Citrus Sinensis ID: 005544

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-------670-------680-------690-

MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGDGSVSDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLISKSEAVDSDITDDEAGSFIVKSQPKHED

cccccEEEEEEEEcccccccccHHHHHHHHHHHHHHHHcccccEEEEEEEccccccccccccccccccEEEEcccccccHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccccccEEEEEEccccccccccHHHHHHHHHHHHHHHHHcccccEEccccccccccccccccHHHHHHHHHHHcccccEEEcHHHHHHHHcccccccccccEEEEEEEEcccccEEEEEEEEEcccccccccccccccccccccccccEEEEEEEEEEcccccccccccccccEEEEccEEEEccHHHHHHHcccccccEEEEEEEEccccccEEEcccEEEEEccccccHHHHHHHHHHHHHHHccEEEEEEEEEccccccEEEEEEccccccccccccEEEEEccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHccccccccccccccccccHHHHcccccccccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccHHHHHHHHHHcccccccccccccccccHHHHHcccccccccccc

ccccccEEEEEEEccHcHccccccHHHHHHHHHHHHHEcccccEEEEEEEcccccccccccccccccEEEEEcccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccEEEEEEccccccccccHHHHHHHHHHHHHHHcEcccccccccccccccccccccccccHHHHHHHHHHccccEEEcHHHHHHHHcccccccccccccccEEEEEccccEEEEEEEEEEEcccccccEEEEEEcccccccccEEEEEEEEEEEcccccccccHHHHHccEcccccEEEccHHHHHHHcccccccEEEEEEEcHHHcccHcccccEEEEEcccccHHHHHHHHHHHHHHHHcccEEEEEEEEcccccccEEEEEEccccccccccccEEEEEcccHHHcccccccccccccccccccHHHHHHHHHHHHHccccccccHHcccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHHcccccccccccccHHHcccccccccccHHHccccHHHHHHHHHHcccccccEccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccccccccccccccccHHHHHHHHccccccccc

MARTREALLLLLDvspsmhsvlPDVEKLCSRLIQKKliygknhevGVILFGTeeteneltkevggyehvKVLQDIKVVDGHLVqslkhlpqgtcagdfLDAIVVGVDMLIKKYgetykgkkhlclitdalcplkdpdvgtkedQVSTIARQMVAFGLRMKNIVVRAslsgephmrVIIENDNLLnifskkssaktlfvdsttslrgarktrdispvtifrgdLELSEKMKIKVWVYKKtgeekfptlkkysdkapstdkfathevkvdyeyksvedpskvvppeqrikgyrygpqvvpissaeweavkfkpeksvkllgftdasNILRHYYMKDVNlfiaepgnsrATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGvltpnvsekinipdsfyfnvlpfaedvrefqfpsfskfpvswqpneqQQEAADNLVKMLdlapsgkgeilqpeltpnpaleRFYHHLelksehqdaappplddslkkitepdptllaeSQSAIDAFCGQfvikenpklkkSTRRflrekpsgsdepngdgsvsdaqavnsmeskpvvtvdkigdltpiqdfeammsrrdcpdWVDKAIEDMKNKIFGLlensneginyPKAVELLVALRKGcileqepkQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLiskseavdsditddeagsfivksqpkhed

MARTREALLLlldvspsmhsvLPDVEKLCSRLIQKKliygknhevgVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFskkssaktlfvdsttslrgarktrdispvtifrgdlelsekmkIKVWvykktgeekfptlkkysdkapstdkfathevkvdyeyksvedpskvvppeqrikgyrygPQVVPISSAEweavkfkpeksvkllgfTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFvikenpklkkstrrflrekpsgsdepngdgsvSDAQAVNSmeskpvvtvdkigDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLlensnegiNYPKAVELLVALRKGCIleqepkqfndVLEKVCKICRKRNFSTFFDFLMSKKLSLISKSeavdsditddeagsfivksqpkhed

******ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGE***********************VKVDYEY**************RIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSW****************************************FY*************************************AIDAFCGQFVIK*******************************************VTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLI****************************

***TREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN***KEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQG*CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST***********ISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFS**********QQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSE**********DSLKKITEP*************AFCGQFVIKENPKL************************************************PIQDFEAMMS**D**DWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLISK*E************************

MARTREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV***********TRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRR**********************AVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLISKSEAVDSDITDDEAGSFIV********

****REALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENP******************************AVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLISK**************************

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		691	2.2.26 [Sep-21-2011]
Q9FQ09		680	ATP-dependent DNA helicas	yes	no	0.975	0.991	0.617	0.0
Q75IP6		688	ATP-dependent DNA helicas	yes	no	0.992	0.997	0.593	0.0
Q54LY5		796	X-ray repair cross-comple	yes	no	0.971	0.842	0.272	1e-74
P27641		732	X-ray repair cross-comple	yes	no	0.962	0.908	0.233	3e-41
P13010		732	X-ray repair cross-comple	yes	no	0.945	0.892	0.226	5e-36
Q7RX73		725	ATP-dependent DNA helicas	N/A	no	0.869	0.828	0.241	6e-34
Q2H6C5		736	ATP-dependent DNA helicas	N/A	no	0.890	0.835	0.235	3e-30
Q2MHH1		725	ATP-dependent DNA helicas	N/A	no	0.920	0.877	0.233	2e-28
Q4WI96		725	ATP-dependent DNA helicas	yes	no	0.888	0.846	0.225	3e-28
Q2MHH2		725	ATP-dependent DNA helicas	yes	no	0.936	0.892	0.225	2e-27

>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 =  877 bits (2266), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 424/687 (61%), Positives = 538/687 (78%), Gaps = 13/687 (1%)

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-SNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKK 659
           EN ++EG    KA+E ++ALRKGC+LEQEPKQFN+ L  + K+C++RN S   +  MSKK
Sbjct: 592 ENCTDEG---DKALECVLALRKGCVLEQEPKQFNEFLNHLFKLCQERNLSHLLEHFMSKK 648

Query: 660 LSLISKSEAVDSDITDDEAGSFIVKSQ 686
           ++LI KSEA DSDI D+ AG FIVK +
Sbjct: 649 ITLIPKSEAADSDIVDENAGDFIVKQE 675

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\|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\|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\|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

>sp\|Q2MHH2\|KU80_ASPOR ATP-dependent DNA helicase II subunit 2 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) 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		691
359489412		690	PREDICTED: ATP-dependent DNA helicase 2	0.998	1.0	0.727	0.0
255541318		684	ku P80 DNA helicase, putative [Ricinus c	0.989	1.0	0.731	0.0
296089149		673	unnamed protein product [Vitis vinifera]	0.973	1.0	0.723	0.0
224130002		700	predicted protein [Populus trichocarpa]	0.986	0.974	0.694	0.0
449433125		691	PREDICTED: ATP-dependent DNA helicase 2	0.997	0.997	0.679	0.0
449525249		691	PREDICTED: ATP-dependent DNA helicase 2	0.997	0.997	0.678	0.0
357469575		683	ATP-dependent DNA helicase 2 subunit [Me	0.985	0.997	0.664	0.0
19401142		683	KAP-2 [Medicago truncatula]	0.985	0.997	0.662	0.0
356512141		687	PREDICTED: ATP-dependent DNA helicase 2	0.989	0.995	0.648	0.0
225453905		688	PREDICTED: ATP-dependent DNA helicase 2	0.986	0.991	0.650	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 = 1042 bits (2695), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 502/690 (72%), Positives = 586/690 (84%)

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 ENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKL 660
           E+S EG NY KA+E LVALRKGC+LEQEPKQFND L  + K C K N ++F + L SK++
Sbjct: 601 EDSYEGDNYLKALEYLVALRKGCVLEQEPKQFNDFLHHLYKYCEKHNLNSFCESLASKEI 660

Query: 661 SLISKSEAVDSDITDDEAGSFIVKSQPKHE 690
            LI+K+EA DS++T+DEA S +VK +PK E
Sbjct: 661 MLINKTEAADSEVTEDEARSLMVKKEPKLE 690

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\|356512141\|ref\|XP_003524779.1\| PREDICTED: ATP-dependent DNA helicase 2 subunit KU80-like [Glycine max]	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

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		691
TAIR\|locus:2023757		680	KU80 [Arabidopsis thaliana (ta	0.975	0.991	0.605	7.4e-224
UNIPROTKB\|Q75IP6		688	KU80 "ATP-dependent DNA helica	0.992	0.997	0.580	2.8e-208
DICTYBASE\|DDB_G0286303		796	ku80 "DNA-dependent protein ki	0.370	0.321	0.305	1.1e-67
UNIPROTKB\|F1NZI1		729	XRCC5 "Uncharacterized protein	0.968	0.917	0.260	5.6e-49
ZFIN\|ZDB-GENE-041008-108		727	xrcc5 "X-ray repair complement	0.654	0.621	0.260	2.6e-42
UNIPROTKB\|F1SS19		733	XRCC5 "Uncharacterized protein	0.661	0.623	0.241	1.2e-40
UNIPROTKB\|G3V817		732	Xrcc5 "Protein Xrcc5" [Rattus	0.659	0.622	0.242	2.3e-40
MGI\|MGI:104517		732	Xrcc5 "X-ray repair complement	0.956	0.903	0.232	2.9e-40
UNIPROTKB\|P13010		732	XRCC5 "X-ray repair cross-comp	0.654	0.617	0.248	1.6e-38
RGD\|3976		683	Xrcc5 "X-ray repair complement	0.917	0.928	0.236	4.9e-37

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

 Score = 2161 (765.8 bits), Expect = 7.4e-224, P = 7.4e-224
 Identities = 416/687 (60%), Positives = 528/687 (76%)

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-SNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFXXXXX 659
             EN ++EG    KA+E ++ALRKGC+LEQEPKQFN+ L  + K+C++RN S   +      
Sbjct:   592 ENCTDEG---DKALECVLALRKGCVLEQEPKQFNEFLNHLFKLCQERNLSHLLEHFMSKK 648

Query:   660 XXXXXXXEAVDSDITDDEAGSFIVKSQ 686
                    EA DSDI D+ AG FIVK +
Sbjct:   649 ITLIPKSEAADSDIVDENAGDFIVKQE 675

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	0.6171	0.9753	0.9911	yes	no
Q75IP6	KU80_ORYSJ	3, ., 6, ., 4, ., 1, 2	0.5939	0.9927	0.9970	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	0.991
3rd Layer	3.6.4	0.976

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		691
cd00873		300	cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku8	3e-99
cd00594		272	cd00594, KU, Ku-core domain; includes the central	3e-66
pfam08785		120	pfam08785, Ku_PK_bind, Ku C terminal domain like	2e-41
pfam02735		200	pfam02735, Ku, Ku70/Ku80 beta-barrel domain	2e-39
smart00559		140	smart00559, Ku78, Ku70 and Ku80 are 70kDa and 80kD	1e-32
cd00788		287	cd00788, KU70, Ku-core domain, Ku70 subfamily; Ku7	8e-22
pfam03731		221	pfam03731, Ku_N, Ku70/Ku80 N-terminal alpha/beta d	2e-19
cd01458		218	cd01458, vWA_ku, Ku70/Ku80 N-terminal domain	2e-19
cd00789		256	cd00789, KU_like, Ku-core domain, Ku-like subfamil	2e-08
TIGR02772		258	TIGR02772, Ku_bact, Ku protein, prokaryotic	1e-07
COG1273		278	COG1273, COG1273, Ku-homolog [Replication, recombi	1e-06
pfam03730		95	pfam03730, Ku_C, Ku70/Ku80 C-terminal arm	7e-04
cd00198		161	cd00198, vWFA, Von Willebrand factor type A (vWA)	8e-04
TIGR00578		584	TIGR00578, ku70, ATP-dependent DNA helicase II, 70	0.004

>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 =  306 bits (786), Expect = 3e-99
 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\|117355 pfam08785, Ku_PK_bind, Ku C terminal domain like	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\|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		691
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
PF08785		120	Ku_PK_bind: Ku C terminal domain like; InterPro: I	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
cd01458		218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	99.92
cd01453		183	vWA_transcription_factor_IIH_type Transcription fa	99.38
cd01451		178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	99.19
cd01452		187	VWA_26S_proteasome_subunit 26S proteasome plays a	99.18
PRK13685		326	hypothetical protein; Provisional	99.16
cd01465		170	vWA_subgroup VWA subgroup: Von Willebrand factor t	99.15
cd01480		186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	99.11
cd01467		180	vWA_BatA_type VWA BatA type: Von Willebrand factor	99.07
cd01472		164	vWA_collagen von Willebrand factor (vWF) type A do	99.05
cd01474		185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	99.04
cd01470		198	vWA_complement_factors Complement factors B and C2	99.02
cd01456		206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	99.01
PRK13406		584	bchD magnesium chelatase subunit D; Provisional	99.0
cd01482		164	vWA_collagen_alphaI-XII-like Collagen: The extrace	98.98
TIGR03436		296	acidobact_VWFA VWFA-related Acidobacterial domain.	98.97
COG1240		261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	98.95
cd01471		186	vWA_micronemal_protein Micronemal proteins: The To	98.94
cd01476		163	VWA_integrin_invertebrates VWA_integrin (invertebr	98.94
cd01469		177	vWA_integrins_alpha_subunit Integrins are a class	98.93
PF13519		172	VWA_2: von Willebrand factor type A domain; PDB: 3	98.93
cd01450		161	vWFA_subfamily_ECM Von Willebrand factor type A (v	98.91
cd01463		190	vWA_VGCC_like VWA Voltage gated Calcium channel li	98.89
cd01473		192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	98.88
PF03730		96	Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR00516	98.88
TIGR02031		589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.87
cd01461		171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	98.87
TIGR00868		863	hCaCC calcium-activated chloride channel protein 1	98.83
cd01455		191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	98.83
cd01466		155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	98.82
cd01475		224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	98.82
cd01454		174	vWA_norD_type norD type: Denitrifying bacteria con	98.8
TIGR02442		633	Cob-chelat-sub cobaltochelatase subunit. A number	98.79
cd01477		193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	98.73
PTZ00441		576	sporozoite surface protein 2 (SSP2); Provisional	98.71
cd00198		161	vWFA Von Willebrand factor type A (vWA) domain was	98.66
smart00327		177	VWA von Willebrand factor (vWF) type A domain. VWA	98.66
PF13768		155	VWA_3: von Willebrand factor type A domain	98.65
cd01464		176	vWA_subfamily VWA subfamily: Von Willebrand factor	98.64
cd01481		165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	98.56
cd01460		266	vWA_midasin VWA_Midasin: Midasin is a member of th	98.55
PF00092		178	VWA: von Willebrand factor type A domain; InterPro	98.5
cd01462		152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	98.44
TIGR03788		596	marine_srt_targ marine proteobacterial sortase tar	98.4
PF04056		193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	98.12
KOG2884		259	consensus 26S proteasome regulatory complex, subun	97.89
cd01457		199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	97.61
COG5148		243	RPN10 26S proteasome regulatory complex, subunit R	97.5
PRK10997		487	yieM hypothetical protein; Provisional	97.09
COG4867		652	Uncharacterized protein with a von Willebrand fact	97.01
PF11265		226	Med25_VWA: Mediator complex subunit 25 von Willebr	96.99
KOG2807		378	consensus RNA polymerase II transcription initiati	96.67
COG4245		207	TerY Uncharacterized protein encoded in toxicity p	96.62
COG2425		437	Uncharacterized protein containing a von Willebran	96.52
PF05762		222	VWA_CoxE: VWA domain containing CoxE-like protein;	96.44
cd01479		244	Sec24-like Sec24-like: Protein and membrane traffi	95.96
TIGR00627		279	tfb4 transcription factor tfb4. This family is bas	95.58
PF10138		200	vWA-TerF-like: vWA found in TerF C terminus ; Inte	95.47
cd01468		239	trunk_domain trunk domain. COPII-coated vesicles c	95.05
PF04811		243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	94.43
TIGR01651		600	CobT cobaltochelatase, CobT subunit. This model de	93.96
COG5242		296	TFB4 RNA polymerase II transcription initiation/nu	93.76
PF03850		276	Tfb4: Transcription factor Tfb4; InterPro: IPR0046	93.24
PF12257		281	DUF3608: Protein of unknown function (DUF3608); In	92.97
COG4548		637	NorD Nitric oxide reductase activation protein [In	92.54
PF11775		219	CobT_C: Cobalamin biosynthesis protein CobT VWA do	92.52
KOG2487		314	consensus RNA polymerase II transcription initiati	92.33
KOG1984		1007	consensus Vesicle coat complex COPII, subunit SFB3	92.2
KOG2326		669	consensus DNA-binding subunit of a DNA-dependent p	92.16
smart00187		423	INB Integrin beta subunits (N-terminal portion of	91.94
cd01478		267	Sec23-like Sec23-like: Protein and membrane traffi	91.81
PLN00162		761	transport protein sec23; Provisional	91.57
PTZ00395		1560	Sec24-related protein; Provisional	91.06
KOG3768		888	consensus DEAD box RNA helicase [General function	89.98
KOG2353		1104	consensus L-type voltage-dependent Ca2+ channel, a	89.81
PF09967		126	DUF2201: VWA-like domain (DUF2201); InterPro: IPR0	87.7
COG5151		421	SSL1 RNA polymerase II transcription initiation/nu	87.16
cd01459		254	vWA_copine_like VWA Copine: Copines are phospholip	84.88
KOG1986		745	consensus Vesicle coat complex COPII, subunit SEC2	80.14

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

Probab=100.00  E-value=2.3e-81  Score=708.94  Aligned_cols=473  Identities=19%  Similarity=0.268  Sum_probs=399.6

Q ss_pred             CCeEEEEEEecCCCccC---------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee
Q 005544            4 TREALLLLLDVSPSMHS---------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD   74 (691)
Q Consensus         4 ~Kea~vflIDvs~sM~~---------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~   74 (691)
                      .|||+|||||||++|++         ++..|++||.+++++|||++++|+||||||||+.|+|++     +|+||+|+++
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            69999999999999996         267899999999999999999999999999999999987     6999999999


Q ss_pred             cCCCCHHHHHHhhcCCCCCC------------CCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCch
Q 005544           75 IKVVDGHLVQSLKHLPQGTC------------AGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKE  142 (691)
Q Consensus        75 l~~~~~~~l~~L~~l~~~~~------------~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~  142 (691)
                      |+.|+++.++.|++|..+.+            .+++.||||+|++||.+ + ++++.+||||||||+++|+.+  ++...
T Consensus        84 L~~p~a~~i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~-~-~~k~~~kRI~lfTd~D~P~~~--~~~~~  159 (584)
T TIGR00578        84 LDNPGAKRILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSD-V-QFRMSHKRIMLFTNEDNPHGN--DSAKA  159 (584)
T ss_pred             CCCCCHHHHHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHh-c-chhhcCcEEEEECCCCCCCCC--chhHH
Confidence            99999999999998754311            23679999999999985 3 346789999999999999985  23344


Q ss_pred             hhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCC----eEeehh-hhHHhhcccccccCCCcc
Q 005544          143 DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA----KTLFVD-STTSLRGARKTRDISPVT  217 (691)
Q Consensus       143 ~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g----~~~~~~-~a~~ll~~~~~k~~~~~~  217 (691)
                      +++..+|++|++.||.|++|+++.  +++|+..      .|+..+....++    ...... ...+++..++.|.+++|+
T Consensus       160 ~~a~~~a~dl~~~gi~ielf~l~~--~~~Fd~s------~Fy~dii~~~~~~~~~~~~~~~~~l~~l~~~l~~k~~~kR~  231 (584)
T TIGR00578       160 SRARTKAGDLRDTGIFLDLMHLKK--PGGFDIS------LFYRDIITDAEDEDLGVHPEESSKLEDLLRKVRAKETRKRA  231 (584)
T ss_pred             HHHHHHHHHHHhcCeEEEEEecCC--CCCCChh------hhhHhhhccccccccccCcchhHHHHHHHHHHhhcccceee
Confidence            566889999999999999999943  3444332      344444321111    111112 244667889999999999


Q ss_pred             eeeeeEEecCCeEEEEEEEeecccccCCC-ceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCCce
Q 005544          218 IFRGDLELSEKMKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV  296 (691)
Q Consensus       218 ~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~  296 (691)
                      .|+|+|+||++++|+|++|.+++++++|. .+.+..+        ...|+.+|+|+ +.+++++|++++++|||+||+++
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            99999999999999999999999987664 4666543        35788888887 57788899999999999999999


Q ss_pred             EeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCC-hhhHHHHHHHHHHHHhcCceEEEEEEecCCC
Q 005544          297 VPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGN-SRATVAVSALARAMKEMNKVAIVRCVWRQGQ  375 (691)
Q Consensus       297 Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~-~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~  375 (691)
                      |+|+++|++++|..++|+|+||||+|.+.|+++|+++++|||+|+++. .+|.+||+||+++|.++++|||||||+|+|+
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            999999999999999999999999999999999999999999999864 4799999999999999999999999999998


Q ss_pred             CceEEEEeeccccCCC-----CCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcC
Q 005544          376 QSVVVGVLTPNVSEKI-----NIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEI  450 (691)
Q Consensus       376 ~p~~v~~L~P~~~~~~-----~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~  450 (691)
                      .|. +++|+|+.++..     ..|+||++++|||+||||.++|++      ...++++|+++|++||++|++.       
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 556889865432     257899999999999999998742      2469999999999999999996       


Q ss_pred             CCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHH-HHHHHHHHHHHh-hcCCccCCcccc
Q 005544          451 LQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL-AESQSAIDAFCG-QFVIKENPKLKK  521 (691)
Q Consensus       451 ~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~-~~~~~~le~~k~-~f~~~~~~~~~~  521 (691)
                      |+|..|+||+|||||++|+++||+++.|.++.|.++     |+...+ +++++.+++|++ +|+.+.+++++.
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 888888876443

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

>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

>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

>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

>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto)	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

>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

>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

>PRK13406 bchD magnesium chelatase subunit D; Provisional	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

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

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

>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

>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

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

>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

>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

>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

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D	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

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

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

>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

>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

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

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

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

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

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

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

>PF13768 VWA_3: von Willebrand factor type A domain	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

>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

>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family	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

>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

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

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

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

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

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

>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

>TIGR01651 CobT cobaltochelatase, CobT subunit	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

>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

>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

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

>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain	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

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

>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region)	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

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

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

>KOG3768 consensus DEAD box RNA helicase [General function prediction only]	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

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

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

>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]	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		691
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		691
1jey_B		565	KU80; double-strand DNA break repair, non-homologo	1e-106
1jey_A		609	KU70; double-strand DNA break repair, non-homologo	3e-84
1q2z_A		120	ATP-dependent DNA helicase II, 80 kDa subunit; KU,	1e-34
1rw2_A		152	ATP-dependent DNA helicase II, 80 kDa subunit; KU8	1e-33
3ism_C		359	CG4930; endonuclease, endonuclease inhibitor compl	8e-15
3ism_C		359	CG4930; endonuclease, endonuclease inhibitor compl	2e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-12
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-07

>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 =  333 bits (854), Expect = e-106
 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

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

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

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		691
d1jeyb1		304	b.131.1.2 (B:242-545) Ku80 subunit middle domain {	2e-72
d1jeya1		281	b.131.1.1 (A:254-534) Ku70 subunit middle domain {	3e-55
d1rw2a_		152	a.118.19.1 (A:) C-terminal domain of Ku80 {Human (	4e-39
d1jeyb2		236	c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain	1e-18
d1jeya2		220	c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain	9e-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 =  234 bits (599), Expect = 2e-72
 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

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

>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		691
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	100.0
d1jeyb2		236	Ku80 subunit N-terminal domain {Human (Homo sapien	99.95
d1jeya2		220	Ku70 subunit N-terminal domain {Human (Homo sapien	99.91
d1shux_		181	Capillary morphogenesis protein 2 domain {Human (H	99.06
d1atza_		184	von Willebrand factor A3 domain, vWA3 {Human (Homo	99.01
d1pt6a_		192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	98.84
d1v7pc_		193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	98.8
d1q0pa_		209	Complement factor B domain {Human (Homo sapiens) [	98.79
d1ijba_		202	von Willebrand factor A1 domain, vWA1 {Human (Homo	98.76
d1n3ya_		189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	98.65
d1mf7a_		194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	98.49
d1mjna_		179	Integrin CD11a/CD18 (Leukocyte function associated	98.04
d1yvra2		174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	97.96
d1tyeb2		248	Integrin beta A domain {Human (Homo sapiens) [TaxI	97.91
d1pd0a3		252	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	90.73
d2qtva3		271	Sec23 {Baker's yeast (Saccharomyces cerevisiae) [T	87.79

>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=0  Score=467.76  Aligned_cols=294  Identities=26%  Similarity=0.453  Sum_probs=264.3

Q ss_pred             CEEEEEEEECCCEEEEEEEEEECCCCCCCCCEEECCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             01555587629818999999403544699725741579987644543026878985047999978932212322238905
Q 005544          217 TIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV  296 (691)
Q Consensus       217 ~~~~g~L~ig~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~V~~ed~~kgy~yG~~~  296 (691)
                      ..|+|+|+||++++|+|++|++++++++|+.+++...+..    ....|++.+.|+.+++++.+|+++|++|||+||+++
T Consensus         4 ~~W~~~L~iG~~l~I~V~~Y~~~~~~k~~~~~~~~~~~~~----~~~~v~~~~~~~~~~~~~~ev~~~di~kgy~yG~~~   79 (304)
T d1jeyb1           4 IHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDAKTL----KKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDI   79 (304)
T ss_dssp             CCEEEEEEETTTEEEEEEEEEEECCCCCCCCCEEEETTTC----CSTTEEEEEEEEESSSSCCEECGGGEEEEEEETTEE
T ss_pred             CCCEEEEEECCCCEEEEEEEECCCCCCCCCCEEEEECCCC----CCCCCEEEEEEEECCCCCCCCCHHHEEEEEEECCEE
T ss_conf             5404569986983999996946712677843799506776----555420699999759998235868936878878968


Q ss_pred             EECCHHHHHHHCCC-CCCCEEEEEEEECCCCCCEECCCC-EEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEECCC
Q ss_conf             74794558865038-975289996740899743000387-0999729999132899999999999659267999886289
Q 005544          297 VPISSAEWEAVKFK-PEKSVKLLGFTDASNILRHYYMKD-VNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQG  374 (691)
Q Consensus       297 Vp~s~~e~~~~k~~-~~k~l~ilGF~~~~~i~~~~~~~~-~~~i~p~~~~~~s~~afsaL~~Al~e~~~vaI~r~v~r~~  374 (691)
                      |||+++|++.+++. +.+||+||||+++++|+++|+|++ +|++.|++++.+|..||+||++||.+++++||||||+|.+
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
T ss_conf             98499998642246899759999886379889867069962999468888437899999999998779099999951489


Q ss_pred             CCCEEEEEEECCCCCCCCCCCEEEEECCCCHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-----CCCC
Q ss_conf             99527999604113778878707982278721026889998878999999998899999999987177999-----9886
Q 005544          375 QQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPS-----GKGE  449 (691)
Q Consensus       375 ~~p~~i~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lId~mdl~~~-----~~~e  449 (691)
                      +. |.+++|+|+++..   ++||++++|||+||+|.++||++.+. ....|+++|+++|++||++|+|++.     ...+
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
T ss_conf             88-4899998741357---88699997786475357677886666-7789999999999999986767543333345446


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             7899999993469899999874149999999992555530599978999879999999823598658865
Q 005544          450 ILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKL  519 (691)
Q Consensus       450 ~~~p~~~~NP~lqr~~~~i~~ral~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~l~~~k~~f~~~~~~~k  519 (691)
                      .|+|+.++||++||||++|+++|++|+.|+|+.++.|.++++|+.++++++++++++++++|+++++++|
T Consensus       235 ~f~p~~~~NP~lq~~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~~~~~~~~fp~~~~~kk  304 (304)
T d1jeyb1         235 LFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKK  304 (304)
T ss_dssp             SCCGGGSCCHHHHHHHHHHHHHHHCTTSCCCCCCHHHHHHHSCCHHHHHHHHHHHHHHHHHSCCEECCCC
T ss_pred             CCCHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             6682437998999999999998559998999987255554365899999989999999973684556899

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

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

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

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

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

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

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

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

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

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