDetvpdeegmarpgVVKAVEEFKLsvygdnydeegdvkvseasrKRKAATenaakecanydwadladkGKLKEMTVQELKLYLMahnlsttgrketLISRILTHMGK

MeldpddvfrdddeesdNEFYQEHEATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYDEEGDVKVSEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK

*************************ATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKG****ADKRILLFTN******************************GISIELLPL****EEFKVSHFYADMIGLEGDDLALFMP*************RKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDI************************AALMKRIDLKDFSVCQFANPSLQRHYAVLQALAL***********************VVKAVEEFKLSVYGD**************************ECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRI******

******DVFRDDDEESDNEFYQEHEATKEYVVYLVDASPKM**************HFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKK****DLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEK**********GSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKG*AKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLA*F****GQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSD*DA**RASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDN**********************************LADKGKLKEMTVQELKLYLMAHN****GRKETLISRILTHMG*

*******************FYQEHEATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYDEEG*******************KECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK

***************SDNEFYQEHEATKEYVVYLVDASPKMFSTT**AEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNY*************************CANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		623	2.2.26 [Sep-21-2011]
Q9FQ08		621	ATP-dependent DNA helicas	yes	no	0.993	0.996	0.702	0.0
Q7F1M0		624	ATP-dependent DNA helicas	yes	no	0.996	0.995	0.656	0.0
O93257		632	X-ray repair cross-comple	yes	no	0.892	0.879	0.323	2e-69
P23475		608	X-ray repair cross-comple	yes	no	0.913	0.935	0.315	2e-60
P12956		609	X-ray repair cross-comple	yes	no	0.905	0.926	0.322	1e-59
Q26228		600	ATP-dependent DNA helicas	N/A	no	0.895	0.93	0.288	1e-55
Q2MHH4		655	ATP-dependent DNA helicas	yes	no	0.919	0.874	0.261	2e-47
Q2MHH3		655	ATP-dependent DNA helicas	N/A	no	0.919	0.874	0.263	3e-47
Q7SA95		645	ATP-dependent DNA helicas	N/A	no	0.942	0.910	0.263	1e-46
Q54MA9		909	ATP-dependent DNA helicas	yes	no	0.624	0.427	0.304	2e-45

>sp\|Q9FQ08\|KU70_ARATH ATP-dependent DNA helicase 2 subunit KU70 OS=Arabidopsis thaliana GN=KU70 PE=1 SV=1	Back alignment and function desciption

 Score =  932 bits (2409), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 439/625 (70%), Positives = 533/625 (85%), Gaps = 6/625 (0%)

Query: 1   MELDPDDVFRDDDEESDNEFYQEHEATKEYVVYLVDASPKMFSTTCPAEDQ-TDETHFHI 59
           MELDPDDVFRD+DE+ +N+F+QE EA+KE+VVYL+DASPKMF +TCP+E++   E+HFHI
Sbjct: 1   MELDPDDVFRDEDEDPENDFFQEKEASKEFVVYLIDASPKMFCSTCPSEEEDKQESHFHI 60

Query: 60  AVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIK 119
           AVSCIAQSLK  IINR  DE+AICFFNTR+KKNLQDLN V+VFNV ER+ +DRPTAR IK
Sbjct: 61  AVSCIAQSLKAHIINRSNDEIAICFFNTREKKNLQDLNGVYVFNVPERDSIDRPTARLIK 120

Query: 120 EFDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDP 179
           EFD IEESF+KEIGSQ GIVS SRENSLY+ALWVAQ LLRKGS KTADKR+ LFTNEDDP
Sbjct: 121 EFDLIEESFDKEIGSQTGIVSDSRENSLYSALWVAQALLRKGSLKTADKRMFLFTNEDDP 180

Query: 180 FGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLA 239
           FGS++ + K DMTRTT+QRAKDAQDLGISIELLPLS PD++F ++ FY D+IGL  D+L 
Sbjct: 181 FGSMRISVKEDMTRTTLQRAKDAQDLGISIELLPLSQPDKQFNITLFYKDLIGLNSDELT 240

Query: 240 LFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLD 299
            FMPS GQKLEDMKDQL+KR+ +KRI KRI+F+I +GLSIELN YAL+RP +PG+ITWLD
Sbjct: 241 EFMPSVGQKLEDMKDQLKKRVLAKRIAKRITFVICDGLSIELNGYALLRPAIPGSITWLD 300

Query: 300 SVTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGF 359
           S TN P+K ERS+IC DTGA+MQ+P +R QPYK +NI F+V+ELS++KR+STGHLRL GF
Sbjct: 301 STTNLPVKVERSYICTDTGAIMQDPIQRIQPYKNQNIMFTVEELSQVKRISTGHLRLLGF 360

Query: 360 KPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVA 419
           KPLS LKDYHNL+PSTF++PSDKEV+GST  FIALHRSM++L RFAVAFYG  + PRLVA
Sbjct: 361 KPLSCLKDYHNLKPSTFLYPSDKEVIGSTRAFIALHRSMIQLERFAVAFYGGTTPPRLVA 420

Query: 420 LVAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTD-AVPRASDDEVKKAAALMK 478
           LVAQDEI   GGQVEPPG++MIYLPY++DIR ++ELHS    A PRASDD++KKA+ALM+
Sbjct: 421 LVAQDEIESDGGQVEPPGINMIYLPYANDIRDIDELHSKPGVAAPRASDDQLKKASALMR 480

Query: 479 RIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEF 538
           R++LKDFSVCQFANP+LQRHYA+LQA+AL+E+++ E +DET+PDEEGM RP VVKA+E+F
Sbjct: 481 RLELKDFSVCQFANPALQRHYAILQAIALDENELRETRDETLPDEEGMNRPAVVKAIEQF 540

Query: 539 KLSVYGDNYDEEGDVKVSEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLY 598
           K S+YGD+ DEE D    E S+KRKA   +  K    YD+ +LA  GKLK++TV ELK Y
Sbjct: 541 KQSIYGDDPDEESDSGAKEKSKKRKAGDADDGK----YDYIELAKTGKLKDLTVVELKTY 596

Query: 599 LMAHNLSTTGRKETLISRILTHMGK 623
           L A+NL  +G+KE LI+RILTH+GK
Sbjct: 597 LTANNLLVSGKKEVLINRILTHIGK 621

Single stranded DNA-dependent ATP-dependent helicase. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair. When associated with KU80, binds to double-stranded telomeric and non-telomeric DNA sequences, but not to single-stranded DNA. Plays a role in maintaining telomere length. Acts as a negative regulator of telomerase. Required for maintenance of the telomeric C-rich strand.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp\|Q7F1M0\|KU70_ORYSJ ATP-dependent DNA helicase 2 subunit KU70 OS=Oryza sativa subsp. japonica GN=KU70 PE=1 SV=1	Back alignment and function description

>sp\|O93257\|XRCC6_CHICK X-ray repair cross-complementing protein 5 OS=Gallus gallus GN=XRCC6 PE=2 SV=1	Back alignment and function description

>sp\|P23475\|XRCC6_MOUSE X-ray repair cross-complementing protein 6 OS=Mus musculus GN=Xrcc6 PE=1 SV=5	Back alignment and function description

>sp\|P12956\|XRCC6_HUMAN X-ray repair cross-complementing protein 6 OS=Homo sapiens GN=XRCC6 PE=1 SV=2	Back alignment and function description

>sp\|Q26228\|KU70_RHIAP ATP-dependent DNA helicase 2 subunit 1 OS=Rhipicephalus appendiculatus GN=ku70 PE=2 SV=1	Back alignment and function description

>sp\|Q2MHH4\|KU70_ASPOR ATP-dependent DNA helicase II subunit 1 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=ku70 PE=3 SV=1	Back alignment and function description

>sp\|Q2MHH3\|KU70_ASPSO ATP-dependent DNA helicase II subunit 1 OS=Aspergillus sojae GN=ku70 PE=3 SV=1	Back alignment and function description

>sp\|Q7SA95\|KU70_NEUCR ATP-dependent DNA helicase II subunit 1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=ku70 PE=3 SV=2	Back alignment and function description

>sp\|Q54MA9\|KU70_DICDI ATP-dependent DNA helicase ku70 OS=Dictyostelium discoideum GN=ku70 PE=3 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		623
112982629		627	Ku70 homolog [Populus nigra]	1.0	0.993	0.818	0.0
224116992		628	predicted protein [Populus trichocarpa]	1.0	0.992	0.812	0.0
255561040		626	ku P70 DNA helicase, putative [Ricinus c	0.998	0.993	0.808	0.0
225433705		623	PREDICTED: ATP-dependent DNA helicase 2	0.963	0.963	0.806	0.0
449502267		625	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	1.0	0.996	0.756	0.0
449468754		625	PREDICTED: ATP-dependent DNA helicase 2	1.0	0.996	0.756	0.0
356576925		633	PREDICTED: ATP-dependent DNA helicase 2	0.988	0.973	0.755	0.0
18394425		621	ATP-dependent DNA helicase 2 subunit KU7	0.993	0.996	0.702	0.0
48995221		629	Ku70-like protein [Vigna radiata]	1.0	0.990	0.705	0.0
297850100		623	hypothetical protein ARALYDRAFT_471898 [	0.993	0.993	0.692	0.0

>gi\|112982629\|dbj\|BAF03493.1\| Ku70 homolog [Populus nigra]	Back alignment and taxonomy information

 Score = 1058 bits (2735), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 513/627 (81%), Positives = 570/627 (90%), Gaps = 4/627 (0%)

Query: 1   MELDPDDVFRDDDEESDNEFYQEHEATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIA 60
           MELDPDD+F+DD+++ D+EFYQ+ E++KE+VVYLVDASPKMFS+TCP+ED  +ETHF IA
Sbjct: 1   MELDPDDIFKDDEDDPDSEFYQQRESSKEFVVYLVDASPKMFSSTCPSEDGKEETHFQIA 60

Query: 61  VSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKE 120
           +SCIAQSLKTQIINR YDEVAICFFNTR+KKNLQDLN  FVFNVAERE LDRPTAR IK+
Sbjct: 61  ISCIAQSLKTQIINRSYDEVAICFFNTREKKNLQDLNGAFVFNVAEREYLDRPTARLIKD 120

Query: 121 FDHIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPF 180
           FD IEESF K+IGSQYGIVSGSRENSLYNALW+AQ LLRKGS+KTADKRILLFTNEDDPF
Sbjct: 121 FDCIEESFTKDIGSQYGIVSGSRENSLYNALWIAQALLRKGSAKTADKRILLFTNEDDPF 180

Query: 181 GSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLAL 240
           GSIKG AK DMTRTT+QRAKDAQDLGISIELLPLS PDEEF VS FY+D+IGLEGD+LA 
Sbjct: 181 GSIKGVAKADMTRTTLQRAKDAQDLGISIELLPLSQPDEEFNVSLFYSDLIGLEGDELAQ 240

Query: 241 FMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDS 300
           FMPSAGQKL+DMKDQLRKRMF+KRIV+RI+  IANGLSIELNTYALIRPT+PGAITWLDS
Sbjct: 241 FMPSAGQKLQDMKDQLRKRMFTKRIVRRITLSIANGLSIELNTYALIRPTLPGAITWLDS 300

Query: 301 VTNHPLKTERSFICADTGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFK 360
           VTN PLKTERSFICADTGALMQEPAKR+QPYK +NI  SV+ELSEIKRVS GHL L GFK
Sbjct: 301 VTNRPLKTERSFICADTGALMQEPAKRYQPYKNDNIMLSVEELSEIKRVSMGHLHLLGFK 360

Query: 361 PLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVAL 420
           PLS LKDYHNLRPSTF+FPSDKEV+GSTCIFIAL RSM+ L RFAVAFYG+ S P+LVAL
Sbjct: 361 PLSCLKDYHNLRPSTFIFPSDKEVIGSTCIFIALLRSMVNLKRFAVAFYGSSSRPQLVAL 420

Query: 421 VAQDEIVRAGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDA-VPRASDDEVKKAAALMKR 479
           VAQDEI+ AGGQVEPPGMHMIYLPYSDD+R VEE+HSDT+A  PRA+D+++KKAAAL+KR
Sbjct: 421 VAQDEIISAGGQVEPPGMHMIYLPYSDDVRHVEEIHSDTNAGAPRATDEQIKKAAALIKR 480

Query: 480 IDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFK 539
           IDLKDFSV QFANP LQRHYAVLQALAL+EDDMPEI DET+PDEEGMARPGVVKAVEEFK
Sbjct: 481 IDLKDFSVFQFANPGLQRHYAVLQALALDEDDMPEINDETLPDEEGMARPGVVKAVEEFK 540

Query: 540 LSVYGDNYDEEGDV---KVSEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELK 596
           LSVYG+NYDEE D+   K S+AS+KRK A ENAAKE ANY+W DLAD G+LK++TV ELK
Sbjct: 541 LSVYGENYDEESDMGNGKASDASKKRKTAVENAAKESANYNWPDLADNGQLKDLTVTELK 600

Query: 597 LYLMAHNLSTTGRKETLISRILTHMGK 623
            YL AHNL  TG+KE LISRILTH+GK
Sbjct: 601 YYLTAHNLPVTGKKEVLISRILTHLGK 627

Source: Populus nigra

Species: Populus nigra

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224116992\|ref\|XP_002317447.1\| predicted protein [Populus trichocarpa] gi\|222860512\|gb\|EEE98059.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255561040\|ref\|XP_002521532.1\| ku P70 DNA helicase, putative [Ricinus communis] gi\|223539210\|gb\|EEF40803.1\| ku P70 DNA helicase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225433705\|ref\|XP_002267875.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU70 [Vitis vinifera] gi\|296089629\|emb\|CBI39448.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449502267\|ref\|XP_004161593.1\| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent DNA helicase 2 subunit KU70-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449468754\|ref\|XP_004152086.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU70-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356576925\|ref\|XP_003556580.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU70-like [Glycine max]	Back alignment and taxonomy information

>gi|18394425|ref|NP_564012.1| ATP-dependent DNA helicase 2 subunit KU70 [Arabidopsis thaliana] gi|75309289|sp|Q9FQ08.1|KU70_ARATH RecName: Full=ATP-dependent DNA helicase 2 subunit KU70; AltName: Full=ATP-dependent DNA helicase 2 subunit 1; AltName: Full=ATP-dependent DNA helicase II 70 kDa subunit gi|12006424|gb|AAG44852.1|AF283759_1 Ku70-like protein [Arabidopsis thaliana] gi|62320632|dbj|BAD95294.1| Ku70-like protein [Arabidopsis thaliana] gi|332191406|gb|AEE29527.1| ATP-dependent DNA helicase 2 subunit KU70 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|48995221\|gb\|AAT48365.1\| Ku70-like protein [Vigna radiata]	Back alignment and taxonomy information

>gi\|297850100\|ref\|XP_002892931.1\| hypothetical protein ARALYDRAFT_471898 [Arabidopsis lyrata subsp. lyrata] gi\|297338773\|gb\|EFH69190.1\| hypothetical protein ARALYDRAFT_471898 [Arabidopsis lyrata subsp. lyrata]	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		623
TAIR\|locus:2035495		621	KU70 "KU70 homolog" [Arabidops	0.966	0.969	0.700	5.7e-233
UNIPROTKB\|Q7F1M0		624	KU70 "ATP-dependent DNA helica	0.964	0.963	0.672	8.3e-225
UNIPROTKB\|O93257		632	XRCC6 "X-ray repair cross-comp	0.905	0.892	0.327	2.4e-69
UNIPROTKB\|F1NED5		624	XRCC6 "X-ray repair cross-comp	0.900	0.899	0.333	2.1e-68
ZFIN\|ZDB-GENE-030131-6420		610	xrcc6 "X-ray repair complement	0.911	0.931	0.325	2.1e-68
UNIPROTKB\|F1NII5		620	XRCC6 "X-ray repair cross-comp	0.903	0.908	0.323	7.4e-66
UNIPROTKB\|E9PT85		609	Xrcc6 "Protein Xrcc6" [Rattus	0.913	0.934	0.312	3.2e-65
UNIPROTKB\|Q6AZ64		608	Xrcc6 "X-ray repair complement	0.913	0.935	0.312	3.2e-65
MGI\|MGI:95606		608	Xrcc6 "X-ray repair complement	0.911	0.934	0.320	5.2e-65
RGD\|2643		609	Xrcc6 "X-ray repair complement	0.913	0.934	0.312	1.1e-64

TAIR\|locus:2035495 KU70 "KU70 homolog" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2247 (796.0 bits), Expect = 5.7e-233, P = 5.7e-233
 Identities = 426/608 (70%), Positives = 517/608 (85%)

Query:    18 NEFYQEHEATKEYVVYLVDASPKMFSTTCPAEDQT-DETHFHIAVSCIAQSLKTQIINRL 76
             N+F+QE EA+KE+VVYL+DASPKMF +TCP+E++   E+HFHIAVSCIAQSLK  IINR 
Sbjct:    18 NDFFQEKEASKEFVVYLIDASPKMFCSTCPSEEEDKQESHFHIAVSCIAQSLKAHIINRS 77

Query:    77 YDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEESFEKEIGSQY 136
              DE+AICFFNTR+KKNLQDLN V+VFNV ER+ +DRPTAR IKEFD IEESF+KEIGSQ 
Sbjct:    78 NDEIAICFFNTREKKNLQDLNGVYVFNVPERDSIDRPTARLIKEFDLIEESFDKEIGSQT 137

Query:   137 GIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTM 196
             GIVS SRENSLY+ALWVAQ LLRKGS KTADKR+ LFTNEDDPFGS++ + K DMTRTT+
Sbjct:   138 GIVSDSRENSLYSALWVAQALLRKGSLKTADKRMFLFTNEDDPFGSMRISVKEDMTRTTL 197

Query:   197 QRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQL 256
             QRAKDAQDLGISIELLPLS PD++F ++ FY D+IGL  D+L  FMPS GQKLEDMKDQL
Sbjct:   198 QRAKDAQDLGISIELLPLSQPDKQFNITLFYKDLIGLNSDELTEFMPSVGQKLEDMKDQL 257

Query:   257 RKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICAD 316
             +KR+ +KRI KRI+F+I +GLSIELN YAL+RP +PG+ITWLDS TN P+K ERS+IC D
Sbjct:   258 KKRVLAKRIAKRITFVICDGLSIELNGYALLRPAIPGSITWLDSTTNLPVKVERSYICTD 317

Query:   317 TGALMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTF 376
             TGA+MQ+P +R QPYK +NI F+V+ELS++KR+STGHLRL GFKPLS LKDYHNL+PSTF
Sbjct:   318 TGAIMQDPIQRIQPYKNQNIMFTVEELSQVKRISTGHLRLLGFKPLSCLKDYHNLKPSTF 377

Query:   377 VFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYGNPSNPRLVALVAQDEIVRAGGQVEPP 436
             ++PSDKEV+GST  FIALHRSM++L RFAVAFYG  + PRLVALVAQDEI   GGQVEPP
Sbjct:   378 LYPSDKEVIGSTRAFIALHRSMIQLERFAVAFYGGTTPPRLVALVAQDEIESDGGQVEPP 437

Query:   437 GMHMIYLPYSDDIRPVEELHSDTD-AVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSL 495
             G++MIYLPY++DIR ++ELHS    A PRASDD++KKA+ALM+R++LKDFSVCQFANP+L
Sbjct:   438 GINMIYLPYANDIRDIDELHSKPGVAAPRASDDQLKKASALMRRLELKDFSVCQFANPAL 497

Query:   496 QRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYDEEGDVKV 555
             QRHYA+LQA+AL+E+++ E +DET+PDEEGM RP VVKA+E+FK S+YGD+ DEE D   
Sbjct:   498 QRHYAILQAIALDENELRETRDETLPDEEGMNRPAVVKAIEQFKQSIYGDDPDEESDSGA 557

Query:   556 SEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLIS 615
              E S+KRKA   +  K    YD+ +LA  GKLK++TV ELK YL A+NL  +G+KE LI+
Sbjct:   558 KEKSKKRKAGDADDGK----YDYIELAKTGKLKDLTVVELKTYLTANNLLVSGKKEVLIN 613

Query:   616 RILTHMGK 623
             RILTH+GK
Sbjct:   614 RILTHIGK 621

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0005958 "DNA-dependent protein kinase-DNA ligase 4 complex" evidence=IEA

GO:0006303 "double-strand break repair via nonhomologous end joining" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0000723 "telomere maintenance" evidence=TAS

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0006281 "DNA repair" evidence=TAS

GO:0009408 "response to heat" evidence=IEP

UNIPROTKB\|Q7F1M0 KU70 "ATP-dependent DNA helicase 2 subunit KU70" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

UNIPROTKB\|O93257 XRCC6 "X-ray repair cross-complementing protein 5" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NED5 XRCC6 "X-ray repair cross-complementing protein 5" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-6420 xrcc6 "X-ray repair complementing defective repair in Chinese hamster cells 6" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NII5 XRCC6 "X-ray repair cross-complementing protein 5" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E9PT85 Xrcc6 "Protein Xrcc6" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q6AZ64 Xrcc6 "X-ray repair complementing defective repair in Chinese hamster cells 6, isoform CRA_a" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:95606 Xrcc6 "X-ray repair complementing defective repair in Chinese hamster cells 6" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|2643 Xrcc6 "X-ray repair complementing defective repair in Chinese hamster cells 6" [Rattus norvegicus (taxid:10116)]	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)
P23475	XRCC6_MOUSE	4, ., 2, ., 9, 9, ., -	0.3151	0.9133	0.9358	yes	no
O93257	XRCC6_CHICK	4, ., 2, ., 9, 9, ., -	0.3239	0.8924	0.8797	yes	no
Q9FQ08	KU70_ARATH	3, ., 6, ., 4, ., 1, 2	0.7024	0.9935	0.9967	yes	no
P12956	XRCC6_HUMAN	4, ., 2, ., 9, 9, ., -	0.3228	0.9052	0.9261	yes	no
Q7F1M0	KU70_ORYSJ	3, ., 6, ., 4, ., 1, 2	0.6565	0.9967	0.9951	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.12	0.979
3rd Layer	3.6.4	0.983

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		623
TIGR00578		584	TIGR00578, ku70, ATP-dependent DNA helicase II, 70	3e-96
cd00788		287	cd00788, KU70, Ku-core domain, Ku70 subfamily; Ku7	2e-84
cd00594		272	cd00594, KU, Ku-core domain; includes the central	1e-56
cd01458		218	cd01458, vWA_ku, Ku70/Ku80 N-terminal domain	9e-48
pfam02735		200	pfam02735, Ku, Ku70/Ku80 beta-barrel domain	5e-45
pfam03731		221	pfam03731, Ku_N, Ku70/Ku80 N-terminal alpha/beta d	4e-44
smart00559		140	smart00559, Ku78, Ku70 and Ku80 are 70kDa and 80kD	4e-34
pfam03730		95	pfam03730, Ku_C, Ku70/Ku80 C-terminal arm	4e-13
pfam02037		35	pfam02037, SAP, SAP domain	2e-07
smart00513		35	smart00513, SAP, Putative DNA-binding (bihelical)	2e-05
cd00873		300	cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku8	1e-04

>gnl\|CDD\|129668 TIGR00578, ku70, ATP-dependent DNA helicase II, 70 kDa subunit (ku70)	Back alignment and domain information

 Score =  306 bits (785), Expect = 3e-96
 Identities = 201/602 (33%), Positives = 308/602 (51%), Gaps = 42/602 (6%)

Query: 31  VVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKK 90
           +++LVDAS  MF     ++ + + T F +++ CI     ++II+   D +A+ F+ T K 
Sbjct: 13  LIFLVDASKAMFE---ESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKD 69

Query: 91  KNLQDLNAVFVFNVAEREQLDRPTARFIKEFDH-IEESFEKEIGSQYGIVSGSRENSLYN 149
           KN  +   ++V      ++LD P A+ I E D    +   K+    YG   GS + SL  
Sbjct: 70  KNSVNFKNIYVL-----QELDNPGAKRILELDQFKGDQGPKKFRDTYG--HGS-DYSLSE 121

Query: 150 ALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISI 209
            LWV   L      + + KRI+LFTNED+P G    +AK    RT   +A D +D GI +
Sbjct: 122 VLWVCANLFSDVQFRMSHKRIMLFTNEDNPHG--NDSAKASRART---KAGDLRDTGIFL 176

Query: 210 ELLPLSPPDEEFKVSHFYADMIGL-EGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKR 268
           +L+ L  P   F +S FY D+I   E +DL +  P    KLED+  ++R +   KR + R
Sbjct: 177 DLMHLKKPGG-FDISLFYRDIITDAEDEDLGVH-PEESSKLEDLLRKVRAKETRKRALSR 234

Query: 269 ISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTG-ALMQEPAKR 327
           +   +   + + +  Y L++     A   L   TN P+KT+      DTG  L+    KR
Sbjct: 235 LKLKLNKDVVMSVGIYNLVQKAGKPAPVKLYRETNEPVKTKTRTFNMDTGSLLLPSDTKR 294

Query: 328 FQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGS 387
            Q Y G  I    +E  E+KR     L+L GFKPLS LK +H+LRPS FV+P +  V GS
Sbjct: 295 SQTYGGRQIYLEKEETEELKRFDPPGLQLMGFKPLSMLKKHHHLRPSLFVYPEESLVRGS 354

Query: 388 TCIFIALHRSMLRLNRFAVAFYGNPSN--PRLVALVAQDEIVRAGG-QVEPPGMHMIYLP 444
           T +F AL +  L     A+  Y +  N  P  VALV Q+E +     QV PPG H+++LP
Sbjct: 355 TTLFSALLQKCLEKEVAALCRYISRRNQPPYFVALVPQEEELDDQKIQVTPPGFHLVFLP 414

Query: 445 YSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQA 504
           ++DD R V            A+ ++V K  A+++++    +    F NP LQ+H+  L+A
Sbjct: 415 FADDKRKVPFTEKVK-----ATPEQVDKMKAIVEKLRFT-YRSDSFENPVLQQHFRNLEA 468

Query: 505 LALEEDDMPEIKDETVPDEEGM-ARPGVVKAVEEFKLSVYGDNYDEEGDV----KVSEAS 559
           LAL+  +  +  D T+P  E M  R G    V+EFK  VY  +Y+ EG V    +  E S
Sbjct: 469 LALDMMEPEQAVDLTLPKVEAMKKRLG--SLVDEFKELVYPPDYNPEGKVAKRKQAGEGS 526

Query: 560 RKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILT 619
           + ++   EN+ +E   +     A KG L ++TV  LK +  A+ L +  +K+ L+  +  
Sbjct: 527 QSKRPKVENSEEELREH-----AKKGTLGKLTVSVLKDFCRAYGLRSGSKKQELLDALTK 581

Query: 620 HM 621
           H 
Sbjct: 582 HF 583

Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast [DNA metabolism, DNA replication, recombination, and repair]. Length = 584

>gnl\|CDD\|238407 cd00788, KU70, Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination	Back alignment and domain information

>gnl\|CDD\|238334 cd00594, KU, Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins	Back alignment and domain information

>gnl\|CDD\|238735 cd01458, vWA_ku, Ku70/Ku80 N-terminal domain	Back alignment and domain information

>gnl\|CDD\|217209 pfam02735, Ku, Ku70/Ku80 beta-barrel domain	Back alignment and domain information

>gnl\|CDD\|217700 pfam03731, Ku_N, Ku70/Ku80 N-terminal alpha/beta domain	Back alignment and domain information

>gnl\|CDD\|128831 smart00559, Ku78, Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen	Back alignment and domain information

>gnl\|CDD\|190729 pfam03730, Ku_C, Ku70/Ku80 C-terminal arm	Back alignment and domain information

>gnl\|CDD\|202100 pfam02037, SAP, SAP domain	Back alignment and domain information

>gnl\|CDD\|128789 smart00513, SAP, Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation	Back alignment and domain information

>gnl\|CDD\|238445 cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		623
TIGR00578		584	ku70 ATP-dependent DNA helicase ii, 70 kDa subunit	100.0
KOG2327		602	consensus DNA-binding subunit of a DNA-dependent p	100.0
cd00788		287	KU70 Ku-core domain, Ku70 subfamily; Ku70 is a sub	100.0
cd00594		272	KU Ku-core domain; includes the central DNA-bindin	100.0
cd00873		300	KU80 Ku-core domain, Ku80 subfamily; Ku80 is a sub	100.0
TIGR02772		258	Ku_bact Ku protein, prokaryotic. Members of this p	100.0
cd00789		256	KU_like Ku-core domain, Ku-like subfamily; compose	100.0
KOG2326		669	consensus DNA-binding subunit of a DNA-dependent p	100.0
PF02735		200	Ku: Ku70/Ku80 beta-barrel domain; InterPro: IPR006	100.0
PF03731		224	Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; Inte	100.0
COG1273		278	Ku-homolog [Replication, recombination, and repair	100.0
cd01458		218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	100.0
smart00559		140	Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of	100.0
PF03730		96	Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR00516	99.39
PF02037		35	SAP: SAP domain; InterPro: IPR003034 The SAP (afte	98.88
cd01452		187	VWA_26S_proteasome_subunit 26S proteasome plays a	98.84
smart00513		35	SAP Putative DNA-binding (bihelical) motif predict	98.65
cd01453		183	vWA_transcription_factor_IIH_type Transcription fa	98.55
cd01471		186	vWA_micronemal_protein Micronemal proteins: The To	98.53
cd01480		186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	98.35
cd01473		192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	98.3
cd01465		170	vWA_subgroup VWA subgroup: Von Willebrand factor t	98.23
PRK13685		326	hypothetical protein; Provisional	98.22
cd00198		161	vWFA Von Willebrand factor type A (vWA) domain was	98.21
cd01454		174	vWA_norD_type norD type: Denitrifying bacteria con	98.2
cd01472		164	vWA_collagen von Willebrand factor (vWF) type A do	98.17
cd01477		193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	98.16
cd01451		178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	98.14
cd01482		164	vWA_collagen_alphaI-XII-like Collagen: The extrace	98.14
PF13519		172	VWA_2: von Willebrand factor type A domain; PDB: 3	98.12
cd01474		185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	98.1
cd01467		180	vWA_BatA_type VWA BatA type: Von Willebrand factor	98.08
cd01456		206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	98.07
cd01469		177	vWA_integrins_alpha_subunit Integrins are a class	98.06
cd01470		198	vWA_complement_factors Complement factors B and C2	98.04
cd01450		161	vWFA_subfamily_ECM Von Willebrand factor type A (v	98.04
cd01476		163	VWA_integrin_invertebrates VWA_integrin (invertebr	97.95
cd01466		155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	97.94
cd01464		176	vWA_subfamily VWA subfamily: Von Willebrand factor	97.91
smart00327		177	VWA von Willebrand factor (vWF) type A domain. VWA	97.87
PRK13406		584	bchD magnesium chelatase subunit D; Provisional	97.82
cd01460		266	vWA_midasin VWA_Midasin: Midasin is a member of th	97.8
cd01462		152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	97.78
cd01463		190	vWA_VGCC_like VWA Voltage gated Calcium channel li	97.77
TIGR00868		863	hCaCC calcium-activated chloride channel protein 1	97.76
PTZ00441		576	sporozoite surface protein 2 (SSP2); Provisional	97.74
cd01461		171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	97.64
COG5148		243	RPN10 26S proteasome regulatory complex, subunit R	97.64
PF12949		35	HeH: HeH/LEM domain; PDB: 2OUT_A.	97.63
TIGR02031		589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.59
PF13768		155	VWA_3: von Willebrand factor type A domain	97.57
cd01475		224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	97.52
TIGR03436		296	acidobact_VWFA VWFA-related Acidobacterial domain.	97.48
PF00092		178	VWA: von Willebrand factor type A domain; InterPro	97.41
cd01481		165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	97.4
COG1240		261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	97.39
PF04056		193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	97.35
TIGR02442		633	Cob-chelat-sub cobaltochelatase subunit. A number	97.32
KOG2884		259	consensus 26S proteasome regulatory complex, subun	97.27
cd01457		199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	97.24
cd01455		191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	97.24
TIGR03788		596	marine_srt_targ marine proteobacterial sortase tar	97.2
PF12257		281	DUF3608: Protein of unknown function (DUF3608); In	96.78
PF07498		43	Rho_N: Rho termination factor, N-terminal domain;	96.11
PRK10997		487	yieM hypothetical protein; Provisional	96.08
cd01468		239	trunk_domain trunk domain. COPII-coated vesicles c	95.81
KOG1984		1007	consensus Vesicle coat complex COPII, subunit SFB3	95.51
cd01479		244	Sec24-like Sec24-like: Protein and membrane traffi	94.85
PF10281		38	Ish1: Putative stress-responsive nuclear envelope	94.7
COG4867		652	Uncharacterized protein with a von Willebrand fact	94.67
PF11265		226	Med25_VWA: Mediator complex subunit 25 von Willebr	92.96
PTZ00395		1560	Sec24-related protein; Provisional	92.04
PF04811		243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	91.62
KOG2807		378	consensus RNA polymerase II transcription initiati	91.6
PF10208		154	Armet: Degradation arginine-rich protein for mis-f	91.23
COG4245		207	TerY Uncharacterized protein encoded in toxicity p	90.72
TIGR00627		279	tfb4 transcription factor tfb4. This family is bas	90.18
KOG2487		314	consensus RNA polymerase II transcription initiati	86.84
KOG2326		669	consensus DNA-binding subunit of a DNA-dependent p	86.75
PF05762		222	VWA_CoxE: VWA domain containing CoxE-like protein;	86.56
PF11775		219	CobT_C: Cobalamin biosynthesis protein CobT VWA do	84.29
COG5028		861	Vesicle coat complex COPII, subunit SEC24/subunit	84.15
PRK14537		230	50S ribosomal protein L20/unknown domain fusion pr	83.07
cd01478		267	Sec23-like Sec23-like: Protein and membrane traffi	80.32

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

Probab=100.00  E-value=6.4e-122  Score=1028.16  Aligned_cols=572  Identities=33%  Similarity=0.528  Sum_probs=513.7

Q ss_pred             hhc-ccceEEEEEEECCccccCCCCCCCCCCCCCHHHHHHHHHHHHHHhhhhccCCCeEEEEEEecCCCCCCCCCCcEEE
Q 006975           23 EHE-ATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFV  101 (623)
Q Consensus        23 ~~~-~~ke~iiflIDvs~sM~~~~~~~~~~~~~s~~~~al~~i~~~~~~kIi~~~~D~vgivl~gt~~t~n~~~~~~i~~  101 (623)
                      +|+ .+|||||||||||++||.+.+.   ++..|+|++|++||+++||+|||++|+|+||||||||++|+|+.+|+|||+
T Consensus         4 ~~~~~~keailflIDvs~sM~~~~~~---~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t~n~~~~~~i~v   80 (584)
T TIGR00578         4 DYKYSGRDSLIFLVDASKAMFEESQG---EDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNSVNFKNIYV   80 (584)
T ss_pred             cccccceeEEEEEEECCHHHcCCCcC---cCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCCCCccCCCceEE
Confidence            454 6899999999999999997652   346899999999999999999999999999999999999999999999999


Q ss_pred             ecccccccCCCCChHHHHHHHHHHHh-HhhhhcccccccCCCCCCCHHHHHHHHHHHHhcCCCCCCCcEEEEEeCCCCCC
Q 006975          102 FNVAEREQLDRPTARFIKEFDHIEES-FEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPF  180 (623)
Q Consensus       102 l~~~~~~~l~~p~~~~ik~L~~l~~~-~~~~~~~~~~~~~~~~~~~l~daL~~a~~~f~~~~~~~~~krI~l~Tn~d~P~  180 (623)
                      +     ++|+.|+++.|++|++|.++ ....+...+|+   ...++|++|||+|++||+++++++++||||||||+|+||
T Consensus        81 ~-----~~L~~p~a~~i~~L~~l~~~~~~~~~~~~~~~---~~~~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~  152 (584)
T TIGR00578        81 L-----QELDNPGAKRILELDQFKGDQGPKKFRDTYGH---GSDYSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPH  152 (584)
T ss_pred             E-----eeCCCCCHHHHHHHHHHhhccCccchhhccCC---CCCCcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCC
Confidence            9     99999999999999999876 23345456665   345799999999999999887899999999999999999


Q ss_pred             CCCccCcchhhHHHHHHHHHHhHhcCceEEEeeCCCCCCCCcccchhhhhcccCCccccccCCCccccHHHHHHHHHhhh
Q 006975          181 GSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFMPSAGQKLEDMKDQLRKRM  260 (623)
Q Consensus       181 ~~~~~~~d~~~~~~~~~~a~dL~~~gI~i~l~~i~~~~~~Fd~~~fy~~i~~~~~~~~~~~~~~~~~~~~~L~~~i~~k~  260 (623)
                      .+     +....++|.++|+||+++||+|++|+|+.+++ ||.++||++|+...+++..+..+...+.+++|++++++|+
T Consensus       153 ~~-----~~~~~~~a~~~a~dl~~~gi~ielf~l~~~~~-Fd~s~Fy~dii~~~~~~~~~~~~~~~~~l~~l~~~l~~k~  226 (584)
T TIGR00578       153 GN-----DSAKASRARTKAGDLRDTGIFLDLMHLKKPGG-FDISLFYRDIITDAEDEDLGVHPEESSKLEDLLRKVRAKE  226 (584)
T ss_pred             CC-----chhHHHHHHHHHHHHHhcCeEEEEEecCCCCC-CChhhhhHhhhccccccccccCcchhHHHHHHHHHHhhcc
Confidence            98     56677888999999999999999999999876 9999999999976554433444555567999999999999


Q ss_pred             hcceeeeeeeEEecCCceEEEEEeeeecccCCCcEeEecCCCCCCceeeeEEeeCCcCccc-cccceeeEecCCeeeecC
Q 006975          261 FSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALM-QEPAKRFQPYKGENIKFS  339 (623)
Q Consensus       261 ~~kR~~~~~~l~lg~~~~I~V~~Y~~~~~~~~~~~~~~~~~~~~~vk~~t~~~~~dt~~~~-~~~~~k~y~yG~~~V~~~  339 (623)
                      +++|++++++|+||++++|+|++|.+++++++++++|++++++++|+++|+|+|.+||+++ +++++|||+|||++|+|+
T Consensus       227 ~~kR~~~~~~L~lg~~~~I~V~~Y~~~~~~~~~~~~~l~~~~~~~v~~~~~~~~~dtg~~V~~~~i~Kgy~yGg~~V~~t  306 (584)
T TIGR00578       227 TRKRALSRLKLKLNKDVVMSVGIYNLVQKAGKPAPVKLYRETNEPVKTKTRTFNMDTGSLLLPSDTKRSQTYGGRQIYLE  306 (584)
T ss_pred             cceeeEEeccEEECCCCEEEEEEEEEEEeecCCceEEEecCCceeeEEEEEEEecCCccccCHHHceeeeeECCEEEecC
Confidence            9999999999999999999999999999999899999999999999999999999999855 589999999999999999


Q ss_pred             HHHHHHhhccCCCcEEEEeeecCCCCCcccccCCcEEEecCCCCCcCcHHHHHHHHHHHHhcCcEEEEEe--cCCCCceE
Q 006975          340 VQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFY--GNPSNPRL  417 (623)
Q Consensus       340 ~ee~~~ik~~~~~~l~llGF~~~~~i~~~~~~~~s~fi~Pd~~~~~gS~~~fsaL~~am~~~~kvaI~r~--r~~s~P~l  417 (623)
                      ++|+++|+.+++|+|+||||+|+++|++||++++|+||+|++..+.||+++|+||+++|++++|||||||  |+|+.|+|
T Consensus       307 ~ee~~~lk~~~~~~l~ilGF~~~s~l~~~~~~~~s~fi~Pde~~~~gs~~afsaL~~~l~~~~kvAI~~~v~r~~~~P~l  386 (584)
T TIGR00578       307 KEETEELKRFDPPGLQLMGFKPLSMLKKHHHLRPSLFVYPEESLVRGSTTLFSALLQKCLEKEVAALCRYISRRNQPPYF  386 (584)
T ss_pred             HHHHHHHhccCCCceEEEeeccHHHCCchhhcCCceEEecCCcccccHHHHHHHHHHHHHhcCcEEEEEEEecCCCCCEE
Confidence            9999999999999999999999999999999999999999999889999999999999999999999999  99999999


Q ss_pred             EEEEeehhhccc-CCCCCCCcEEEEecCCccCCCCCccCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCCCCCCChhHH
Q 006975          418 VALVAQDEIVRA-GGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQ  496 (623)
Q Consensus       418 vaL~P~~~~~~~-~~q~~p~g~~li~LPfadDiR~~~~~~~~~~~~~~~~~eq~~~a~~lI~~l~l~~y~p~~~~NP~lq  496 (623)
                      |||+|+.+..++ +.|..|+|||+++|||+||||++++..     ...++++|+++|++||++|+++ |+|+.|+||+||
T Consensus       387 vaL~P~~~~~d~~~~q~~p~G~~l~~LPfadDIR~~~~~~-----~~~~~~e~~~~a~~LI~~l~~~-y~P~~~~NP~LQ  460 (584)
T TIGR00578       387 VALVPQEEELDDQKIQVTPPGFHLVFLPFADDKRKVPFTE-----KVKATPEQVDKMKAIVEKLRFT-YRSDSFENPVLQ  460 (584)
T ss_pred             EEEeCCcccccccCCccCCCeEEEEecCchhhccCCCCcc-----cCCCCHHHHHHHHHHHHhcCCC-CCcccCCChHHH
Confidence            999999887776 458899999999999999999988642     3579999999999999999997 999999999999


Q ss_pred             HHHHHHHHhhcCcCCCCCCCCCCCCChhhhccccchHHHHHHHHhhcCCCCCCcccc-ccchh--hhchhhhhhhhhhcc
Q 006975          497 RHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYDEEGDV-KVSEA--SRKRKAATENAAKEC  573 (623)
Q Consensus       497 ~~y~~lea~Al~~~~~~~~~D~t~P~~~~i~~~~~~~~i~~fk~~~~~~~~~~~~~~-~~~~~--~~k~~~~~~~~~~~~  573 (623)
                      |||++|+|+||+++.|+++.|.|+|++++|++|++ +.+++|++.+++..+++.... +++.+  ++.+++    +..+.
T Consensus       461 ~hY~~LealAL~~~~~~~~~D~tlp~~~~i~~r~~-~~i~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~k~----~~~~~  535 (584)
T TIGR00578       461 QHFRNLEALALDMMEPEQAVDLTLPKVEAMKKRLG-SLVDEFKELVYPPDYNPEGKVAKRKQAGEGSQSKR----PKVEN  535 (584)
T ss_pred             HHHHHHHHHhCCCCCCCCCcccccCCHHHHHHHHH-HHHHHHHHHhcccccCcccccccccCCCCCccccc----CCCCc
Confidence            99999999999999999999999999999999998 899999999998878776532 22111  111111    11124


Q ss_pred             chHHHHHHHHcCCcccccHHHHHHHHHHcCCCCCCChHHHHHHHHHhhc
Q 006975          574 ANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMG  622 (623)
Q Consensus       574 ~~~~~~~~~~~g~l~kltv~~LK~~l~~~~~~~~gkK~dLi~~i~~~l~  622 (623)
                      +..+|+.+|++|+|+||||+|||+||+++|++++||||||||||++||+
T Consensus       536 ~~~~~~~~~~~~~l~kltv~~Lk~~l~~~g~~~~~kKadLi~~i~~~~~  584 (584)
T TIGR00578       536 SEEELREHAKKGTLGKLTVSVLKDFCRAYGLRSGSKKQELLDALTKHFK  584 (584)
T ss_pred             CHHHHHHHHHcCChhhccHHHHHHHHHHcCCCccccHHHHHHHHHHHhC
Confidence            5778999999999999999999999999999999999999999999985

>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]	Back alignment and domain information

>cd00788 KU70 Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination	Back alignment and domain information

>cd00594 KU Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins	Back alignment and domain information

>cd00873 KU80 Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination	Back alignment and domain information

>TIGR02772 Ku_bact Ku protein, prokaryotic	Back alignment and domain information

>cd00789 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku	Back alignment and domain information

>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]	Back alignment and domain information

>PF02735 Ku: Ku70/Ku80 beta-barrel domain; InterPro: IPR006164 The Ku heterodimer is composed of Ku70 and Ku80 (or Ku86), 70 kDa and 80 kDa subunits of an ATP-dependent DNA helicase, which contributes to genomic integrity through its ability to bind DNA double-stranded breaks and facilitate repair by the non-homologous end-joining pathway	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

>COG1273 Ku-homolog [Replication, recombination, and repair]	Back alignment and domain information

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

>smart00559 Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen	Back alignment and domain information

>PF03730 Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR005160 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

>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []	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

>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation	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

>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell	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

>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

>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

>PRK13685 hypothetical protein; Provisional	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

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

>cd01477 vWA_F09G8-8_type VWA F09G8	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

>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

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

>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

>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

>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

>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation	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

>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

>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

>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

>smart00327 VWA von Willebrand factor (vWF) type A domain	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

>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

>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

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

>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional	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

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

>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A	Back alignment and domain information

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

>PF13768 VWA_3: von Willebrand factor type A domain	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

>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain	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

>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

>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]	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

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

>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]	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

>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

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

>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length	Back alignment and domain information

>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts	Back alignment and domain information

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

>cd01468 trunk_domain trunk domain	Back alignment and domain information

>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]	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

>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues []	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

>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

>PTZ00395 Sec24-related protein; Provisional	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

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]	Back alignment and domain information

>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein)	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

>TIGR00627 tfb4 transcription factor tfb4	Back alignment and domain information

>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]	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

>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain	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

>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional	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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		623
1jeq_A		609	Crystal Structure Of The Ku Heterodimer Length = 60		4e-61

>pdb|1JEQ|A Chain A, Crystal Structure Of The Ku Heterodimer Length = 609

Back alignment and structure

Iteration: 1

Score = 232 bits (592), Expect = 4e-61, Method: Compositional matrix adjust. Identities = 196/607 (32%), Positives = 309/607 (50%), Gaps = 43/607 (7%) Query: 26 ATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFF 85 + ++ +++LVDAS MF + +ED+ T F +++ CI ++II+ D +A+ F+ Sbjct: 33 SGRDSLIFLVDASKAMFESQ--SEDEL--TPFDMSIQCIQSVYISKIISSDRDLLAVVFY 88 Query: 86 NTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIE-ESFEKEIGSQYGIVSGSRE 144 T K KN + ++V ++LD P A+ I E D + + +K G GS + Sbjct: 89 GTEKDKNSVNFKNIYVL-----QELDNPGAKRILELDQFKGQQGQKRFQDMMG--HGS-D 140 Query: 145 NSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQD 204 SL LWV L K + KRI+LFTNED+P G+ +AK RT +A D +D Sbjct: 141 YSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGN--DSAKASRART---KAGDLRD 195 Query: 205 LGISIELLPLSPPDEEFKVSHFYADMIGL-EGDDLALFMPSAGQKLEDMKDQLRKRMFSK 263 GI ++L+ L P F +S FY D+I + E +DL + + KLED+ ++R + K Sbjct: 196 TGIFLDLMHLKKPGG-FDISLFYRDIISIAEDEDLRVHFEESS-KLEDLLRKVRAKETRK 253 Query: 264 RIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTE-RSFICADTGALMQ 322 R + R+ + + I + Y L++ + L TN P+KT+ R+F + G L+ Sbjct: 254 RALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLP 313 Query: 323 EPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDK 382 KR Q Y I +E E+KR L L GFKPL LK +H LRPS FV+P + Sbjct: 314 SDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEES 373 Query: 383 EVVGSTCIFIALHRSMLRLNRFAVAFYGNPSN--PRLVALVAQ-DEIVRAGGQVEPPGMH 439 V+GS+ +F AL L A+ Y N P VALV Q +E+ QV PPG Sbjct: 374 LVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQ 433 Query: 440 MIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHY 499 +++LP++DD R + T+ + A+ ++V K A+++++ + F NP LQ+H+ Sbjct: 434 LVFLPFADDKRKM----PFTEKI-MATPEQVGKMKAIVEKLRFT-YRSDSFENPVLQQHF 487 Query: 500 AVLQALALEEDDMPEIKDETVPDEEGM-ARPGVVKAVEEFKLSVYGDNYDEEGDVKV--- 555 L+ALAL+ + + D T+P E M R G + V+EFK VY +Y+ EG V Sbjct: 488 RNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSL--VDEFKELVYPPDYNPEGKVTKRKH 545 Query: 556 -SEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLI 614 +E S ++ E + +E + KG L + TV LK A+ L + +K+ L+ Sbjct: 546 DNEGSGSKRPKVEYSEEELKTH-----ISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL 600 Query: 615 SRILTHM 621 + H Sbjct: 601 EALTKHF 607

PyMOL of 1jeq

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		623
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	1e-120
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	4e-68
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-11
1jjr_A		151	KU70, thyroid autoantigen; DNA repair protein, pro	4e-07
2kvu_A		75	MKL/myocardin-like protein 1; SAP motif, DNA/RNA b	3e-04

>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 Length = 609	Back alignment and structure

 Score =  369 bits (947), Expect = e-120
 Identities = 178/623 (28%), Positives = 294/623 (47%), Gaps = 30/623 (4%)

Query: 4   DPDDVFRDDDEESDNEFYQEH-EATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVS 62
              D   ++++E + E   ++  + ++ +++LVDAS  MF +    + + + T F +++ 
Sbjct: 10  TEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFES----QSEDELTPFDMSIQ 65

Query: 63  CIAQSLKTQIINRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFD 122
           CI     ++II+   D +A+ F+ T K KN  +   ++V       +LD P A+ I E D
Sbjct: 66  CIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQ-----ELDNPGAKRILELD 120

Query: 123 HIEESFEKEIGSQYGIVSGSRENSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGS 182
             +    ++      ++    + SL   LWV   L      K + KRI+LFTNED+P G+
Sbjct: 121 QFKGQQGQK--RFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGN 178

Query: 183 IKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIGLEGDDLALFM 242
                 +        +A D +D GI ++L+ L  P   F +S FY D+I +  D+     
Sbjct: 179 -----DSAKASRARTKAGDLRDTGIFLDLMHLKKPGG-FDISLFYRDIISIAEDEDLRVH 232

Query: 243 PSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVT 302
                KLED+  ++R +   KR + R+   +   + I +  Y L++  +      L   T
Sbjct: 233 FEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRET 292

Query: 303 NHPLKTERSFICADTGA-LMQEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKP 361
           N P+KT+       TG  L+    KR Q Y    I    +E  E+KR     L L GFKP
Sbjct: 293 NEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKP 352

Query: 362 LSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFYG--NPSNPRLVA 419
           L  LK +H LRPS FV+P +  V+GS+ +F AL    L     A+  Y       P  VA
Sbjct: 353 LVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVA 412

Query: 420 LVAQDEIVR-AGGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMK 478
           LV Q+E +     QV PPG  +++LP++DD R +            A+ ++V K  A+++
Sbjct: 413 LVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEK-----IMATPEQVGKMKAIVE 467

Query: 479 RIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEF 538
           ++    +    F NP LQ+H+  L+ALAL+  +  +  D T+P  E M +  +   V+EF
Sbjct: 468 KLRF-TYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKR-LGSLVDEF 525

Query: 539 KLSVYGDNYDEEGDVKVSEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLY 598
           K  VY  +Y+ EG            + ++    E +  +      KG L + TV  LK  
Sbjct: 526 KELVYPPDYNPEGK-VTKRKHDNEGSGSKRPKVEYSEEELKTHISKGTLGKFTVPMLKEA 584

Query: 599 LMAHNLSTTGRKETLISRILTHM 621
             A+ L +  +K+ L+  +  H 
Sbjct: 585 CRAYGLKSGLKKQELLEALTKHF 607

PyMOL of 1jey

>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* Length = 565	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2kvu_A MKL/myocardin-like protein 1; SAP motif, DNA/RNA binding, structural genomics, northeast structural genomics consortium (NESG), PSI-2; NMR {Homo sapiens} PDB: 2kw9_A Length = 75	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		623
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	100.0
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	100.0
1jjr_A		151	KU70, thyroid autoantigen; DNA repair protein, pro	99.31
1jjr_A		151	KU70, thyroid autoantigen; DNA repair protein, pro	99.03
4b4t_W		268	RPN10, 26S proteasome regulatory subunit RPN10; hy	98.98
2x5n_A		192	SPRPN10, 26S proteasome regulatory subunit RPN10;	98.86
2do1_A		55	Nuclear protein HCC-1; SAP domain, structural geno	98.83
1zrj_A		50	E1B-55KDA-associated protein 5 isoform C; SAP doma	98.77
1h1j_S		51	THO1 protein; SAP domain, DNA binding; NMR {Saccha	98.77
2rnn_A		114	E3 SUMO-protein ligase SIZ1; SUMO ligase, DNA bind	98.76
2kvu_A		75	MKL/myocardin-like protein 1; SAP motif, DNA/RNA b	98.71
1q0p_A		223	Complement factor B; VON willebrand factor, MAC-1,	98.31
3ibs_A		218	Conserved hypothetical protein BATB; structural ge	98.31
4hqo_A		266	Sporozoite surface protein 2; malaria, gliding mot	98.24
1ijb_A		202	VON willebrand factor; dinucleotide-binding fold,	98.19
2xgg_A		178	Microneme protein 2; A/I domain, cell adhesion, hy	98.17
4hqf_A		281	Thrombospondin-related anonymous protein, trap; ma	98.13
1shu_X		182	Anthrax toxin receptor 2; alpha/beta rossmann fold	98.07
4fx5_A		464	VON willebrand factor type A; structural genomics,	98.03
1v7p_C		200	Integrin alpha-2; snake venom, C-type lectin, anta	98.02
1atz_A		189	VON willebrand factor; collagen-binding, hemostasi	98.0
1rrk_A		497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	98.0
2odp_A		509	Complement C2; C3/C5 convertase, complement serin	97.96
3n2n_F		185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	97.95
1pt6_A		213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	97.95
3hrz_D		741	Complement factor B; serine protease, glycosilated	97.9
2b2x_A		223	Integrin alpha-1; computational design, antibody-a	97.89
2x31_A		189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	97.71
1n3y_A		198	Integrin alpha-X; alpha/beta rossmann fold, cell a	97.64
1mf7_A		194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	97.41
3zqk_A		199	VON willebrand factor; blood clotting, adamts-13,	97.26
1mjn_A		179	Integrin alpha-L; rossmann fold, immune system; 1.	96.86
2ww8_A		893	RRGA, cell WALL surface anchor family protein; IGG	96.86
3k6s_A		1095	Integrin alpha-X; cell receptor, adhesion molecule	96.2
2rno_A		110	Putative DNA-binding protein; SUMO ligase, sumoyla	96.16
3rag_A		242	Uncharacterized protein; structural genomics, PSI-	95.44
1yvr_A		538	RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein,	95.14
2out_A		131	MU-like prophage flumu protein GP35, protein HI150	94.6
2nvo_A		535	RO sixty-related protein, RSR; alpha helical repea	94.57
2iue_A		212	Pactolus I-domain; membrane protein, CD, ITC, limb	93.79
2jx3_A		131	Protein DEK; alpha helix, SAF/SAP motif, DNA bindi	93.32
1v66_A		65	Protein inhibitor of activated STAT protein 1; fou	93.17
3fcs_B		690	Integrin beta-3; beta propeller, rossmann fold, EG	92.05
1y02_A		120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	89.57
2ld7_A		94	Histone deacetylase complex subunit SAP30; transcr	87.41
3skq_A		249	Mitochondrial distribution and morphology protein;	87.05
3t3p_B		472	Integrin beta-3; integrin, cell adhesion, blood cl	86.83
1m2o_A		768	SEC23, protein transport protein SEC23, SEC23P; zi	85.67
2nut_A		769	Protein transport protein SEC23A; human copii SEC2	85.61
2do5_A		58	Splicing factor 3B subunit 2; SAP domain, structur	84.73
3vi3_B		454	Integrin beta-1; beta propeller fold, rossman fold	80.48

>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

Probab=100.00  E-value=4.7e-110  Score=944.60  Aligned_cols=592  Identities=31%  Similarity=0.485  Sum_probs=445.0

Q ss_pred             CCCCC--CCCCCCCc--ccchhhh--hhhhc-ccceEEEEEEECCccccCCCCCCCCCCCCCHHHHHHHHHHHHHHhhhh
Q 006975            1 MELDP--DDVFRDDD--EESDNEF--YQEHE-ATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQII   73 (623)
Q Consensus         1 ~~~~~--~~~~~~~~--~~~~~~~--~~~~~-~~ke~iiflIDvs~sM~~~~~~~~~~~~~s~~~~al~~i~~~~~~kIi   73 (623)
                      |+-|+  ++.|+||+  +|+||+.  ..+|. ++||+||||||||+||+.+..    +...|+|++|++||.++|++||+
T Consensus         1 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ke~ivf~IDvS~SM~~~d~----~~~~srl~~a~~~v~~~i~~kii   76 (609)
T 1jey_A            1 MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQS----EDELTPFDMSIQCIQSVYISKII   76 (609)
T ss_dssp             ---------------------------------CEEEEEEEEECSGGGGCCCS----SSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcccccccccccccccchhhhhccccccccCceEEEEEEECCHHHcCCCC----CCCCChHHHHHHHHHHHHHHhhC
Confidence            56687  68899866  3333332  24564 799999999999999999764    24579999999999999999999


Q ss_pred             ccCCCeEEEEEEecCCCCCCCCCCcEEEecccccccCCCCChHHHHHHHHHHHh-HhhhhcccccccCCCCCCCHHHHHH
Q 006975           74 NRLYDEVAICFFNTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIEES-FEKEIGSQYGIVSGSRENSLYNALW  152 (623)
Q Consensus        74 ~~~~D~vgivl~gt~~t~n~~~~~~i~~l~~~~~~~l~~p~~~~ik~L~~l~~~-~~~~~~~~~~~~~~~~~~~l~daL~  152 (623)
                      ++++|+||||+|||+.++|+.+|+|||++     ++|+.|+++.++.|.++++. ....+...+|.   ...++|.+|||
T Consensus        77 ~~~~D~vGlVlfgt~~t~n~l~~d~i~v~-----~~L~~~~~~~ik~l~~l~~~~~~~~~~~~~g~---~~~t~l~daL~  148 (609)
T 1jey_A           77 SSDRDLLAVVFYGTEKDKNSVNFKNIYVL-----QELDNPGAKRILELDQFKGQQGQKRFQDMMGH---GSDYSLSEVLW  148 (609)
T ss_dssp             TTCCCEEEEEEESCSSCBSTTCCTTEEEE-----EEEECCCHHHHHHHHTTSHHHHHHHHHHHHCC---SCCCCHHHHHH
T ss_pred             CCCCCeEEEEEEccCCCCCcCCCCCeEEE-----ecCCCCCHHHHHHHHHHhhcccchhhhhhcCC---CCCCCHHHHHH
Confidence            99999999999999999999999999999     99999999999999998752 11122223332   35789999999


Q ss_pred             HHHHHHhcCCCCCCCcEEEEEeCCCCCCCCCccCcchhhHHHHHHHHHHhHhcCceEEEeeCCCCCCCCcccchhhhhcc
Q 006975          153 VAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQDLGISIELLPLSPPDEEFKVSHFYADMIG  232 (623)
Q Consensus       153 ~a~~~f~~~~~~~~~krI~l~Tn~d~P~~~~~~~~d~~~~~~~~~~a~dL~~~gI~i~l~~i~~~~~~Fd~~~fy~~i~~  232 (623)
                      +|+++|+++++++.+||||||||+++|++.     +...+..+.+.|++|++.||.|.+|+|+.++. ||.++||.+++.
T Consensus       149 ~a~~~f~~~~~k~~~k~IiL~TDg~~p~~~-----~~~~~~~~~~~a~~l~~~gI~i~~igig~~~~-fd~~~fy~~~~~  222 (609)
T 1jey_A          149 VCANLFSDVQFKMSHKRIMLFTNEDNPHGN-----DSAKASRARTKAGDLRDTGIFLDLMHLKKPGG-FDISLFYRDIIS  222 (609)
T ss_dssp             HHHHHHHTCSSCEEEEEEEEEESCSCTTTT-----CHHHHHHHHHHHHHHHHHTEEEEEEEBCCTTC-CCTTTTGGGTCC
T ss_pred             HHHHHHHhhchhhcCCEEEEEcCCCCCCCC-----chHHHHHHHHHHHHHHhcCcEEEEEecCCCCc-cchhhhhhhhhc
Confidence            999999987667789999999999999987     55556778889999999999999999998765 999999999987


Q ss_pred             cCCccccccCCCccccHHHHHHHHHhhhhcceeeeeeeEEecCCceEEEEEeeeecccCCCcEeEecCCCCCCceeeeEE
Q 006975          233 LEGDDLALFMPSAGQKLEDMKDQLRKRMFSKRIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSF  312 (623)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~L~~~i~~k~~~kR~~~~~~l~lg~~~~I~V~~Y~~~~~~~~~~~~~~~~~~~~~vk~~t~~  312 (623)
                      ...++...........+++|++++++|.+++|++|+++|+||++++|||++|+++++++++++++++++++++|+++++|
T Consensus       223 ~~~~~~~~~~~~~~~~l~~ll~~i~~k~~~~R~~~~g~l~lg~~v~I~V~~Y~~t~~~~~~~~~~l~~~~~~~V~~~~~~  302 (609)
T 1jey_A          223 IAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRT  302 (609)
T ss_dssp             --------CCCCCBCSHHHHHHHHHHHHSCCCCSEEEEEESSSSCEEEEEEECSBCCCCCCCCEEEETTTTEEEEEEEEE
T ss_pred             cccccchhcccCchhhHHHHHHHHHhhhccceeeeeeeeEECCCCEEEEEEEeecccccCCCcEEEcccCCccceEEEEE
Confidence            65443322233344678999999999999999999999999999999999999999998899999999999999999999


Q ss_pred             eeCCcCccc-cccceeeEecCCeeeecCHHHHHHhhccCCCcEEEEeeecCCCCCcccccCCcEEEecCCCCCcCcHHHH
Q 006975          313 ICADTGALM-QEPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIF  391 (623)
Q Consensus       313 ~~~dt~~~~-~~~~~k~y~yG~~~V~~~~ee~~~ik~~~~~~l~llGF~~~~~i~~~~~~~~s~fi~Pd~~~~~gS~~~f  391 (623)
                      +|++||+.+ +++++|||+|||++|+|+++|++.++..++|+|+|+||+|+++|+++|++++||||+|++..+.||+++|
T Consensus       303 ~~~~~g~~V~~~di~kgy~yg~~~V~~~~ee~~~~k~~~~~~i~ilgFv~~~~i~~~~~~~~~~~l~P~~~~~~~s~~af  382 (609)
T 1jey_A          303 FNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLF  382 (609)
T ss_dssp             EETTTCCBCCGGGEEEEEEETTEEEEECHHHHHHTTCCSCSEEEEEEEEEGGGSCGGGCCSCCEEEEECTTTEETHHHHH
T ss_pred             EeCCCCCccChhhceeeeeeCCeeeccCHHHHHHHhccCCCceEEEeecchHhCchhhccCCceEEecCCCCccchHHHH
Confidence            999999865 6999999999999999999999999999999999999999999999999999999999998888999999


Q ss_pred             HHHHHHHHhcCcEEEEEe--cCCCCceEEEEEeehhhccc-CCCCCCCcEEEEecCCccCCCCCccCCCCCCCCCCCCHH
Q 006975          392 IALHRSMLRLNRFAVAFY--GNPSNPRLVALVAQDEIVRA-GGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDD  468 (623)
Q Consensus       392 saL~~am~~~~kvaI~r~--r~~s~P~lvaL~P~~~~~~~-~~q~~p~g~~li~LPfadDiR~~~~~~~~~~~~~~~~~e  468 (623)
                      +||++||.++++||||||  |.++.|+||||+|+.+..++ ++|..|+||++++|||+||||.++++.     ...++++
T Consensus       383 saL~~al~~~~kvaIar~v~r~~~~p~l~aL~P~~~~~d~~~~q~~~~gl~l~~Lpf~ddvR~~~f~~-----~~~~~~~  457 (609)
T 1jey_A          383 SALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTE-----KIMATPE  457 (609)
T ss_dssp             HHHHHHHHHTTEEEEEEEECSSSCCCEEEEEEEECCEECTTCCEEECSEEEEEECCCGGGBCCCCCCC-----CCCCCHH
T ss_pred             HHHHHHHHhcCcEEEEEEEecCCCCCEEEEEeCccccccccCCcCCCCeeEEEecCccccccCCCCcc-----cCCCCHH
Confidence            999999999999999998  89999999999999875443 557789999999999999999987643     5679999


Q ss_pred             HHHHHHHHHhhcCCCCCCCCCCCChhHHHHHHHHHHhhcCcCCCCCCCCCCCCChhhhccccchHHHHHHHHhhcCCCCC
Q 006975          469 EVKKAAALMKRIDLKDFSVCQFANPSLQRHYAVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNYD  548 (623)
Q Consensus       469 q~~~a~~lI~~l~l~~y~p~~~~NP~lq~~y~~lea~Al~~~~~~~~~D~t~P~~~~i~~~~~~~~i~~fk~~~~~~~~~  548 (623)
                      |+++|++||++|+++ |+|+.|+||++|+||++|+++|++++.|+++.|.|+|+++.|.++++ +++++|++++|+..++
T Consensus       458 ~l~~a~~lI~~m~~~-~~p~~~~np~lq~~~~~i~a~al~~~~~~~~~d~t~p~~~~~~~~~~-~~~~~~k~~~f~~~~~  535 (609)
T 1jey_A          458 QVGKMKAIVEKLRFT-YRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLG-SLVDEFKELVYPPDYN  535 (609)
T ss_dssp             HHHHHHHHHHHTBCC-CCTTSCCCHHHHHHHHHHHHHHTTCSSCCCCCCTTSCCHHHHHHHHT-THHHHHHHHHSCSCC-
T ss_pred             HHHHHHHHHHhcccC-CCcccCCCHHHHHHHHHHHHHhcCCCCCCCCCCcccCCHHHHHHHHH-HHHHHHHHhhcccccc
Confidence            999999999999998 99999999999999999999999999998899999999999988888 8999999998888887


Q ss_pred             Ccccc-cc-chh---hhchhhhhhhhhhccchHHHHHHHHcCCcccccHHHHHHHHHHcCCCCCCChHHHHHHHHHhhcC
Q 006975          549 EEGDV-KV-SEA---SRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLISRILTHMGK  623 (623)
Q Consensus       549 ~~~~~-~~-~~~---~~k~~~~~~~~~~~~~~~~~~~~~~~g~l~kltv~~LK~~l~~~~~~~~gkK~dLi~~i~~~l~~  623 (623)
                      +.... ++ +..   +.||.      ..+.+..+|+++|++|+|++|||+|||+||+++|++++|||||||+||++||+|
T Consensus       536 ~~~~~~~~k~~~~~~~~k~~------k~~~~~~~~~~~~~~g~l~~~tv~~Lk~~l~~~~~~~~~kK~~li~~i~~~~~~  609 (609)
T 1jey_A          536 PEGKVTKRKHDNEGSGSKRP------KVEYSEEELKTHISKGTLGKFTVPMLKEACRAYGLKSGLKKQELLEALTKHFQD  609 (609)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             chhccccccccccCCccccc------cCcCCHHHHHHHHHCCCchhccHHHHHHHHHHcCCCCCCcHHHHHHHHHHHhcC
Confidence            65411 11 100   01111      124478899999999999999999999999999999999999999999999986

PyMOL of 1jey

>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

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

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

>2do1_A Nuclear protein HCC-1; SAP domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.140.2.1	Back alignment and structure

>1zrj_A E1B-55KDA-associated protein 5 isoform C; SAP domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.140.2.1	Back alignment and structure

>1h1j_S THO1 protein; SAP domain, DNA binding; NMR {Saccharomyces cerevisiae} SCOP: a.140.2.1 PDB: 2wqg_A	Back alignment and structure

>2rnn_A E3 SUMO-protein ligase SIZ1; SUMO ligase, DNA binding, sumoylation, metal-binding, nucLeu phosphoprotein, UBL conjugation pathway; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2kvu_A MKL/myocardin-like protein 1; SAP motif, DNA/RNA binding, structural genomics, northeast structural genomics consortium (NESG), PSI-2; NMR {Homo sapiens} PDB: 2kw9_A	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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>2rno_A Putative DNA-binding protein; SUMO ligase, sumoylation, metal-BI zinc-finger, ligase; NMR {Oryza sativa subsp}	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

>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

>2out_A MU-like prophage flumu protein GP35, protein HI1507 in MU-like prophage flumu region...; structural genomics, hypothetical protein; NMR {Haemophilus influenzae} SCOP: a.140.3.2 d.344.1.1	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

>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

>2jx3_A Protein DEK; alpha helix, SAF/SAP motif, DNA binding, chromosomal rearrangement, DNA-binding, nucleus, phosphorylation, proto oncogene; NMR {Homo sapiens}	Back alignment and structure

>1v66_A Protein inhibitor of activated STAT protein 1; four helix bundle, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.140.2.1	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

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1	Back alignment and structure

>2ld7_A Histone deacetylase complex subunit SAP30; transcription; NMR {Mus musculus}	Back alignment and structure

>3skq_A Mitochondrial distribution and morphology protein; 14-3-3-like membrane protein, mitochondrial ribosome, respir chain biogenesis; 2.10A {Saccharomyces cerevisiae}	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

>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

>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

>2do5_A Splicing factor 3B subunit 2; SAP domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	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

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		623
d1jeya1		281	b.131.1.1 (A:254-534) Ku70 subunit middle domain {	1e-74
d1jeyb1		304	b.131.1.2 (B:242-545) Ku80 subunit middle domain {	4e-48
d1jeya2		220	c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain	4e-26
d1jeyb2		236	c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain	8e-11
d1jeqa1		51	a.140.2.1 (A:559-609) DNA binding C-terminal domai	4e-09
d1h1js_		44	a.140.2.1 (S:) S/mar DNA-binding protein Tho1 {Bak	6e-06
d1zrja1		37	a.140.2.1 (A:1-37) Heterogeneous nuclear ribonucle	3e-05

>d1jeya1 b.131.1.1 (A:254-534) Ku70 subunit middle domain {Human (Homo sapiens) [TaxId: 9606]} Length = 281	Back information, alignment and structure


class: All beta proteins
fold: SPOC domain-like
superfamily: SPOC domain-like
family: Ku70 subunit middle domain
domain: Ku70 subunit middle domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  238 bits (609), Expect = 1e-74
 Identities = 93/288 (32%), Positives = 141/288 (48%), Gaps = 11/288 (3%)

Query: 264 RIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGA-LMQ 322
           R + R+   +   + I +  Y L++  +      L   TN P+KT+       TG  L+ 
Sbjct: 1   RALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLP 60

Query: 323 EPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDK 382
              KR Q Y    I    +E  E+KR     L L GFKPL  LK +H LRPS FV+P + 
Sbjct: 61  SDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEES 120

Query: 383 EVVGSTCIFIALHRSMLRLNRFAVAFY--GNPSNPRLVALVAQDEIVR-AGGQVEPPGMH 439
            V+GS+ +F AL    L     A+  Y       P  VALV Q+E +     QV PPG  
Sbjct: 121 LVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQ 180

Query: 440 MIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHY 499
           +++LP++DD R +            A+ ++V K  A+++++    +    F NP LQ+H+
Sbjct: 181 LVFLPFADDKRKMPFTEK-----IMATPEQVGKMKAIVEKLRF-TYRSDSFENPVLQQHF 234

Query: 500 AVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNY 547
             L+ALAL+  +  +  D T+P  E M +  +   V+EFK  VY  +Y
Sbjct: 235 RNLEALALDLMEPEQAVDLTLPKVEAMNKR-LGSLVDEFKELVYPPDY 281

PyMOL of d1jeya1

>d1jeyb1 b.131.1.2 (B:242-545) Ku80 subunit middle domain {Human (Homo sapiens) [TaxId: 9606]} Length = 304	Back information, alignment and structure

>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

>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

>d1jeqa1 a.140.2.1 (A:559-609) DNA binding C-terminal domain of ku70 {Human (Homo sapiens) [TaxId: 9606]} Length = 51	Back information, alignment and structure

>d1h1js_ a.140.2.1 (S:) S/mar DNA-binding protein Tho1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 44	Back information, alignment and structure

>d1zrja1 a.140.2.1 (A:1-37) Heterogeneous nuclear ribonucleoprotein U-like protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 37	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		623
d1jeya1		281	Ku70 subunit middle domain {Human (Homo sapiens) [	100.0
d1jeyb1		304	Ku80 subunit middle domain {Human (Homo sapiens) [	100.0
d1jeya2		220	Ku70 subunit N-terminal domain {Human (Homo sapien	99.97
d1jeyb2		236	Ku80 subunit N-terminal domain {Human (Homo sapien	99.84
d1jeqa1		51	DNA binding C-terminal domain of ku70 {Human (Homo	99.5
d1zrja1		37	Heterogeneous nuclear ribonucleoprotein U-like pro	98.89
d1h1js_		44	S/mar DNA-binding protein Tho1 {Baker's yeast (Sac	98.89
d1shux_		181	Capillary morphogenesis protein 2 domain {Human (H	98.18
d1q0pa_		209	Complement factor B domain {Human (Homo sapiens) [	98.08
d1atza_		184	von Willebrand factor A3 domain, vWA3 {Human (Homo	97.93
d1v7pc_		193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	97.85
d1pt6a_		192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	97.84
d2do1a1		42	Nuclear protein hcc-1 {Human (Homo sapiens) [TaxId	97.8
d1ijba_		202	von Willebrand factor A1 domain, vWA1 {Human (Homo	97.71
d1n3ya_		189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	97.19
d1mf7a_		194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	97.14
d1yvra2		174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	96.92
d1mjna_		179	Integrin CD11a/CD18 (Leukocyte function associated	96.29
d1tyeb2		248	Integrin beta A domain {Human (Homo sapiens) [TaxI	95.95
d1y02a1		44	Rififylin (FYVE-RING finger protein Sakura) {Human	94.85
d2qtva3		271	Sec23 {Baker's yeast (Saccharomyces cerevisiae) [T	93.16
d1pd0a3		252	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	92.65
d1a62a1		47	Rho termination factor, N-terminal domain {Escheri	92.14
d1v66a_		65	p53 binding domain of protein inhibitor of activat	91.61
d1kcfa1		36	Mitochondrial resolvase ydc2 N-terminal domain {Fi	88.95

>d1jeya1 b.131.1.1 (A:254-534) Ku70 subunit middle domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All beta proteins
fold: SPOC domain-like
superfamily: SPOC domain-like
family: Ku70 subunit middle domain
domain: Ku70 subunit middle domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4.7e-65  Score=521.06  Aligned_cols=277  Identities=34%  Similarity=0.507  Sum_probs=265.0

Q ss_pred             eeeeeeeEEecCCceEEEEEeeeecccCCCcEeEecCCCCCCceeeeEEeeCCcCcccc-ccceeeEecCCeeeecCHHH
Q 006975          264 RIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTERSFICADTGALMQ-EPAKRFQPYKGENIKFSVQE  342 (623)
Q Consensus       264 R~~~~~~l~lg~~~~I~V~~Y~~~~~~~~~~~~~~~~~~~~~vk~~t~~~~~dt~~~~~-~~~~k~y~yG~~~V~~~~ee  342 (623)
                      |++++++|+||++++|+|++|+++++++++++++++++++++|+.+|+|+|.+||++++ ++++|||+|||++|+|+++|
T Consensus         1 R~~~~~~l~ig~~v~I~V~~Y~~~~~~~~~~~~~l~~~t~~~v~~~~~~v~~~tg~~v~~~di~kgy~yG~~~V~~~~ee   80 (281)
T d1jeya1           1 RALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEE   80 (281)
T ss_dssp             CCSEEEEEESSSSCEEEEEEECSBCCCCCCCCEEEETTTTEEEEEEEEEEETTTCCBCCGGGEEEEEEETTEEEEECHHH
T ss_pred             CccEEeEEEeCCCcEEEEEEEeCccccCCCccEEEECCCCCEeeEEEEEEcCCCCcccChHHceeEEEECCEEEEecHHH
Confidence            78999999999999999999999999999999999999999999999999999999665 89999999999999999999


Q ss_pred             HHHhhccCCCcEEEEeeecCCCCCcccccCCcEEEecCCCCCcCcHHHHHHHHHHHHhcCcEEEEEe--cCCCCceEEEE
Q 006975          343 LSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDKEVVGSTCIFIALHRSMLRLNRFAVAFY--GNPSNPRLVAL  420 (623)
Q Consensus       343 ~~~ik~~~~~~l~llGF~~~~~i~~~~~~~~s~fi~Pd~~~~~gS~~~fsaL~~am~~~~kvaI~r~--r~~s~P~lvaL  420 (623)
                      +++|+..++|||+||||+++++|+++|++++++||+|++.+..||+++|+||++||+++++||||||  |+++.|+||||
T Consensus        81 ~~~ik~~~~~~l~llGF~~~~~i~~~~~~~~s~~i~p~~~~~~gs~~af~aL~~al~~~~kvaI~r~v~r~~~~p~lvaL  160 (281)
T d1jeya1          81 TEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVAL  160 (281)
T ss_dssp             HHHTTCCSCSEEEEEEEEEGGGSCGGGCCSCCEEEEECTTTEETHHHHHHHHHHHHHHTTEEEEEEEECSSSCCCEEEEE
T ss_pred             HhhhccCCCCeEEEEEEEcHHHCCHHHcCCCcEEEEeCCccccchHHHHHHHHHHHHHcCCEEEEEEEEcCCCCcEEEEE
Confidence            9999999999999999999999999999999999999999899999999999999999999999998  99999999999


Q ss_pred             Eeehhhccc-CCCCCCCcEEEEecCCccCCCCCccCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCCCCCCCChhHHHHH
Q 006975          421 VAQDEIVRA-GGQVEPPGMHMIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHY  499 (623)
Q Consensus       421 ~P~~~~~~~-~~q~~p~g~~li~LPfadDiR~~~~~~~~~~~~~~~~~eq~~~a~~lI~~l~l~~y~p~~~~NP~lq~~y  499 (623)
                      +|+.+..++ +.+..|+|||+++|||+||||++++..     ...++++|+++|++||++|+++ |+|+.|+||+||+||
T Consensus       161 ~P~~~~~~~~~~~~~~~g~~li~LPfaddvR~~~~~~-----~~~~~~eql~~a~~lI~~l~~~-~~p~~~~NP~lq~~~  234 (281)
T d1jeya1         161 VPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTE-----KIMATPEQVGKMKAIVEKLRFT-YRSDSFENPVLQQHF  234 (281)
T ss_dssp             EEECCEECTTCCEEECSEEEEEECCCGGGBCCCCCCC-----CCCCCHHHHHHHHHHHHHTBCC-CCTTSCCCHHHHHHH
T ss_pred             EccccccccccccccCCeEEEEEcCChhhccCCCCcC-----CCCCCHHHHHHHHHHHHhcccC-CChhhCCCHHHHHHH
Confidence            999988876 457789999999999999999987654     5578999999999999999997 999999999999999


Q ss_pred             HHHHHhhcCcCCCCCCCCCCCCChhhhccccchHHHHHHHHhhcCCCC
Q 006975          500 AVLQALALEEDDMPEIKDETVPDEEGMARPGVVKAVEEFKLSVYGDNY  547 (623)
Q Consensus       500 ~~lea~Al~~~~~~~~~D~t~P~~~~i~~~~~~~~i~~fk~~~~~~~~  547 (623)
                      ++|+|+||+++.|+++.|.|+|+++.|.+|++ +++++|++++||++|
T Consensus       235 ~~l~a~al~~~~p~~~~D~t~P~~~~~~kr~~-~~~~~~~~~v~p~~y  281 (281)
T d1jeya1         235 RNLEALALDLMEPEQAVDLTLPKVEAMNKRLG-SLVDEFKELVYPPDY  281 (281)
T ss_dssp             HHHHHHHTTCSSCCCCCCTTSCCHHHHHHHHT-THHHHHHHHHSCSCC
T ss_pred             HHHHHHhcCCCCCCCCCCccCCChHHHHHHHH-HHHHHHHHhhCCCCC
Confidence            99999999999999999999999999999988 899999999999876

PyMOL of d1jeya1

>d1jeyb1 b.131.1.2 (B:242-545) Ku80 subunit middle domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

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

>d1jeqa1 a.140.2.1 (A:559-609) DNA binding C-terminal domain of ku70 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zrja1 a.140.2.1 (A:1-37) Heterogeneous nuclear ribonucleoprotein U-like protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h1js_ a.140.2.1 (S:) S/mar DNA-binding protein Tho1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

>d1q0pa_ c.62.1.1 (A:) Complement factor B 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

>d1v7pc_ c.62.1.1 (C:) Integrin alpha2-beta1 {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

>d2do1a1 a.140.2.1 (A:5-46) Nuclear protein hcc-1 {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

>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

>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

>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

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

>d1y02a1 a.140.2.1 (A:71-114) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}	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

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

>d1a62a1 a.140.3.1 (A:1-47) Rho termination factor, N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1v66a_ a.140.2.1 (A:) p53 binding domain of protein inhibitor of activated STAT protein 1, PIAS-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1kcfa1 a.140.2.1 (A:3-38) Mitochondrial resolvase ydc2 N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}	Back information, alignment and structure