Citrus Sinensis ID: 006065

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-------630-------640-------650-------660--

MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGDGSVSDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFSYAS

cccccEEEEEEEEcccccccccHHHHHHHHHHHHHHHHcccccEEEEEEEccccccccccccccccccEEEEcccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcccccccEEEEEEEccccccccccHHcHHHHHHHHHHHHHHcccccEEccccccccccccccccccHHHHHHHHHccccccEEcHHHHHHHHcccccccccccEEEEEEEEcccccEEEEEEEEEccccccccccccccccccccccccEEEEEEEEEEEccccccccccccccccEEcccEEEEccHHHHHHHcccccccEEEEEEEEccccccEEEcccEEEEEcccccHHHHHHHHHHHHHHHHccEEEEEEEEEccccccEEEEEEEcccccccccccEEEEEcccccHHcccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccccccccccccccccccHHHHcccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEcc

ccccccEEEEEEEccHcHccccccHHHHHHHHHHHHHEcccccEEEEEEEcccccccccccccccccEEEEEcccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccEEEEEEccccccccccHHHHHHHHHHHHHHHcEcccccccccccccccccccccccccHHHHHHHHHHccccEEEcHHHHHHHHcccccccccccccccEEEEEccccEEEEEEEEEEEcccccccEEEEEEccccccccccEEEEEEEEEEcccccccccHHHHHccccccccEEEccHHHHHHHcccccccEEEEEEEcHHHcccHcccccEEEEEcccccHHHHHHHHHHHHHHHHcccEEEEEEEEcccccccEEEEEEccccccccccccEEEEEcccHHHHccccccccccccccccccHHHHHHHHHHHHHccccccccHHcccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHccccccccccccHHHHcccccccccccHHHccccHHHHHHHHHHHcccccEEEcccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccc

MARTREALLLLLDvspsmhsvlPDVEKLCSRLIQKKliygknhevGVILFGTeeteneltkevggyehvKVLQDIKVVDGHLVqslkhlpqgtcagdfLDAIVVGVDMLIKKYgetykgkkhlclitdalcplkdpdvgtkedQVSTIARQMVAFGLRMKNIVVRAslsgephmrVIIENDNLLnifskkssaktlfvdsttslrgarktrdispvtifrgdLELSEKMKIKVWVYKKtgeekfptlkkysdkapstdkfathevkvdyeyksvedpskvvppeqrikgyrygpqvvpissaeweavkfkpeksvkllgftdasNILRHYYMKDVNlfiaepgnsrATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGvltpnvsekinipdsfyfnvlpfaedvrefqfpsfskfpvswqpneqQQEAADNLVKMLdlapsgkgeilqpeltpnpaleRFYHHLelksehqdaappplddslkkitepdptllaeSQSAIDAFCGQfvikenpklkkSTRRflrekpsgsdepngdgsvsdaqavnsmeskpvvtvdkigdltpiqdfeammsrrdcpdWVDKAIEDMKNKIFGLlensneginyPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFwdnsclndmssivtfsyas

MARTREALLLlldvspsmhsvLPDVEKLCSRLIQKKliygknhevgVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFskkssaktlfvdsttslrgarktrdispvtifrgdlelsekmkIKVWvykktgeekfptlkkysdkapstdkfathevkvdyeyksvedpskvvppeqrikgyrygPQVVPISSAEweavkfkpeksvkllgfTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFvikenpklkkstrrflrekpsgsdepngdgsvSDAQAVNSmeskpvvtvdkigDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFSYAS

******ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGE***********************VKVDYEY**************RIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSW****************************************FY*************************************AIDAFCGQFVIK*******************************************VTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFS***

***TREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN*****VGGYEHVKVLQDIKVVDGHLVQSLKHLPQ**CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST************SPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPST*****HEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSE**********DSLKKITEP*************AFCGQFVIKENPKLK**********************************************TPIQDFEAMMSRRDC*DWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFSY**

MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV***********TRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRR**********************AVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFSYAS

****REALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPK**************************DAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQVYLSVSFFLLWFAFAFWDNSCLNDMSSIVTFSYA*

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SSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiii

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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		662	2.2.26 [Sep-21-2011]
Q9FQ09		680	ATP-dependent DNA helicas	yes	no	0.929	0.904	0.622	0.0
Q75IP6		688	ATP-dependent DNA helicas	yes	no	0.941	0.905	0.612	0.0
Q54LY5		796	X-ray repair cross-comple	yes	no	0.927	0.771	0.275	4e-68
P27641		732	X-ray repair cross-comple	yes	no	0.903	0.816	0.229	1e-33
Q7RX73		725	ATP-dependent DNA helicas	N/A	no	0.820	0.748	0.244	2e-28
P13010		732	X-ray repair cross-comple	yes	no	0.898	0.812	0.223	2e-28
Q6C7B9		726	ATP-dependent DNA helicas	yes	no	0.709	0.647	0.259	1e-26
Q2H6C5		736	ATP-dependent DNA helicas	N/A	no	0.833	0.75	0.235	9e-26
Q2MHH1		725	ATP-dependent DNA helicas	N/A	no	0.842	0.769	0.233	1e-23
Q4WI96		725	ATP-dependent DNA helicas	yes	no	0.845	0.772	0.222	5e-23

>sp\|Q9FQ09\|KU80_ARATH ATP-dependent DNA helicase 2 subunit KU80 OS=Arabidopsis thaliana GN=KU80 PE=1 SV=1	Back alignment and function desciption

 Score =  808 bits (2087), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/628 (62%), Positives = 495/628 (78%), Gaps = 13/628 (2%)

Query: 1   MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELT 60
           MAR RE L+L+LDV P+M SVLPDVEK CS L+QKKLIY K  EVG+++FGTEET NEL 
Sbjct: 1   MARNREGLVLVLDVGPAMRSVLPDVEKACSMLLQKKLIYNKYDEVGIVVFGTEETGNELA 60

Query: 61  KEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGK 120
           +E+GGYE+V VL++I+VVD    + +K LP+GT AGDFLDA++VG+DMLIK YG  +KGK
Sbjct: 61  REIGGYENVTVLRNIRVVDELAAEHVKQLPRGTVAGDFLDALIVGMDMLIKMYGNAHKGK 120

Query: 121 KHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN 180
           K +CLIT+A CP KDP  GTK+DQVSTIA +M A G++M++IV+R++LSG+ H RVI EN
Sbjct: 121 KRMCLITNAACPTKDPFEGTKDDQVSTIAMKMAAEGIKMESIVMRSNLSGDAHERVIEEN 180

Query: 181 DNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTG 240
           D+LL +FS  + AKT+ VDS  SL G+ KTR ++PVT+FRGDLE++  MKIKVWVYKK  
Sbjct: 181 DHLLTLFSSNAIAKTVNVDSPLSLLGSLKTRRVAPVTLFRGDLEINPTMKIKVWVYKKVA 240

Query: 241 EEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPIS 300
           EE+ PTLK YSDKAP TDKFA HEVKVDY+YK   + ++V+ PE+RIKG+RYGPQV+PIS
Sbjct: 241 EERLPTLKMYSDKAPPTDKFAKHEVKVDYDYKVTAESTEVIAPEERIKGFRYGPQVIPIS 300

Query: 301 SAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKE 360
             + E +KFK +K +KLLGFT+ASNILRHYYMKDVN+ + +P   ++ +AVSA+AR MKE
Sbjct: 301 PDQIETLKFKTDKGMKLLGFTEASNILRHYYMKDVNIVVPDPSKEKSVLAVSAIAREMKE 360

Query: 361 MNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFP 420
            NKVAIVRCVWR GQ +VVVGVLTPNVSE+ + PDSFYFNVLPFAEDVREF FPSF+K P
Sbjct: 361 TNKVAIVRCVWRNGQGNVVVGVLTPNVSERDDTPDSFYFNVLPFAEDVREFPFPSFNKLP 420

Query: 421 VSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPP 480
            SW+P+EQQQ  ADNLVKMLDLAPS + E+L+P+LTPNP L+RFY +LELKS+  DA  P
Sbjct: 421 SSWKPDEQQQAVADNLVKMLDLAPSAEEEVLKPDLTPNPVLQRFYEYLELKSKSTDATLP 480

Query: 481 PLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGD 540
           P+D + K++ E DP L + ++S +D F G F +KENPKLKK+++R LR+KPSGSD+ +  
Sbjct: 481 PMDGTFKRLMEQDPELSSNNKSIMDTFRGSFEVKENPKLKKASKRLLRDKPSGSDDEDNR 540

Query: 541 GSVSDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLL 600
               DA+     E+K    +D +GD  PIQDFEAM+SRRD  DW +KAI  MKN I  L+
Sbjct: 541 MITYDAK-----ENK----IDIVGDANPIQDFEAMISRRDKTDWTEKAITQMKNLIMKLV 591

Query: 601 EN-SNEGINYPKAVELLVALRKGCILEQ 627
           EN ++EG    KA+E ++ALRKGC+LEQ
Sbjct: 592 ENCTDEG---DKALECVLALRKGCVLEQ 616

Single stranded DNA-dependent ATP-dependent helicase. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair. When associated with KU70, 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. Binds to and recombines double-stranded T-DNA molecules.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp\|Q75IP6\|KU80_ORYSJ ATP-dependent DNA helicase 2 subunit KU80 OS=Oryza sativa subsp. japonica GN=KU80 PE=1 SV=1	Back alignment and function description

>sp\|Q54LY5\|XRCC5_DICDI X-ray repair cross-complementing protein 5 OS=Dictyostelium discoideum GN=ku80 PE=3 SV=1	Back alignment and function description

>sp\|P27641\|XRCC5_MOUSE X-ray repair cross-complementing protein 5 OS=Mus musculus GN=Xrcc5 PE=2 SV=4	Back alignment and function description

>sp\|Q7RX73\|KU80_NEUCR ATP-dependent DNA helicase II subunit 2 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=ku80 PE=3 SV=2	Back alignment and function description

>sp\|P13010\|XRCC5_HUMAN X-ray repair cross-complementing protein 5 OS=Homo sapiens GN=XRCC5 PE=1 SV=3	Back alignment and function description

>sp\|Q6C7B9\|KU80_YARLI ATP-dependent DNA helicase II subunit 2 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=KU80 PE=3 SV=1	Back alignment and function description

>sp\|Q2H6C5\|KU80_CHAGB ATP-dependent DNA helicase II subunit 2 OS=Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) GN=KU80 PE=3 SV=1	Back alignment and function description

>sp\|Q2MHH1\|KU80_ASPSO ATP-dependent DNA helicase II subunit 2 OS=Aspergillus sojae GN=ku80 PE=3 SV=1	Back alignment and function description

>sp\|Q4WI96\|KU80_ASPFU ATP-dependent DNA helicase II subunit 2 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=ku80 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		662
359489412		690	PREDICTED: ATP-dependent DNA helicase 2	0.947	0.908	0.748	0.0
255541318		684	ku P80 DNA helicase, putative [Ricinus c	0.938	0.907	0.748	0.0
296089149		673	unnamed protein product [Vitis vinifera]	0.921	0.906	0.744	0.0
224130002		700	predicted protein [Populus trichocarpa]	0.935	0.884	0.713	0.0
449433125		691	PREDICTED: ATP-dependent DNA helicase 2	0.945	0.905	0.695	0.0
449525249		691	PREDICTED: ATP-dependent DNA helicase 2	0.945	0.905	0.693	0.0
357469575		683	ATP-dependent DNA helicase 2 subunit [Me	0.936	0.907	0.677	0.0
19401142		683	KAP-2 [Medicago truncatula]	0.936	0.907	0.676	0.0
225453905		688	PREDICTED: ATP-dependent DNA helicase 2	0.968	0.931	0.663	0.0
356512141		687	PREDICTED: ATP-dependent DNA helicase 2	0.957	0.922	0.654	0.0

>gi\|359489412\|ref\|XP_002273349.2\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  974 bits (2518), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 469/627 (74%), Positives = 540/627 (86%)

Query: 1   MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELT 60
           MAR +EALLLLLDVSPSMH+ LP+VEKLCS L+QKKLIY KN EVG++LFGTE+T NELT
Sbjct: 1   MARNKEALLLLLDVSPSMHTFLPEVEKLCSMLLQKKLIYSKNDEVGIVLFGTEDTNNELT 60

Query: 61  KEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGK 120
           KEVGGYEHV VL+ IKVVDG LV++L+ LP+GT AGDFLDAIVVG+DMLIKK+G T KGK
Sbjct: 61  KEVGGYEHVVVLRHIKVVDGDLVEALQQLPRGTVAGDFLDAIVVGMDMLIKKFGSTNKGK 120

Query: 121 KHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN 180
           K LCLIT ALCP+KDP  GTKEDQ+ TIA QM A G++++ IV R  LSG   MR++ EN
Sbjct: 121 KRLCLITSALCPIKDPYEGTKEDQIGTIAEQMSAHGMKLECIVARGRLSGNVDMRIMDEN 180

Query: 181 DNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTG 240
           D LL +FS K++AKTL+V++ TSL GA +TR I+PVTIFRGDLELS KM+IKVWVYKKT 
Sbjct: 181 DLLLKLFSTKTTAKTLYVETPTSLLGALRTRSIAPVTIFRGDLELSPKMRIKVWVYKKTA 240

Query: 241 EEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPIS 300
           EE+FPTLK+YSD+AP TDKFATHEVKVD+EYKSVE+ SKVVPPEQRIKGYRYGPQV+PIS
Sbjct: 241 EERFPTLKQYSDQAPPTDKFATHEVKVDFEYKSVEESSKVVPPEQRIKGYRYGPQVIPIS 300

Query: 301 SAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKE 360
           SAEWEAVKFKPEK VKLLGFTDASN++RHYYM DVN+FIAEP N++A +AVSALARAMKE
Sbjct: 301 SAEWEAVKFKPEKGVKLLGFTDASNVMRHYYMHDVNIFIAEPSNTKAMLAVSALARAMKE 360

Query: 361 MNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFP 420
           MNKVAI+RCVWRQGQ SVV+G+LTPNVS+K +IPDSFYFNVLP+AEDVREFQFPSFS  P
Sbjct: 361 MNKVAILRCVWRQGQGSVVIGILTPNVSDKDDIPDSFYFNVLPYAEDVREFQFPSFSNLP 420

Query: 421 VSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPP 480
            SWQPNE+QQEAADNLVKMLDLAPSG  E L P+LTPNP LERFY HLELKS+H DAA P
Sbjct: 421 ASWQPNEEQQEAADNLVKMLDLAPSGSKETLLPDLTPNPVLERFYRHLELKSKHPDAAVP 480

Query: 481 PLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGD 540
           PLD+SLKKITEPDP LL++++  IDAF  +F +KENPKLKKSTRR LRE+PSG +E    
Sbjct: 481 PLDESLKKITEPDPKLLSQNKPIIDAFRRRFELKENPKLKKSTRRLLRERPSGLNEEASM 540

Query: 541 GSVSDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLL 600
           G  SD QA+ S+E+   V V+KIGD TPIQDFEAMMS RD P+WV KAI +MKNKIF L+
Sbjct: 541 GDGSDGQAIKSIENTSTVGVEKIGDSTPIQDFEAMMSCRDSPEWVGKAINEMKNKIFDLV 600

Query: 601 ENSNEGINYPKAVELLVALRKGCILEQ 627
           E+S EG NY KA+E LVALRKGC+LEQ
Sbjct: 601 EDSYEGDNYLKALEYLVALRKGCVLEQ 627

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255541318\|ref\|XP_002511723.1\| ku P80 DNA helicase, putative [Ricinus communis] gi\|223548903\|gb\|EEF50392.1\| ku P80 DNA helicase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|296089149\|emb\|CBI38852.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224130002\|ref\|XP_002320725.1\| predicted protein [Populus trichocarpa] gi\|222861498\|gb\|EEE99040.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449433125\|ref\|XP_004134348.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449525249\|ref\|XP_004169630.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357469575\|ref\|XP_003605072.1\| ATP-dependent DNA helicase 2 subunit [Medicago truncatula] gi\|355506127\|gb\|AES87269.1\| ATP-dependent DNA helicase 2 subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|19401142\|gb\|AAL87543.1\|AF293343_1 KAP-2 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|225453905\|ref\|XP_002273329.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356512141\|ref\|XP_003524779.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Glycine max]	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		662
TAIR\|locus:2023757		680	KU80 [Arabidopsis thaliana (ta	0.929	0.904	0.622	2.1e-210
UNIPROTKB\|Q75IP6		688	KU80 "ATP-dependent DNA helica	0.941	0.905	0.612	3.6e-199
DICTYBASE\|DDB_G0286303		796	ku80 "DNA-dependent protein ki	0.386	0.321	0.305	2e-64
UNIPROTKB\|F1NZI1		729	XRCC5 "Uncharacterized protein	0.903	0.820	0.266	2.1e-41
ZFIN\|ZDB-GENE-041008-108		727	xrcc5 "X-ray repair complement	0.586	0.533	0.267	4.7e-38
UNIPROTKB\|F1SS19		733	XRCC5 "Uncharacterized protein	0.589	0.532	0.246	5.1e-35
UNIPROTKB\|G3V817		732	Xrcc5 "Protein Xrcc5" [Rattus	0.587	0.531	0.248	5.7e-35
MGI\|MGI:104517		732	Xrcc5 "X-ray repair complement	0.897	0.811	0.233	1.1e-34
UNIPROTKB\|P13010		732	XRCC5 "X-ray repair cross-comp	0.587	0.531	0.253	2.2e-33
RGD\|3976		683	Xrcc5 "X-ray repair complement	0.856	0.830	0.239	1.3e-31

TAIR\|locus:2023757 KU80 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2034 (721.1 bits), Expect = 2.1e-210, P = 2.1e-210
 Identities = 391/628 (62%), Positives = 495/628 (78%)

Query:     1 MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELT 60
             MAR RE L+L+LDV P+M SVLPDVEK CS L+QKKLIY K  EVG+++FGTEET NEL 
Sbjct:     1 MARNREGLVLVLDVGPAMRSVLPDVEKACSMLLQKKLIYNKYDEVGIVVFGTEETGNELA 60

Query:    61 KEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGK 120
             +E+GGYE+V VL++I+VVD    + +K LP+GT AGDFLDA++VG+DMLIK YG  +KGK
Sbjct:    61 REIGGYENVTVLRNIRVVDELAAEHVKQLPRGTVAGDFLDALIVGMDMLIKMYGNAHKGK 120

Query:   121 KHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN 180
             K +CLIT+A CP KDP  GTK+DQVSTIA +M A G++M++IV+R++LSG+ H RVI EN
Sbjct:   121 KRMCLITNAACPTKDPFEGTKDDQVSTIAMKMAAEGIKMESIVMRSNLSGDAHERVIEEN 180

Query:   181 DNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTG 240
             D+LL +FS  + AKT+ VDS  SL G+ KTR ++PVT+FRGDLE++  MKIKVWVYKK  
Sbjct:   181 DHLLTLFSSNAIAKTVNVDSPLSLLGSLKTRRVAPVTLFRGDLEINPTMKIKVWVYKKVA 240

Query:   241 EEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPIS 300
             EE+ PTLK YSDKAP TDKFA HEVKVDY+YK   + ++V+ PE+RIKG+RYGPQV+PIS
Sbjct:   241 EERLPTLKMYSDKAPPTDKFAKHEVKVDYDYKVTAESTEVIAPEERIKGFRYGPQVIPIS 300

Query:   301 SAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKE 360
               + E +KFK +K +KLLGFT+ASNILRHYYMKDVN+ + +P   ++ +AVSA+AR MKE
Sbjct:   301 PDQIETLKFKTDKGMKLLGFTEASNILRHYYMKDVNIVVPDPSKEKSVLAVSAIAREMKE 360

Query:   361 MNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFP 420
              NKVAIVRCVWR GQ +VVVGVLTPNVSE+ + PDSFYFNVLPFAEDVREF FPSF+K P
Sbjct:   361 TNKVAIVRCVWRNGQGNVVVGVLTPNVSERDDTPDSFYFNVLPFAEDVREFPFPSFNKLP 420

Query:   421 VSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPP 480
              SW+P+EQQQ  ADNLVKMLDLAPS + E+L+P+LTPNP L+RFY +LELKS+  DA  P
Sbjct:   421 SSWKPDEQQQAVADNLVKMLDLAPSAEEEVLKPDLTPNPVLQRFYEYLELKSKSTDATLP 480

Query:   481 PLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGD 540
             P+D + K++ E DP L + ++S +D F G F +KENPKLKK+++R LR+KPSGSD+ +  
Sbjct:   481 PMDGTFKRLMEQDPELSSNNKSIMDTFRGSFEVKENPKLKKASKRLLRDKPSGSDDEDNR 540

Query:   541 GSVSDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLL 600
                 DA+     E+K    +D +GD  PIQDFEAM+SRRD  DW +KAI  MKN I  L+
Sbjct:   541 MITYDAK-----ENK----IDIVGDANPIQDFEAMISRRDKTDWTEKAITQMKNLIMKLV 591

Query:   601 EN-SNEGINYPKAVELLVALRKGCILEQ 627
             EN ++EG    KA+E ++ALRKGC+LEQ
Sbjct:   592 ENCTDEG---DKALECVLALRKGCVLEQ 616

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0015074 "DNA integration" evidence=TAS

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

GO:0006302 "double-strand break repair" evidence=IMP

GO:0006342 "chromatin silencing" evidence=RCA

GO:0016572 "histone phosphorylation" evidence=RCA

GO:0051567 "histone H3-K9 methylation" evidence=RCA

UNIPROTKB\|Q75IP6 KU80 "ATP-dependent DNA helicase 2 subunit KU80" [Oryza sativa Japonica Group (taxid:39947)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0286303 ku80 "DNA-dependent protein kinase (DNAPK) subunit" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NZI1 XRCC5 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-041008-108 xrcc5 "X-ray repair complementing defective repair in Chinese hamster cells 5" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SS19 XRCC5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|G3V817 Xrcc5 "Protein Xrcc5" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:104517 Xrcc5 "X-ray repair complementing defective repair in Chinese hamster cells 5" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|P13010 XRCC5 "X-ray repair cross-complementing protein 5" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

RGD\|3976 Xrcc5 "X-ray repair complementing defective repair in Chinese hamster cells 5" [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)
Q9FQ09	KU80_ARATH	3, ., 6, ., 4, ., 1, 2	0.6226	0.9290	0.9044	yes	no
Q75IP6	KU80_ORYSJ	3, ., 6, ., 4, ., 1, 2	0.6120	0.9410	0.9055	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	0.946
3rd Layer	3.6.4	0.963

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		662
cd00873		300	cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku8	1e-100
cd00594		272	cd00594, KU, Ku-core domain; includes the central	2e-67
pfam02735		200	pfam02735, Ku, Ku70/Ku80 beta-barrel domain	4e-40
smart00559		140	smart00559, Ku78, Ku70 and Ku80 are 70kDa and 80kD	7e-33
cd00788		287	cd00788, KU70, Ku-core domain, Ku70 subfamily; Ku7	3e-22
pfam03731		221	pfam03731, Ku_N, Ku70/Ku80 N-terminal alpha/beta d	7e-20
cd01458		218	cd01458, vWA_ku, Ku70/Ku80 N-terminal domain	8e-20
pfam08785		120	pfam08785, Ku_PK_bind, Ku C terminal domain like	3e-17
cd00789		256	cd00789, KU_like, Ku-core domain, Ku-like subfamil	1e-08
TIGR02772		258	TIGR02772, Ku_bact, Ku protein, prokaryotic	6e-08
COG1273		278	COG1273, COG1273, Ku-homolog [Replication, recombi	6e-07
pfam03730		95	pfam03730, Ku_C, Ku70/Ku80 C-terminal arm	3e-04
cd00198		161	cd00198, vWFA, Von Willebrand factor type A (vWA)	8e-04
TIGR00578		584	TIGR00578, ku70, ATP-dependent DNA helicase II, 70	0.001

>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

 Score =  309 bits (793), Expect = e-100
 Identities = 116/305 (38%), Positives = 163/305 (53%), Gaps = 8/305 (2%)

Query: 216 VTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVE 275
           V  F+G L L   + I V +YKKT EE+ P LKK SD    T + A  +VK +  Y   +
Sbjct: 1   VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAEK-TGEDAFEDVKSERSYDVND 59

Query: 276 DPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDV 335
           D    V  E  IKGYRYG  +VP+S  + EA K    K + +LGF  ASN+ R+Y M + 
Sbjct: 60  DDKTEVEKEDLIKGYRYGRDIVPLSEEDEEATKLSTSKGLDILGFIKASNVPRYYLMGES 119

Query: 336 NLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPD 395
           +  + +  +  A +A SAL RA+ E++K AI R V++       +GVL P + E     +
Sbjct: 120 SYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN-SEPQLGVLFPRIKED---YE 175

Query: 396 SFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSG---KGEILQ 452
                 LPFAEDVR+++FPS  K      P E+Q EA D+LV  +DL         E L+
Sbjct: 176 CLVLVRLPFAEDVRQYRFPSLDKLKTPNLPTEEQLEAMDDLVDSMDLDDDEEDDPEEALK 235

Query: 453 PELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFV 512
           P+ TPNP L+R Y  L  ++ H D   PPL   L +  EP   +L +S+ A+     +F 
Sbjct: 236 PDETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFP 295

Query: 513 IKENP 517
           +KE P
Sbjct: 296 LKEVP 300

The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity. Length = 300

>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\|217209 pfam02735, Ku, Ku70/Ku80 beta-barrel 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\|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\|217700 pfam03731, Ku_N, Ku70/Ku80 N-terminal alpha/beta domain	Back alignment and domain information

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

>gnl\|CDD\|117355 pfam08785, Ku_PK_bind, Ku C terminal domain like	Back alignment and domain information

>gnl\|CDD\|238408 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

>gnl\|CDD\|234004 TIGR02772, Ku_bact, Ku protein, prokaryotic	Back alignment and domain information

>gnl\|CDD\|224192 COG1273, COG1273, Ku-homolog [Replication, recombination, and repair]	Back alignment and domain information

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

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		662
TIGR00578		584	ku70 ATP-dependent DNA helicase ii, 70 kDa subunit	100.0
KOG2326		669	consensus DNA-binding subunit of a DNA-dependent p	100.0
cd00873		300	KU80 Ku-core domain, Ku80 subfamily; Ku80 is a sub	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
KOG2327		602	consensus DNA-binding subunit of a DNA-dependent p	100.0
cd00789		256	KU_like Ku-core domain, Ku-like subfamily; compose	100.0
TIGR02772		258	Ku_bact Ku protein, prokaryotic. Members of this p	100.0
PF02735		200	Ku: Ku70/Ku80 beta-barrel domain; InterPro: IPR006	100.0
COG1273		278	Ku-homolog [Replication, recombination, and repair	100.0
smart00559		140	Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of	100.0
PF03731		224	Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; Inte	99.95
PF08785		120	Ku_PK_bind: Ku C terminal domain like; InterPro: I	99.93
cd01458		218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	99.92
cd01453		183	vWA_transcription_factor_IIH_type Transcription fa	99.41
cd01452		187	VWA_26S_proteasome_subunit 26S proteasome plays a	99.25
PRK13685		326	hypothetical protein; Provisional	99.22
cd01451		178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	99.2
cd01465		170	vWA_subgroup VWA subgroup: Von Willebrand factor t	99.16
cd01480		186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	99.13
cd01467		180	vWA_BatA_type VWA BatA type: Von Willebrand factor	99.12
cd01472		164	vWA_collagen von Willebrand factor (vWF) type A do	99.09
cd01474		185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	99.07
cd01470		198	vWA_complement_factors Complement factors B and C2	99.03
TIGR03436		296	acidobact_VWFA VWFA-related Acidobacterial domain.	99.03
PRK13406		584	bchD magnesium chelatase subunit D; Provisional	99.01
cd01456		206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	99.0
cd01482		164	vWA_collagen_alphaI-XII-like Collagen: The extrace	98.99
PF13519		172	VWA_2: von Willebrand factor type A domain; PDB: 3	98.96
cd01473		192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	98.96
cd01471		186	vWA_micronemal_protein Micronemal proteins: The To	98.96
cd01469		177	vWA_integrins_alpha_subunit Integrins are a class	98.94
cd01450		161	vWFA_subfamily_ECM Von Willebrand factor type A (v	98.93
cd01476		163	VWA_integrin_invertebrates VWA_integrin (invertebr	98.93
PF03730		96	Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR00516	98.92
COG1240		261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	98.91
cd01463		190	vWA_VGCC_like VWA Voltage gated Calcium channel li	98.91
cd01461		171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	98.9
cd01475		224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	98.87
cd01455		191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	98.86
TIGR02031		589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.86
TIGR00868		863	hCaCC calcium-activated chloride channel protein 1	98.84
cd01466		155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	98.82
cd01454		174	vWA_norD_type norD type: Denitrifying bacteria con	98.81
cd01477		193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	98.78
TIGR02442		633	Cob-chelat-sub cobaltochelatase subunit. A number	98.78
PTZ00441		576	sporozoite surface protein 2 (SSP2); Provisional	98.73
smart00327		177	VWA von Willebrand factor (vWF) type A domain. VWA	98.72
cd00198		161	vWFA Von Willebrand factor type A (vWA) domain was	98.7
cd01460		266	vWA_midasin VWA_Midasin: Midasin is a member of th	98.69
cd01464		176	vWA_subfamily VWA subfamily: Von Willebrand factor	98.67
PF13768		155	VWA_3: von Willebrand factor type A domain	98.65
PF00092		178	VWA: von Willebrand factor type A domain; InterPro	98.55
cd01481		165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	98.54
cd01462		152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	98.47
TIGR03788		596	marine_srt_targ marine proteobacterial sortase tar	98.41
PF04056		193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	98.15
KOG2884		259	consensus 26S proteasome regulatory complex, subun	97.84
cd01457		199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	97.7
COG5148		243	RPN10 26S proteasome regulatory complex, subunit R	97.46
PRK10997		487	yieM hypothetical protein; Provisional	97.05
KOG2807		378	consensus RNA polymerase II transcription initiati	96.81
COG4867		652	Uncharacterized protein with a von Willebrand fact	96.78
COG4245		207	TerY Uncharacterized protein encoded in toxicity p	96.64
PF11265		226	Med25_VWA: Mediator complex subunit 25 von Willebr	96.63
PF05762		222	VWA_CoxE: VWA domain containing CoxE-like protein;	96.43
COG2425		437	Uncharacterized protein containing a von Willebran	96.38
cd01479		244	Sec24-like Sec24-like: Protein and membrane traffi	96.17
TIGR00627		279	tfb4 transcription factor tfb4. This family is bas	95.68
PF10138		200	vWA-TerF-like: vWA found in TerF C terminus ; Inte	95.67
cd01468		239	trunk_domain trunk domain. COPII-coated vesicles c	95.57
PF04811		243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	95.11
COG4548		637	NorD Nitric oxide reductase activation protein [In	93.89
COG5242		296	TFB4 RNA polymerase II transcription initiation/nu	93.55
cd01478		267	Sec23-like Sec23-like: Protein and membrane traffi	93.19
PF12257		281	DUF3608: Protein of unknown function (DUF3608); In	92.98
PF03850		276	Tfb4: Transcription factor Tfb4; InterPro: IPR0046	92.83
TIGR01651		600	CobT cobaltochelatase, CobT subunit. This model de	92.79
KOG2487		314	consensus RNA polymerase II transcription initiati	92.71
PTZ00395		1560	Sec24-related protein; Provisional	92.4
PF11775		219	CobT_C: Cobalamin biosynthesis protein CobT VWA do	92.3
PLN00162		761	transport protein sec23; Provisional	92.13
KOG2326		669	consensus DNA-binding subunit of a DNA-dependent p	91.75
KOG1984		1007	consensus Vesicle coat complex COPII, subunit SFB3	91.68
smart00187		423	INB Integrin beta subunits (N-terminal portion of	90.21
PF09967		126	DUF2201: VWA-like domain (DUF2201); InterPro: IPR0	89.61
KOG2353		1104	consensus L-type voltage-dependent Ca2+ channel, a	89.59
cd01459		254	vWA_copine_like VWA Copine: Copines are phospholip	88.5
COG5151		421	SSL1 RNA polymerase II transcription initiation/nu	87.06
COG2718		423	Uncharacterized conserved protein [Function unknow	84.64
KOG1986		745	consensus Vesicle coat complex COPII, subunit SEC2	84.55
KOG3768		888	consensus DEAD box RNA helicase [General function	80.2
TIGR02877		371	spore_yhbH sporulation protein YhbH. This protein	80.18
PF04285		421	DUF444: Protein of unknown function (DUF444); Inte	80.15
PF07002		146	Copine: Copine; InterPro: IPR010734 This represent	80.13

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

Probab=100.00  E-value=1.3e-81  Score=707.11  Aligned_cols=473  Identities=19%  Similarity=0.267  Sum_probs=400.0

Q ss_pred             CCeEEEEEEeCCCCcCCc---------hhHHHHHHHHHHHHHHhccCccEEEEEEEcCCCcCccccccCCCcccEEEEec
Q 006065            4 TREALLLLLDVSPSMHSV---------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD   74 (662)
Q Consensus         4 ~Kea~vflIDvs~sM~~~---------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~~~~~y~nI~v~~~   74 (662)
                      .|||+|||||||++|+++         +..|++|+.+++++|||++++|+||||||||++|+|++     +|+||+|+++
T Consensus         9 ~keailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t~n~~-----~~~~i~v~~~   83 (584)
T TIGR00578         9 GRDSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNSV-----NFKNIYVLQE   83 (584)
T ss_pred             ceeEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCCCCcc-----CCCceEEEee
Confidence            699999999999999962         67899999999999999999999999999999999987     6999999999


Q ss_pred             cCCCCHHHHHHhhcCCCCCC------------CCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCch
Q 006065           75 IKVVDGHLVQSLKHLPQGTC------------AGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKE  142 (662)
Q Consensus        75 l~~~~~~~l~~L~~l~~~~~------------~gd~~daL~va~d~l~~~~~~kk~~~krIvLiTD~~~p~~~~~~~~~~  142 (662)
                      |+.|+++.++.|++|..+.+            .+++.||||+|++||.+ ++ +++.+||||||||+++|+..  +....
T Consensus        84 L~~p~a~~i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~-~~-~k~~~kRI~lfTd~D~P~~~--~~~~~  159 (584)
T TIGR00578        84 LDNPGAKRILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSD-VQ-FRMSHKRIMLFTNEDNPHGN--DSAKA  159 (584)
T ss_pred             CCCCCHHHHHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHh-cc-hhhcCcEEEEECCCCCCCCC--chhHH
Confidence            99999999999998754311            24779999999999986 33 46789999999999999985  23344


Q ss_pred             hhHHHHHHHHhhCCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhccCC----eeeehh-chHHhhcccccccCCcce
Q 006065          143 DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA----KTLFVD-STTSLRGARKTRDISPVT  217 (662)
Q Consensus       143 ~~~~~ia~~l~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~L~~l~~~~~g----~~~~~~-~a~~ll~~~~~k~~~~~~  217 (662)
                      +++..+|++|++.||.|++|+++.  +++++.      ..|+..+....++    ...... ...+++..++.|.+++|+
T Consensus       160 ~~a~~~a~dl~~~gi~ielf~l~~--~~~Fd~------s~Fy~dii~~~~~~~~~~~~~~~~~l~~l~~~l~~k~~~kR~  231 (584)
T TIGR00578       160 SRARTKAGDLRDTGIFLDLMHLKK--PGGFDI------SLFYRDIITDAEDEDLGVHPEESSKLEDLLRKVRAKETRKRA  231 (584)
T ss_pred             HHHHHHHHHHHhcCeEEEEEecCC--CCCCCh------hhhhHhhhccccccccccCcchhHHHHHHHHHHhhcccceee
Confidence            566889999999999999999853  333332      2344444321111    111111 234667889999999999


Q ss_pred             eeeeeeeecCCeEEEEEEEeecccccCCC-ceEeccCCCCCccccccceEEEEEEEecCCCCCCCCccccccceeeCCee
Q 006065          218 IFRGDLELSEKMKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV  296 (662)
Q Consensus       218 ~~~g~L~ig~~l~I~V~~Y~~~~~~k~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~  296 (662)
                      .|+|+|+||++++|+|++|.+++++++|. .+.+..+        ...|+.+|+|+ +.+++++|+++|++|||+||+++
T Consensus       232 ~~~~~L~lg~~~~I~V~~Y~~~~~~~~~~~~~l~~~~--------~~~v~~~~~~~-~~dtg~~V~~~~i~Kgy~yGg~~  302 (584)
T TIGR00578       232 LSRLKLKLNKDVVMSVGIYNLVQKAGKPAPVKLYRET--------NEPVKTKTRTF-NMDTGSLLLPSDTKRSQTYGGRQ  302 (584)
T ss_pred             EEeccEEECCCCEEEEEEEEEEEeecCCceEEEecCC--------ceeeEEEEEEE-ecCCccccCHHHceeeeeECCEE
Confidence            99999999999999999999999987665 4666543        36799999898 47788899999999999999999


Q ss_pred             EeCChhhHHhhccCCCccEEEEeEeeCCCCcchhccCCeEEEEcCCCC-hhhHHHHHHHHHHHHhcCceeEEEEEecCCC
Q 006065          297 VPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGN-SRATVAVSALARAMKEMNKVAIVRCVWRQGQ  375 (662)
Q Consensus       297 Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~-~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~  375 (662)
                      |+|+++|++++|..++|+|+||||+|.+.|+++|++++++||+|+++. .+|.+||+||+++|.++++|||||||+|+|+
T Consensus       303 V~~t~ee~~~lk~~~~~~l~ilGF~~~s~l~~~~~~~~s~fi~Pde~~~~gs~~afsaL~~~l~~~~kvAI~~~v~r~~~  382 (584)
T TIGR00578       303 IYLEKEETEELKRFDPPGLQLMGFKPLSMLKKHHHLRPSLFVYPEESLVRGSTTLFSALLQKCLEKEVAALCRYISRRNQ  382 (584)
T ss_pred             EecCHHHHHHHhccCCCceEEEeeccHHHCCchhhcCCceEEecCCcccccHHHHHHHHHHHHHhcCcEEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999999854 4799999999999999999999999999998


Q ss_pred             CceEEEEeeccccCC-----CCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcc
Q 006065          376 QSVVVGVLTPNVSEK-----INIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEI  450 (662)
Q Consensus       376 ~p~~v~~L~P~~~~~-----~~~~~~l~~v~LPfaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~  450 (662)
                      .|. +++|+|+.++.     +..|+||++++|||+||||+++|++      ...++++|+++|++||++|+++       
T Consensus       383 ~P~-lvaL~P~~~~~d~~~~q~~p~G~~l~~LPfadDIR~~~~~~------~~~~~~e~~~~a~~LI~~l~~~-------  448 (584)
T TIGR00578       383 PPY-FVALVPQEEELDDQKIQVTPPGFHLVFLPFADDKRKVPFTE------KVKATPEQVDKMKAIVEKLRFT-------  448 (584)
T ss_pred             CCE-EEEEeCCcccccccCCccCCCeEEEEecCchhhccCCCCcc------cCCCCHHHHHHHHHHHHhcCCC-------
Confidence            755 55788997532     2357899999999999999998742      2469999999999999999997       


Q ss_pred             CCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCChHHH-HHHHHHHHHHHh-hcCCccCCCccc
Q 006065          451 LQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL-AESQSAIDAFCG-QFVIKENPKLKK  521 (662)
Q Consensus       451 ~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~-~~~~~~l~~~k~-~f~~~~~~~k~~  521 (662)
                      |+|+.|+||+|||||++|+++||+++.|.++.|.++     |+...+ +++++.+++|++ +|+.+++++++.
T Consensus       449 y~P~~~~NP~LQ~hY~~LealAL~~~~~~~~~D~tl-----p~~~~i~~r~~~~i~~~~~~~~~~~~~~~~~~  516 (584)
T TIGR00578       449 YRSDSFENPVLQQHFRNLEALALDMMEPEQAVDLTL-----PKVEAMKKRLGSLVDEFKELVYPPDYNPEGKV  516 (584)
T ss_pred             CCcccCCChHHHHHHHHHHHHhCCCCCCCCCccccc-----CCHHHHHHHHHHHHHHHHHHhcccccCccccc
Confidence            999999999999999999999999999988888654     554445 478999999999 888888876543

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.

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

>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

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

>TIGR02772 Ku_bact Ku protein, prokaryotic	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

>COG1273 Ku-homolog [Replication, recombination, and repair]	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

>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

>PF08785 Ku_PK_bind: Ku C terminal domain like; InterPro: IPR014893 The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired	Back alignment and domain information

>cd01458 vWA_ku Ku70/Ku80 N-terminal domain	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

>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

>PRK13685 hypothetical protein; Provisional	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

>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

>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

>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

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

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

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

>PRK13406 bchD magnesium chelatase subunit D; Provisional	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

>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

>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

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

>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

>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

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

>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

>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

>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

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

>TIGR00868 hCaCC calcium-activated chloride channel protein 1	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

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

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

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

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

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

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

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

>PF13768 VWA_3: von Willebrand factor type A 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

>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

>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein	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

>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

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

>PRK10997 yieM hypothetical protein; Provisional	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

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

>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

>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

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

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

>TIGR00627 tfb4 transcription factor tfb4	Back alignment and domain information

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

>cd01468 trunk_domain trunk domain	Back alignment and domain information

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

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

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

>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

>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

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

>TIGR01651 CobT cobaltochelatase, CobT subunit	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

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

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

>PLN00162 transport protein sec23; Provisional	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

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

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

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

>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]	Back alignment and domain information

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

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

>COG2718 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

>KOG3768 consensus DEAD box RNA helicase [General function prediction only]	Back alignment and domain information

>TIGR02877 spore_yhbH sporulation protein YhbH	Back alignment and domain information

>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56	Back alignment and domain information

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		662
1jeq_B		565	Crystal Structure Of The Ku Heterodimer Length = 56		3e-27

>pdb|1JEQ|B Chain B, Crystal Structure Of The Ku Heterodimer Length = 565

Back alignment and structure

Iteration: 1

Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust. Identities = 130/549 (23%), Positives = 243/549 (44%), Gaps = 70/549 (12%) Query: 1 MART--REALLLLLDVSPSMHSVLPDVE-------KLCSRLIQKKLIYGKNHEVGVILFG 51 M R+ + A++L +DV +M + +P +E K+ + +Q+++ E+ ++LFG Sbjct: 1 MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG 60 Query: 52 TEETENELTKEVGG--YEHVKVLQDIKVVDGHLVQSLKHLPQ-GTCAGDFLDAIVVGVDM 108 T+ T+N L+ GG Y+++ V + + + D L++ ++ Q G+ DFLDA++V +D+ Sbjct: 61 TDGTDNPLS---GGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDV 117 Query: 109 LI---------KKYGETYK------GKKHLCLITDAL--CPL-----------KDPDVGT 140 + K++ E + K L +I +L C + K+ G Sbjct: 118 IQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGD 177 Query: 141 KEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN-DNLLNIFSKKSSAKTLFVD 199 + D + +F L+ + L + + +E D L I+S S + L V Sbjct: 178 RGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCV- 236 Query: 200 STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDK 259 + + P L + + I++ YK +E+ K + Sbjct: 237 ----FKKIERHSIHWPCR-----LTIGSNLSIRIAAYKSILQERV----KKTWTVVDAKT 283 Query: 260 FATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPE-KSVKLL 318 +++ + Y +D V E I+G+RYG +VP S + E +K+K E K +L Sbjct: 284 LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL 343 Query: 319 GFTDASNILRHYYMKDVNL-FIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQS 377 GF +S + R ++M + L A + A VA+S+L A+ +++ VAIVR + + + + Sbjct: 344 GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDK-RAN 402 Query: 378 VVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLV 437 VGV P++ + + LPF ED+R++ F S K + P E Q A D L+ Sbjct: 403 PQVGVAFPHIKHNY---ECLVYVQLPFMEDLRQYMFSSL-KNSKKYAPTEAQLNAVDALI 458 Query: 438 KMLDLAPSGKG-----EILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEP 492 + LA + ++ PNP +R + L ++ H PP+ + + P Sbjct: 459 DSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNP 518 Query: 493 DPTLLAESQ 501 + +SQ Sbjct: 519 PAEVTTKSQ 527

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		662
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	1e-109
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	1e-86
1q2z_A		120	ATP-dependent DNA helicase II, 80 kDa subunit; KU,	7e-14
1rw2_A		152	ATP-dependent DNA helicase II, 80 kDa subunit; KU8	2e-13
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
3ism_C		359	CG4930; endonuclease, endonuclease inhibitor compl	1e-04

>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

 Score =  340 bits (873), Expect = e-109
 Identities = 120/580 (20%), Positives = 238/580 (41%), Gaps = 60/580 (10%)

Query: 1   MART--REALLLLLDVSPSMHSVLPDVE-------KLCSRLIQKKLIYGKNHEVGVILFG 51
           M R+  + A++L +DV  +M + +P +E       K+ +  +Q+++      E+ ++LFG
Sbjct: 1   MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG 60

Query: 52  TEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQ-GTCAGDFLDAIVVGVDMLI 110
           T+ T+N L+     Y+++ V + + + D  L++ ++   Q G+   DFLDA++V +D++ 
Sbjct: 61  TDGTDNPLSGG-DQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQ 119

Query: 111 KKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSG 170
            +       K+H+ + TD             + Q+  I   +    + ++  +  +    
Sbjct: 120 HETIGKKFEKRHIEIFTDLSSR-------FSKSQLDIIIHSLKKCDISLQFFLPFSLGKE 172

Query: 171 EP---------HMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPV----- 216
           +           +     +  L  I  ++     +      SL G     +I        
Sbjct: 173 DGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLR 232

Query: 217 ------------TIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHE 264
                         +   L +   + I++  YK   +E+        D           +
Sbjct: 233 KLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDA----KTLKKED 288

Query: 265 VKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKP-EKSVKLLGFTDA 323
           ++ +  Y   +D    V  E  I+G+RYG  +VP S  + E +K+K   K   +LGF  +
Sbjct: 289 IQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKS 348

Query: 324 SNILRHYYMKD-VNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGV 382
           S + R ++M + V    A   +  A VA+S+L  A+ +++ VAIVR  + +   +  VGV
Sbjct: 349 SQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRA-NPQVGV 407

Query: 383 LTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDL 442
             P++       +   +  LPF ED+R++ F S       + P E Q  A D L+  + L
Sbjct: 408 AFPHIKHN---YECLVYVQLPFMEDLRQYMFSSLKN-SKKYAPTEAQLNAVDALIDSMSL 463

Query: 443 APSGKG-----EILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL 497
           A   +      ++      PNP  +R +  L  ++ H     PP+   +  +  P   + 
Sbjct: 464 AKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVT 523

Query: 498 AESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEP 537
            +SQ  +      F + E  K  + T + + +        
Sbjct: 524 TKSQIPLSKIKTLFPLIEAKKKDQVTAQEIFQDNHEDGPT 563

PyMOL of 1jey

>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

>1q2z_A ATP-dependent DNA helicase II, 80 kDa subunit; KU, DNA repair, protein structure, spectroscopy, DNA-PK, KU86, KU80, protein binding; NMR {Homo sapiens} SCOP: a.118.19.1 Length = 120	Back alignment and structure

>1rw2_A ATP-dependent DNA helicase II, 80 kDa subunit; KU80, NHEJ, structure, DNA-PK, DNA binding protein; NMR {Homo sapiens} SCOP: a.118.19.1 Length = 152	Back alignment and structure

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

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

>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

>3ism_C CG4930; endonuclease, endonuclease inhibitor complex, metal complex, hydrolase, hydrolase inhibitor-hydrolase complex; 2.20A {Drosophila melanogaster} Length = 359	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		662
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	100.0
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	100.0
1rw2_A		152	ATP-dependent DNA helicase II, 80 kDa subunit; KU8	99.93
1q2z_A		120	ATP-dependent DNA helicase II, 80 kDa subunit; KU,	99.92
4b4t_W		268	RPN10, 26S proteasome regulatory subunit RPN10; hy	99.44
2x5n_A		192	SPRPN10, 26S proteasome regulatory subunit RPN10;	99.39
3ibs_A		218	Conserved hypothetical protein BATB; structural ge	99.24
3ism_C		359	CG4930; endonuclease, endonuclease inhibitor compl	99.2
1ijb_A		202	VON willebrand factor; dinucleotide-binding fold,	99.13
2b2x_A		223	Integrin alpha-1; computational design, antibody-a	99.11
1pt6_A		213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	99.08
1q0p_A		223	Complement factor B; VON willebrand factor, MAC-1,	99.08
1shu_X		182	Anthrax toxin receptor 2; alpha/beta rossmann fold	99.06
1v7p_C		200	Integrin alpha-2; snake venom, C-type lectin, anta	99.04
1n3y_A		198	Integrin alpha-X; alpha/beta rossmann fold, cell a	99.04
3n2n_F		185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	99.04
4hqo_A		266	Sporozoite surface protein 2; malaria, gliding mot	99.01
1atz_A		189	VON willebrand factor; collagen-binding, hemostasi	99.0
4hqf_A		281	Thrombospondin-related anonymous protein, trap; ma	98.98
2xgg_A		178	Microneme protein 2; A/I domain, cell adhesion, hy	98.98
1mf7_A		194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	98.93
2odp_A		509	Complement C2; C3/C5 convertase, complement serin	98.92
4fx5_A		464	VON willebrand factor type A; structural genomics,	98.84
2x31_A		189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	98.79
3ism_C		359	CG4930; endonuclease, endonuclease inhibitor compl	98.77
1rrk_A		497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	98.76
3hrz_D		741	Complement factor B; serine protease, glycosilated	98.75
3zqk_A		199	VON willebrand factor; blood clotting, adamts-13,	98.71
3k6s_A		1095	Integrin alpha-X; cell receptor, adhesion molecule	98.42
1mjn_A		179	Integrin alpha-L; rossmann fold, immune system; 1.	98.42
1yvr_A		538	RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein,	97.93
2nvo_A		535	RO sixty-related protein, RSR; alpha helical repea	97.89
2ww8_A		893	RRGA, cell WALL surface anchor family protein; IGG	97.71
3rag_A		242	Uncharacterized protein; structural genomics, PSI-	97.71
2iue_A		212	Pactolus I-domain; membrane protein, CD, ITC, limb	97.11
3rag_A		242	Uncharacterized protein; structural genomics, PSI-	96.47
3fcs_B		690	Integrin beta-3; beta propeller, rossmann fold, EG	96.43
3k6s_B		687	Integrin beta-2; cell receptor, adhesion molecule,	95.82
1pcx_A		810	Protein transport protein SEC24; 2.50A {Saccharomy	95.76
3vi3_B		454	Integrin beta-1; beta propeller fold, rossman fold	95.69
2nut_A		769	Protein transport protein SEC23A; human copii SEC2	95.67
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	95.13
3t3p_B		472	Integrin beta-3; integrin, cell adhesion, blood cl	94.56
3v4v_B		503	Integrin beta-7; cell adhesion, madcam-1, membrane	94.56
1m2o_A		768	SEC23, protein transport protein SEC23, SEC23P; zi	94.38
3eh1_A		751	Protein transport protein SEC24B; copii coat prote	93.1
3efo_B		770	SEC24 related gene family, member D; copii, coat p	92.22
3eh2_A		766	Protein transport protein SEC24C; copii-coat prote	92.09

>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

Probab=100.00  E-value=4.6e-86  Score=748.88  Aligned_cols=506  Identities=23%  Similarity=0.389  Sum_probs=433.8

Q ss_pred             CCC--CCeEEEEEEeCCCCcCC-------chhHHHHHHHHHHHHHHhccCccEEEEEEEcCCCcCccccccCCCcccEEE
Q 006065            1 MAR--TREALLLLLDVSPSMHS-------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKV   71 (662)
Q Consensus         1 ma~--~Kea~vflIDvs~sM~~-------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~~~~~y~nI~v   71 (662)
                      ||.  +||++|||||+|+||++       .|+.|++++..++++||+++++|+||||+|||+.+.|+++.+ ++|+||++
T Consensus         1 ~~~~~~ke~iv~~iDvS~SM~~~d~~~~srl~~ak~~i~~~i~~ki~~~~~D~vGlv~f~~~~~~~plt~d-~~y~~i~v   79 (565)
T 1jey_B            1 MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPLSGG-DQYQNITV   79 (565)
T ss_dssp             -----CCEEEEEEEECCGGGGCCBTTBCCHHHHHHHHHHHHHHHHHHTTCCCEEEEEEESCSSCBSTTCTT-TCSTTEEE
T ss_pred             CCCCCCceEEEEEEECChHhcccCCCCCCcHHHHHHHHHHHHHHHhcCCCCCEEEEEEEccCCCCCccccc-cCCCceEE
Confidence            665  56999999999999986       378899999999999999999999999999999999998655 68999999


Q ss_pred             EeccCCCCHHHHHHhhc-CCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHH
Q 006065           72 LQDIKVVDGHLVQSLKH-LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIAR  150 (662)
Q Consensus        72 ~~~l~~~~~~~l~~L~~-l~~~~~~gd~~daL~va~d~l~~~~~~kk~~~krIvLiTD~~~p~~~~~~~~~~~~~~~ia~  150 (662)
                      +++|+.++++.++.|.+ +..+...+++.+||++|+++|.+.+.+++..+|||||||||++|++.       +++..+++
T Consensus        80 l~~l~~~~~~~l~~l~~~l~~~~~~t~i~~al~~A~~~l~~~~~~~k~~~krIiLlTDg~~~~~~-------~~~~~~a~  152 (565)
T 1jey_B           80 HRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHETIGKKFEKRHIEIFTDLSSRFSK-------SQLDIIIH  152 (565)
T ss_dssp             EEEEECCCHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHHSSSSCCSEEEEEEECCCCSCCCC-------TTHHHHHH
T ss_pred             eecCCCCCHHHHHHHHhhccCCCccccHHHHHHHHHHHHHHHhhcccccccEEEEEeCCCCCCCH-------HHHHHHHH
Confidence            99999999999999998 76665678999999999999987544444467999999999999853       57899999


Q ss_pred             HHhhCCcEEE-EEeeccC-----CC----------------CCCCcchhhhhhHHHHHHhhccCC-----eeeehhchHH
Q 006065          151 QMVAFGLRMK-NIVVRAS-----LS----------------GEPHMRVIIENDNLLNIFSKKSSA-----KTLFVDSTTS  203 (662)
Q Consensus       151 ~l~~~gI~l~-vi~i~~~-----~~----------------~~~~~~~~~~ne~~L~~l~~~~~g-----~~~~~~~a~~  203 (662)
                      .+++.||.|+ +||++.+     ++                ++........|+.+|+.+++.++|     .+++++++++
T Consensus       153 ~l~~~gI~i~~vig~g~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~e~~L~~ia~~~~G~~~~s~~~~~~~~~~  232 (565)
T 1jey_B          153 SLKKCDISLQFFLPFSLGKEDGSGDRGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLR  232 (565)
T ss_dssp             HHHHTTEEEEEEESSCCC----------CCCCTTCSSCCCCTTTSCHHHHHHHHHHHHHHHHHHCGGGGGGEEEHHHHTT
T ss_pred             HHHhcCcEEEEEeccCCCcCCcccccccccccccccccccchhccccchhhhHHHHHHHHHhcCCCcccceeecHHHHHH
Confidence            9999999999 8887631     10                111112335789999999999999     8999999999


Q ss_pred             hhcccccccCCcceeeeeeeeecCCeEEEEEEEeecccccC-CCceEeccCCCCCccccccceEEEEEEEecCCCCCCCC
Q 006065          204 LRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKF-PTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVP  282 (662)
Q Consensus       204 ll~~~~~k~~~~~~~~~g~L~ig~~l~I~V~~Y~~~~~~k~-p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~  282 (662)
                      ++..++.+.++++ .|+|.|+||+.++|+|++|++|+++++ +.++.......     ....|+.+++|+.+++++++|+
T Consensus       233 ~l~~~k~~~~r~~-~~~g~l~lg~~v~I~V~~Y~~~~~~~~~~~~~~l~~~~~-----~~~~V~~~~~y~v~~~~~~~V~  306 (565)
T 1jey_B          233 KLCVFKKIERHSI-HWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTL-----KKEDIQKETVYCLNDDDETEVL  306 (565)
T ss_dssp             SSTTTGGGCCCCC-CEEEEEEETTTEEEEEEEEEEECCCCCCCCCEEEETTTC-----CSTTEEEEEEEEESSSSCCEEC
T ss_pred             HhccCcceeeccc-ccccceEECCCcEEEEEEEeeehhcccCCceEEecCccC-----CCcceEEEEEEEecCCCCcccC
Confidence            9999999888876 799999999889999999999999984 44433332210     1357999999965788999999


Q ss_pred             ccccccceeeCCeeEeCChhhHHhhccCCC-ccEEEEeEeeCCCCcchhccCCe-EEEEcCCCChhhHHHHHHHHHHHHh
Q 006065          283 PEQRIKGYRYGPQVVPISSAEWEAVKFKPE-KSVKLLGFTDASNILRHYYMKDV-NLFIAEPGNSRATVAVSALARAMKE  360 (662)
Q Consensus       283 ~ed~~kgy~yG~~~Vp~s~~e~~~~k~~~~-~~l~ilGF~~~~~i~~~~~~~~~-~~i~p~~~~~~s~~afsaL~~Am~e  360 (662)
                      ++|++|||+||+++|+|+++|++.+++.+. ++|+|+||++.++|+++|+++++ ||++|++++.+|..||+||++||.+
T Consensus       307 ~~di~kgy~yg~~~V~~~~ee~~~~~~~~~~~~l~ilgFv~~~~i~~~~~~~~s~y~l~p~~~~~~s~~af~aL~~al~~  386 (565)
T 1jey_B          307 KEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDD  386 (565)
T ss_dssp             GGGEEEEEEETTEEEECCHHHHHHHSCCCCCSEEEEEEEEEGGGSCGGGCEEEEEEEEEECTTCHHHHHHHHHHHHHHHH
T ss_pred             hHHeeeeEecCCeeeccCHHHHHHhcccCCCCcEEEEeeccHHHCCHhhccCCceEEEeCCCCChhhHHHHHHHHHHHHH
Confidence            999999999999999999999999999875 99999999999999999999976 8999988888999999999999999


Q ss_pred             cCceeEEEEEecCCCCceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHc
Q 006065          361 MNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKML  440 (662)
Q Consensus       361 ~~~vaI~r~v~r~~~~p~~v~~L~P~~~~~~~~~~~l~~v~LPfaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m  440 (662)
                      +++|||||||+|.++. |.+|+|+|+++..   ++||++++|||+||||.++||++... ....|+++|+++|++||++|
T Consensus       387 ~~kvaIar~v~r~~~~-p~l~aL~P~~~~~---~~gl~l~~Lpf~ddvR~~~f~~l~~~-~~~~~~~~~l~~a~~lId~m  461 (565)
T 1jey_B          387 LDMVAIVRYAYDKRAN-PQVGVAFPHIKHN---YECLVYVQLPFMEDLRQYMFSSLKNS-KKYAPTEAQLNAVDALIDSM  461 (565)
T ss_dssp             TTEEEEEEEESSSSSC-CEEEEEEEEECSS---CEEEEEEECCCGGGBCCCCCCCSTTC-SSSCCCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEEEEcCCCC-cEEEEEeccccCC---CCeEEEEccCCHHHcccccCCCCCcc-ccCCCCHHHHHHHHHHHHhc
Confidence            9999999999999975 5577999997654   47999999999999999999998632 24579999999999999999


Q ss_pred             CCCCCC-----CCccCCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCChHHHHHHHHHHHHHHhhcCCcc
Q 006065          441 DLAPSG-----KGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKE  515 (662)
Q Consensus       441 ~l~~~~-----~~e~~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~l~~~k~~f~~~~  515 (662)
                      +++..+     .++.|+|+.++||++||||++|+++|++++.|+|+++++|.++++||+.+.++++++|++|+++|++++
T Consensus       462 ~~~~~~~~~~~~~~~~~p~~~~np~lq~~~~~i~~kal~~~~~~p~~d~~l~~~~~p~~~~~~~~~~~l~~~k~~f~~~~  541 (565)
T 1jey_B          462 SLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIE  541 (565)
T ss_dssp             BCEECCTTSSCCEESCCGGGSCCHHHHHHHHHHHHHHHCTTSCCCCCCHHHHHHHSCCHHHHHHHHHHHHHHHHHSCCEE
T ss_pred             cCCcccccCcchhcccCcccCCCHHHHHHHHHHHHHhcCCCCCCCCcCHHHHhhcCCCHHHHHHHHHHHHHHHHhCCcee
Confidence            996311     123599999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccchhhhc
Q 006065          516 NPKLKKSTRRFL  527 (662)
Q Consensus       516 ~~~k~~~~~~~~  527 (662)
                      +  |+|+++..|
T Consensus       542 ~--~~k~~~~~~  551 (565)
T 1jey_B          542 A--KKKDQVTAQ  551 (565)
T ss_dssp             C--CCC------
T ss_pred             h--hcccchhhH
Confidence            9  444445555

PyMOL of 1jey

>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

>1rw2_A ATP-dependent DNA helicase II, 80 kDa subunit; KU80, NHEJ, structure, DNA-PK, DNA binding protein; NMR {Homo sapiens} SCOP: a.118.19.1	Back alignment and structure

>1q2z_A ATP-dependent DNA helicase II, 80 kDa subunit; KU, DNA repair, protein structure, spectroscopy, DNA-PK, KU86, KU80, protein binding; NMR {Homo sapiens} SCOP: a.118.19.1	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

>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

>3ism_C CG4930; endonuclease, endonuclease inhibitor complex, metal complex, hydrolase, hydrolase inhibitor-hydrolase complex; 2.20A {Drosophila melanogaster}	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

>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

>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

>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

>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

>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

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

>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

>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

>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

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

>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

>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

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

>3ism_C CG4930; endonuclease, endonuclease inhibitor complex, metal complex, hydrolase, hydrolase inhibitor-hydrolase complex; 2.20A {Drosophila melanogaster}	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

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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

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

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

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

>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

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

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

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

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		662
d1jeyb1		304	b.131.1.2 (B:242-545) Ku80 subunit middle domain {	6e-74
d1jeya1		281	b.131.1.1 (A:254-534) Ku70 subunit middle domain {	3e-56
d1jeyb2		236	c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain	2e-19
d1rw2a_		152	a.118.19.1 (A:) C-terminal domain of Ku80 {Human (	1e-16
d1jeya2		220	c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain	4e-10

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


class: All beta proteins
fold: SPOC domain-like
superfamily: SPOC domain-like
family: Ku80 subunit middle domain
domain: Ku80 subunit middle domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  238 bits (608), Expect = 6e-74
 Identities = 76/307 (24%), Positives = 136/307 (44%), Gaps = 16/307 (5%)

Query: 219 FRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPS 278
           +   L +   + I++  YK   +E+        D           +++ +  Y   +D  
Sbjct: 6   WPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVD----AKTLKKEDIQKETVYCLNDDDE 61

Query: 279 KVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPE-KSVKLLGFTDASNILRHYYMKDVNL 337
             V  E  I+G+RYG  +VP S  + E +K+K E K   +LGF  +S + R ++M +  L
Sbjct: 62  TEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVL 121

Query: 338 FI-AEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDS 396
            + A   +  A VA+S+L  A+ +++ VAIVR  + +   +  VGV  P++    +  + 
Sbjct: 122 KVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRA-NPQVGVAFPHIK---HNYEC 177

Query: 397 FYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKG-----EIL 451
             +  LPF ED+R++ F S       + P E Q  A D L+  + LA   +      ++ 
Sbjct: 178 LVYVQLPFMEDLRQYMFSSLKN-SKKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLEDLF 236

Query: 452 QPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQF 511
                PNP  +R +  L  ++ H     PP+   +  +  P   +  +SQ  +      F
Sbjct: 237 PTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLF 296

Query: 512 VIKENPK 518
            + E  K
Sbjct: 297 PLIEAKK 303

PyMOL of d1jeyb1

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

>d1rw2a_ a.118.19.1 (A:) C-terminal domain of Ku80 {Human (Homo sapiens) [TaxId: 9606]} Length = 152	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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		662
d1jeyb1		304	Ku80 subunit middle domain {Human (Homo sapiens) [	100.0
d1jeya1		281	Ku70 subunit middle domain {Human (Homo sapiens) [	100.0
d1rw2a_		152	C-terminal domain of Ku80 {Human (Homo sapiens) [T	99.94
d1jeyb2		236	Ku80 subunit N-terminal domain {Human (Homo sapien	99.91
d1jeya2		220	Ku70 subunit N-terminal domain {Human (Homo sapien	99.86
d1shux_		181	Capillary morphogenesis protein 2 domain {Human (H	99.0
d1atza_		184	von Willebrand factor A3 domain, vWA3 {Human (Homo	98.91
d1pt6a_		192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	98.72
d1n3ya_		189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	98.68
d1v7pc_		193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	98.65
d1ijba_		202	von Willebrand factor A1 domain, vWA1 {Human (Homo	98.64
d1q0pa_		209	Complement factor B domain {Human (Homo sapiens) [	98.62
d1mf7a_		194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	98.43
d1mjna_		179	Integrin CD11a/CD18 (Leukocyte function associated	98.11
d1yvra2		174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	97.9
d1tyeb2		248	Integrin beta A domain {Human (Homo sapiens) [TaxI	97.86
d2qtva3		271	Sec23 {Baker's yeast (Saccharomyces cerevisiae) [T	95.16
d1pd0a3		252	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	94.68

>d1jeyb1 b.131.1.2 (B:242-545) Ku80 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: Ku80 subunit middle domain
domain: Ku80 subunit middle domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=8.2e-60  Score=490.28  Aligned_cols=293  Identities=26%  Similarity=0.464  Sum_probs=263.3

Q ss_pred             eeeeeeeeecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceEEEEEEEecCCCCCCCCccccccceeeCCee
Q 006065          217 TIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV  296 (662)
Q Consensus       217 ~~~~g~L~ig~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~  296 (662)
                      ..|+|+|+||++++|+|++|++++++++|+.+++...+.    .....|++.++|+.+++++.+|+++|++|||+||+++
T Consensus         4 ~~W~~~L~iG~~l~I~V~~Y~~~~~~k~~~~~~~~~~~~----~~~~~v~~~~~~~~~~~~~~ev~~~di~kgy~yG~~~   79 (304)
T d1jeyb1           4 IHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKT----LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDI   79 (304)
T ss_dssp             CCEEEEEEETTTEEEEEEEEEEECCCCCCCCCEEEETTT----CCSTTEEEEEEEEESSSSCCEECGGGEEEEEEETTEE
T ss_pred             ccceeeEEEcCCcEEEEEeEecCcccCCCccEEEeecCC----cccccceeEEEEEEcCCCCcccChHHeeEEEEECCeE
Confidence            469999999999999999999999999998777754321    1235688888898788889999999999999999999


Q ss_pred             EeCChhhHHhhccCC-CccEEEEeEeeCCCCcchhccCC-eEEEEcCCCChhhHHHHHHHHHHHHhcCceeEEEEEecCC
Q 006065          297 VPISSAEWEAVKFKP-EKSVKLLGFTDASNILRHYYMKD-VNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQG  374 (662)
Q Consensus       297 Vp~s~~e~~~~k~~~-~~~l~ilGF~~~~~i~~~~~~~~-~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~  374 (662)
                      |||+++|++++++.+ .+||+||||+++++|+++|+|++ +|++.|++++.+|..||+||++||.+++++||||||+|.+
T Consensus        80 V~~~~ee~~~~~~~~~~~~l~ilGF~~~~~i~~~~~~~~~~~~~~~~~~~~~s~~af~aL~~am~~~~~vaI~r~v~r~~  159 (304)
T d1jeyb1          80 VPFSKVDEEQMKYKSEGKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKR  159 (304)
T ss_dssp             EECCHHHHHHHSCCCCCSEEEEEEEEEGGGSCGGGCEEEEEEEEEECTTCHHHHHHHHHHHHHHHHTTEEEEEEEESSSS
T ss_pred             EEcCHHHHhhhcccCCCCeEEEEEEecHHHCCHhHccCCceEEEecCCCCchHHHHHHHHHHHHHHCCcEEEEEEeccCC
Confidence            999999999999874 68999999999999999999998 5677788888999999999999999999999999999999


Q ss_pred             CCceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCC-----CCc
Q 006065          375 QQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSG-----KGE  449 (662)
Q Consensus       375 ~~p~~v~~L~P~~~~~~~~~~~l~~v~LPfaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~-----~~e  449 (662)
                      +. |.+|+|+|+++..   ++||++++|||+||||.++||++.+. ....|+++|+++|++||++|+|+..+     ..+
T Consensus       160 ~~-p~l~aL~P~~~~~---~~g~~l~~LPf~ddvR~~~f~~~~~~-~~~~~~~eq~~~~~~lI~~m~l~~~~~~~~~~~~  234 (304)
T d1jeyb1         160 AN-PQVGVAFPHIKHN---YECLVYVQLPFMEDLRQYMFSSLKNS-KKYAPTEAQLNAVDALIDSMSLAKKDEKTDTLED  234 (304)
T ss_dssp             SC-CEEEEEEEEECSS---CEEEEEEECCCGGGBCCCCCCCSTTC-SSSCCCHHHHHHHHHHHHHTBCEECCTTSSCCEE
T ss_pred             CC-cEEEEEEEecccC---CCeEEEEECCchHhccCcCCCCcccc-CCCCCCHHHHHHHHHHHHhCcCcccccccccccc
Confidence            86 5577999998764   57999999999999999999999764 45679999999999999999996432     346


Q ss_pred             cCCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCChHHHHHHHHHHHHHHhhcCCccCCC
Q 006065          450 ILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPK  518 (662)
Q Consensus       450 ~~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~l~~~k~~f~~~~~~~  518 (662)
                      .|+|+.++||++||||++|+++|++|+.++|+.+++|.++++|+.++++++++.+++++++|+++++++
T Consensus       235 ~f~p~~~~NP~lq~~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~~~~~~~~fp~~~~~k  303 (304)
T d1jeyb1         235 LFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKK  303 (304)
T ss_dssp             SCCGGGSCCHHHHHHHHHHHHHHHCTTSCCCCCCHHHHHHHSCCHHHHHHHHHHHHHHHHHSCCEECCC
T ss_pred             ccChhhCCCHHHHHHHHHHHHHhcCCCCCCCCCChhhhhhcccCHHHHHHHHHHHHHHHHhcCccccCC
Confidence            799999999999999999999999999999999999999999999999999999999999999988764

PyMOL of d1jeyb1

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

>d1rw2a_ a.118.19.1 (A:) C-terminal domain of Ku80 {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

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

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

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

>d1pt6a_ c.62.1.1 (A:) Integrin alpha1-beta1 {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

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

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

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

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

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

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

>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