Citrus Sinensis ID: 047048

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240
Protein Sequence
METRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVPASRARGRKRISRK
Secondary Structure (PSIPRED)
ccccEEEEEEEcccccccEEEEEEEEccEEEEEEEcccccEEEEccHHHHHHHHHHccccHHHHHHHHHHHHccccccccEEEEEccccEEEEEEEEEEEcEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEccHHHHHHHHHHHHHHHHHccccccHHcccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEEccccccEEEEEEEccccEEEEEEcccccEEEcccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEEccccccccEEEEEEEEcccEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHccccccccccccccccccccccccccccccccccccccccccccEccc
Coil and Loop (DISEMBL)
metrqtclkleiphatdpifvkgtwfqshfdlSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYlgfqqpgcvygftdaadgckrLSWTfekegtklewrwkcgpapnskkvpaGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAVMGDlqqeeeestdetesfdegtdddkseeepakditstsigvpasrargrkrisrk
Flexible Loop (DISEMBL)
metrqtclkleiphatdpiFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEgtklewrwkcgpapnskkvpAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQavmgdlqqeeeestdetesfdegtdddkseeepakditstsigvpasrargrkrisrk
Low Complexity Region (SEG)
METRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAVMGDLQQeeeestdetesfdegtdddKSEEEPAKDITSTSIGVPASRARGRKRISRK
Disordered region (IsUnstruct)
******CLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLN**************************************************************************
Disordered Region (DISOPRED)
*****TC**LEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDAN************ERFKNEKLEFESAIYAKFLGVLNSKK***********************************************************************
Disordered Region (DISEMBL)
METRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAV************************************STSIG***************
Disordered Region (DISPRO)
**TRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAV********************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
METRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVPASRARGRKRISRK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	240	2.2.26 [Sep-21-2011]
Q682V0	264	DNA repair protein XRCC4	yes	no	0.933	0.848	0.606	6e-80
Q13426	336	DNA repair protein XRCC4	yes	no	0.845	0.604	0.240	2e-06

>sp|Q682V0|XRCC4_ARATH DNA repair protein XRCC4 OS=Arabidopsis thaliana GN=XRCC4 PE=1 SV=2

 Score =  296 bits (759), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 154/254 (60%), Positives = 187/254 (73%), Gaps = 30/254 (11%)

Query: 3   TRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVT 62
           T+ TCL+LEI  A DPIFVKGTW  S FD+S+TDG ++W+CNA+EE+V +RAA WDQPV+
Sbjct: 23  TKHTCLRLEISGA-DPIFVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQWDQPVS 81

Query: 63  EYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAG 122
           EY+KLAE+YLGFQQP  VY F+DA +G KRLSWTFEKEGTKLEWRWKC P+ +SKK+  G
Sbjct: 82  EYLKLAEQYLGFQQPNSVYSFSDALEGSKRLSWTFEKEGTKLEWRWKCKPSDDSKKITVG 141

Query: 123 ILDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLN 166
           ILDFLM+ANIRLS                AE+CLAQ E+  +EK EFESA YAKFL VLN
Sbjct: 142 ILDFLMEANIRLSEEVVNKTRSFEKMRSEAERCLAQGEKLCDEKTEFESATYAKFLSVLN 201

Query: 167 SKKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEG-TDDDKSEEEPAKDITSTSIG 225
           +KK+KLR L+DK     V+     EEEESTD+ ESF+ G +DD+KSEEE +K  TS    
Sbjct: 202 AKKAKLRALRDKEDSVRVV-----EEEESTDKAESFESGRSDDEKSEEEASKKATS---- 252

Query: 226 VPASRARGRKRISR 239
              S+ARG KR +R
Sbjct: 253 ---SKARGGKRAAR 263

May be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair. May bind to DNA. The LIG4-XRCC4 complex is probably responsible for the NHEJ ligation step, and XRCC4 may enhance the joining activity of LIG4.
Arabidopsis thaliana (taxid: 3702)

>sp|Q13426|XRCC4_HUMAN DNA repair protein XRCC4 OS=Homo sapiens GN=XRCC4 PE=1 SV=2

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 34/237 (14%)

Query: 20  FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
           F++ +W    +S F +++TDG +AW    SE ++   A        +Y+ +L +  L   
Sbjct: 19  FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78

Query: 76  QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
            P  VY F  + + C    + FEK    + +R   +      N  +V   ++ + +D   
Sbjct: 79  GPADVYTFNFSKESC---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIA 135

Query: 133 RLSAEKCLAQSE-------------RFK---NEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
              A+    Q E             RF+   + K   E+ +Y +F+ VLN KK+K+R L 
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLH 195

Query: 177 DKL--SKQAVMGDLQQE------EEESTDETESFDEGTDDDKSEEEPAKDITSTSIG 225
           +KL  + Q    D++QE       E + D    +DE TD++   +     + S ++ 
Sbjct: 196 NKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQTDLSGLASAAVS 252

Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	240
359477612	259	PREDICTED: DNA repair protein XRCC4 [Vit	0.979	0.907	0.657	4e-93
297737175	258	unnamed protein product [Vitis vinifera]	0.979	0.910	0.657	4e-93
255551927	265	DNA-repair protein XRCC4, putative [Rici	0.975	0.883	0.686	3e-92
112982631	255	XRCC4 homolog [Populus nigra]	0.970	0.913	0.628	7e-85
224111038	233	predicted protein [Populus trichocarpa]	0.866	0.892	0.671	8e-83
22331270	264	DNA repair protein XRCC4 [Arabidopsis th	0.933	0.848	0.606	3e-78
51968676	248	putative double strand break repair prot	0.933	0.903	0.606	6e-78
357441033	256	DNA repair protein XRCC4 [Medicago trunc	0.970	0.910	0.611	2e-77
297831034	248	hypothetical protein ARALYDRAFT_479818 [	0.933	0.903	0.594	6e-74
356576495	256	PREDICTED: DNA repair protein XRCC4-like	0.975	0.914	0.592	7e-74

>gi|359477612|ref|XP_002284388.2| PREDICTED: DNA repair protein XRCC4 [Vitis vinifera]

 Score =  346 bits (888), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 165/251 (65%), Positives = 203/251 (80%), Gaps = 16/251 (6%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R +CLKL+IP+ ++PIF+K TWF SHF LSITDGL+AWLCNASE++V++RAA WDQPV++
Sbjct: 6   RHSCLKLQIPNQSEPIFIKATWFPSHFHLSITDGLHAWLCNASEDEVRERAAQWDQPVSD 65

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           YI LAER+LGFQQPG VYGF+DA DG +RLSWTFEKEGTKLEWRWKCG +P+S+   AG+
Sbjct: 66  YIALAERFLGFQQPGSVYGFSDAGDGHRRLSWTFEKEGTKLEWRWKCGLSPDSRSTTAGV 125

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLM+ANIRLS                AEKCLAQSE+F NEK EFESAIYAKFLGVLNS
Sbjct: 126 LDFLMNANIRLSEEVVIKTQSFERLKVEAEKCLAQSEKFNNEKAEFESAIYAKFLGVLNS 185

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVP 227
           KK+KLREL+D++SK+   G L QEE+ESTD+T SFD+ +D++  EEE +K++T TS  V 
Sbjct: 186 KKAKLRELRDQISKEETTGKLPQEEDESTDKTLSFDDESDNEAIEEESSKNLTGTSKHVS 245

Query: 228 ASRARGRKRIS 238
            SR RGRKR++
Sbjct: 246 TSRPRGRKRVA 256

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737175|emb|CBI26376.3| unnamed protein product [Vitis vinifera]

 Score =  346 bits (888), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 165/251 (65%), Positives = 203/251 (80%), Gaps = 16/251 (6%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R +CLKL+IP+ ++PIF+K TWF SHF LSITDGL+AWLCNASE++V++RAA WDQPV++
Sbjct: 6   RHSCLKLQIPNQSEPIFIKATWFPSHFHLSITDGLHAWLCNASEDEVRERAAQWDQPVSD 65

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           YI LAER+LGFQQPG VYGF+DA DG +RLSWTFEKEGTKLEWRWKCG +P+S+   AG+
Sbjct: 66  YIALAERFLGFQQPGSVYGFSDAGDGHRRLSWTFEKEGTKLEWRWKCGLSPDSRSTTAGV 125

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLM+ANIRLS                AEKCLAQSE+F NEK EFESAIYAKFLGVLNS
Sbjct: 126 LDFLMNANIRLSEEVVIKTQSFERLKVEAEKCLAQSEKFNNEKAEFESAIYAKFLGVLNS 185

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVP 227
           KK+KLREL+D++SK+   G L QEE+ESTD+T SFD+ +D++  EEE +K++T TS  V 
Sbjct: 186 KKAKLRELRDQISKEETTGKLPQEEDESTDKTLSFDDESDNEAIEEESSKNLTGTSKHVS 245

Query: 228 ASRARGRKRIS 238
            SR RGRKR++
Sbjct: 246 TSRPRGRKRVA 256

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255551927|ref|XP_002517008.1| DNA-repair protein XRCC4, putative [Ricinus communis] gi|223543643|gb|EEF45171.1| DNA-repair protein XRCC4, putative [Ricinus communis]

 Score =  343 bits (881), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 175/255 (68%), Positives = 198/255 (77%), Gaps = 21/255 (8%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R TCLKLEI   T+PIFVKGTWF SHF LSITDGLNAW+CNA+E QVK+RAA WDQPV+E
Sbjct: 14  RHTCLKLEI---TEPIFVKGTWFDSHFHLSITDGLNAWVCNATEGQVKERAAQWDQPVSE 70

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           YI LAE YLGFQQPG +Y F DA D  KRLSWTFEKEGTKLEWRWKC P+P++K   AGI
Sbjct: 71  YINLAEHYLGFQQPGSIYRFADAGDSHKRLSWTFEKEGTKLEWRWKCQPSPDNKMTTAGI 130

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLMDANIRLS                A+KCL QSERF  EK EFES+IYAKFL VLNS
Sbjct: 131 LDFLMDANIRLSEEVVKKTHSFERLKEEADKCLTQSERFAGEKTEFESSIYAKFLAVLNS 190

Query: 168 KKSKLRELQDKLSKQAVMGDL-QQEEEESTDETESFDE-GTDDDKSEEEPAKDITSTSIG 225
           KK KLR+L+D+LSK+   G L Q+EEEESTD+TESF+E  +D DKSEEEP + +T TS  
Sbjct: 191 KKRKLRQLRDQLSKKEASGKLPQEEEEESTDKTESFEEDSSDGDKSEEEPPEKVTGTSED 250

Query: 226 VPASRARGRKRISRK 240
            P+SR RGRKRI+RK
Sbjct: 251 KPSSRGRGRKRITRK 265

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|112982631|dbj|BAF03494.1| XRCC4 homolog [Populus nigra]

 Score =  319 bits (817), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 159/253 (62%), Positives = 194/253 (76%), Gaps = 20/253 (7%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R TCLKLEIP   +PIF+KGTWF  HF+LSITDGLN+W CNA+EE+V+ RAA WDQPV+ 
Sbjct: 7   RHTCLKLEIP---EPIFIKGTWFPFHFNLSITDGLNSWFCNATEEEVRGRAAQWDQPVST 63

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           YI+LAE++LGFQ PG VY FTDA +G KRLSWTFEKEGTKLEWRWKC P+P++KK    I
Sbjct: 64  YIQLAEKHLGFQIPGSVYKFTDAGEGNKRLSWTFEKEGTKLEWRWKCQPSPDTKKTTTLI 123

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLMDANIRLS                AEKCLAQSE+F ++K+EFE+A+YAKFLGVLNS
Sbjct: 124 LDFLMDANIRLSEEVVRKTQSFERLKGEAEKCLAQSEKFNSQKMEFEAAVYAKFLGVLNS 183

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVP 227
           KK KLREL+D+LSK+ + G+  QE E+S D+TESFD G+DD+KS E+P + +  TS   P
Sbjct: 184 KKRKLRELRDQLSKKEISGESAQEGEDS-DKTESFDRGSDDEKSVEKPREKLAGTSKDPP 242

Query: 228 ASRARGRKRISRK 240
             R   RK+I+ K
Sbjct: 243 PRRGYVRKKITHK 255

Source: Populus nigra

Species: Populus nigra

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111038|ref|XP_002315726.1| predicted protein [Populus trichocarpa] gi|222864766|gb|EEF01897.1| predicted protein [Populus trichocarpa]

 Score =  312 bits (799), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 153/228 (67%), Positives = 184/228 (80%), Gaps = 20/228 (8%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R TCLKLEIP   +PIF+KGTWF  HF+LSITDGLN+W CNA+EE+V+DRAA WDQPV+ 
Sbjct: 7   RHTCLKLEIP---EPIFIKGTWFPFHFNLSITDGLNSWFCNATEEEVRDRAAQWDQPVST 63

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           YI+LAE++LGFQ PG VY FTDA +G KRLSWTFEKEGTKLEWRWKC P+P++KK    I
Sbjct: 64  YIQLAEKHLGFQIPGSVYKFTDAGEGNKRLSWTFEKEGTKLEWRWKCQPSPDTKKTTTLI 123

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLMDANIRLS                AEKCLAQSE+F ++K+EFE+A+YAKFLGVLNS
Sbjct: 124 LDFLMDANIRLSEEVVRKTQSFEQLKGEAEKCLAQSEKFNSQKMEFEAAVYAKFLGVLNS 183

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEP 215
           KK KLREL+D+LSK+ + G+  QEEE+S D+TESFD G+DD+KS E+P
Sbjct: 184 KKRKLRELRDQLSKKEISGESAQEEEDS-DKTESFDRGSDDEKSVEKP 230

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22331270|ref|NP_188951.2| DNA repair protein XRCC4 [Arabidopsis thaliana] gi|238479872|ref|NP_001154639.1| DNA repair protein XRCC4 [Arabidopsis thaliana] gi|85701292|sp|Q682V0.2|XRCC4_ARATH RecName: Full=DNA repair protein XRCC4 gi|9800643|gb|AAF91285.2|AF233528_1 putative double strand break repair protein [Arabidopsis thaliana] gi|9294200|dbj|BAB02102.1| unnamed protein product [Arabidopsis thaliana] gi|332643196|gb|AEE76717.1| DNA repair protein XRCC4 [Arabidopsis thaliana] gi|332643197|gb|AEE76718.1| DNA repair protein XRCC4 [Arabidopsis thaliana]

 Score =  296 bits (759), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 154/254 (60%), Positives = 187/254 (73%), Gaps = 30/254 (11%)

Query: 3   TRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVT 62
           T+ TCL+LEI  A DPIFVKGTW  S FD+S+TDG ++W+CNA+EE+V +RAA WDQPV+
Sbjct: 23  TKHTCLRLEISGA-DPIFVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQWDQPVS 81

Query: 63  EYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAG 122
           EY+KLAE+YLGFQQP  VY F+DA +G KRLSWTFEKEGTKLEWRWKC P+ +SKK+  G
Sbjct: 82  EYLKLAEQYLGFQQPNSVYSFSDALEGSKRLSWTFEKEGTKLEWRWKCKPSDDSKKITVG 141

Query: 123 ILDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLN 166
           ILDFLM+ANIRLS                AE+CLAQ E+  +EK EFESA YAKFL VLN
Sbjct: 142 ILDFLMEANIRLSEEVVNKTRSFEKMRSEAERCLAQGEKLCDEKTEFESATYAKFLSVLN 201

Query: 167 SKKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEG-TDDDKSEEEPAKDITSTSIG 225
           +KK+KLR L+DK     V+     EEEESTD+ ESF+ G +DD+KSEEE +K  TS    
Sbjct: 202 AKKAKLRALRDKEDSVRVV-----EEEESTDKAESFESGRSDDEKSEEEASKKATS---- 252

Query: 226 VPASRARGRKRISR 239
              S+ARG KR +R
Sbjct: 253 ---SKARGGKRAAR 263

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51968676|dbj|BAD43030.1| putative double strand break repair protein (XRCC4) [Arabidopsis thaliana] gi|56461768|gb|AAV91340.1| At1g61410 [Arabidopsis thaliana] gi|61656135|gb|AAX49370.1| At1g61410 [Arabidopsis thaliana]

 Score =  296 bits (757), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 154/254 (60%), Positives = 187/254 (73%), Gaps = 30/254 (11%)

Query: 3   TRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVT 62
           T+ TCL+LEI  A DPIFVKGTW  S FD+S+TDG ++W+CNA+EE+V +RAA WDQPV+
Sbjct: 7   TKHTCLRLEISGA-DPIFVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQWDQPVS 65

Query: 63  EYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAG 122
           EY+KLAE+YLGFQQP  VY F+DA +G KRLSWTFEKEGTKLEWRWKC P+ +SKK+  G
Sbjct: 66  EYLKLAEQYLGFQQPNSVYSFSDALEGSKRLSWTFEKEGTKLEWRWKCKPSDDSKKITVG 125

Query: 123 ILDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLN 166
           ILDFLM+ANIRLS                AE+CLAQ E+  +EK EFESA YAKFL VLN
Sbjct: 126 ILDFLMEANIRLSEEVVNKTRSFEKMRSEAERCLAQGEKLCDEKTEFESATYAKFLSVLN 185

Query: 167 SKKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEG-TDDDKSEEEPAKDITSTSIG 225
           +KK+KLR L+DK     V+     EEEESTD+ ESF+ G +DD+KSEEE +K  TS    
Sbjct: 186 AKKAKLRALRDKEDSVRVV-----EEEESTDKAESFESGRSDDEKSEEEASKKATS---- 236

Query: 226 VPASRARGRKRISR 239
              S+ARG KR +R
Sbjct: 237 ---SKARGGKRAAR 247

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357441033|ref|XP_003590794.1| DNA repair protein XRCC4 [Medicago truncatula] gi|355479842|gb|AES61045.1| DNA repair protein XRCC4 [Medicago truncatula]

 Score =  294 bits (753), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 154/252 (61%), Positives = 182/252 (72%), Gaps = 19/252 (7%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R TCLKL++    + IFVKGTWF +HF+LSITDG  +W CNASE++VK RAA WDQPV E
Sbjct: 6   RHTCLKLQLTEE-ESIFVKGTWFNTHFNLSITDGSTSWHCNASEDEVKQRAAQWDQPVEE 64

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           Y++L+ERYLGFQQP  VY F DA D  KRLSWTFEK G  L WRWKC  +P+ KK  A I
Sbjct: 65  YVELSERYLGFQQPESVYAFADAGDAHKRLSWTFEKGGMTLHWRWKCMKSPDCKKTTAEI 124

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLMDANIRLS                AEKCLAQSER  NE++EFES IY KFLGVLNS
Sbjct: 125 LDFLMDANIRLSEEVVIKTELFEKTKVEAEKCLAQSERIANERVEFESQIYTKFLGVLNS 184

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVP 227
           KK+KLREL+D+LSKQ   GD   +EEE  ++TESFDE +DD KS+E+P K ITS+S    
Sbjct: 185 KKAKLRELRDQLSKQG-NGDKSPQEEEDPEKTESFDEESDDGKSDEDPQKCITSSSKDAG 243

Query: 228 ASRARGRKRISR 239
           A++ R R R +R
Sbjct: 244 ATK-RSRPRRTR 254

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831034|ref|XP_002883399.1| hypothetical protein ARALYDRAFT_479818 [Arabidopsis lyrata subsp. lyrata] gi|297329239|gb|EFH59658.1| hypothetical protein ARALYDRAFT_479818 [Arabidopsis lyrata subsp. lyrata]

 Score =  283 bits (723), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 151/254 (59%), Positives = 184/254 (72%), Gaps = 30/254 (11%)

Query: 3   TRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVT 62
           T+ TCL+LEI  A DPIFVKGTW  SHFD+S+TDG ++W+CNA+EE+V +RAA WDQPV+
Sbjct: 7   TKHTCLRLEISGA-DPIFVKGTWHNSHFDISVTDGSSSWICNATEEEVAERAAQWDQPVS 65

Query: 63  EYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAG 122
           EY++LAERYLGFQQP  VYGF+DA +G KRLSWTFEKEGTKLEWRWKC P+ +SKK+  G
Sbjct: 66  EYLELAERYLGFQQPNSVYGFSDALEGSKRLSWTFEKEGTKLEWRWKCKPSHDSKKITVG 125

Query: 123 ILDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLN 166
           ILDFL++ANIRLS                AE+CLAQ E+   EK EFE+A YAKFL VLN
Sbjct: 126 ILDFLLEANIRLSEEVVNKTRSFEKMKCEAERCLAQGEKLCEEKTEFENATYAKFLSVLN 185

Query: 167 SKKSKLRELQDKL-SKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIG 225
           +KK+KLR L+DK  S +AV      EEEESTD+TESFD G  D++      +     S  
Sbjct: 186 AKKAKLRALRDKGDSVRAV------EEEESTDKTESFDSGRSDNE------QSEEEASKK 233

Query: 226 VPASRARGRKRISR 239
             +S+ARGRKR  R
Sbjct: 234 ASSSKARGRKRAVR 247

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356576495|ref|XP_003556366.1| PREDICTED: DNA repair protein XRCC4-like [Glycine max]

 Score =  282 bits (722), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 150/253 (59%), Positives = 175/253 (69%), Gaps = 19/253 (7%)

Query: 4   RQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTE 63
           R +C KL IP   +PIFVK TWF +HF L++TDG+ AW C+ S E+VK RAA WD PV+E
Sbjct: 7   RFSCSKLLIPKG-EPIFVKATWFPTHFHLAVTDGITAWHCHPSAEEVKQRAAQWDLPVSE 65

Query: 64  YIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPAGI 123
           Y+ L+ERYLG QQPG VY F DA D  KRLSWTFEKEG  L WRWKC  +P+SKK    I
Sbjct: 66  YLNLSERYLGLQQPGSVYAFDDAGDSHKRLSWTFEKEGMTLLWRWKCLLSPDSKKSNVEI 125

Query: 124 LDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVLNS 167
           LDFLM +NI LS                AEKCL QSER  NE+LEFES IYAKFLGVLNS
Sbjct: 126 LDFLMGSNINLSDKVVTENELFEKMKVEAEKCLTQSERIANERLEFESEIYAKFLGVLNS 185

Query: 168 KKSKLRELQDKLSKQAVMGDLQQEEEESTDETESFDEGTDDDKSEEEPAKDITSTSIGVP 227
           KKSKLR L+DKLSKQ      +  EEE TD+TESFDE  D ++S+E+P KDITS+S  V 
Sbjct: 186 KKSKLRVLRDKLSKQE--NSEKSPEEEDTDKTESFDEENDFERSDEDPQKDITSSSKEVM 243

Query: 228 ASRARGRKRISRK 240
           A++    KRI  K
Sbjct: 244 ANKPSHPKRIRHK 256

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	240
TAIR|locus:2094593	264	XRCC4 "homolog of X-ray repair	0.941	0.856	0.555	7.4e-66
TAIR|locus:2197679	118	AT1G61410 [Arabidopsis thalian	0.4	0.813	0.394	7.4e-11
UNIPROTKB|Q13426	336	XRCC4 "DNA repair protein XRCC	0.520	0.372	0.271	0.00016
UNIPROTKB|F1REZ3	246	XRCC4 "Uncharacterized protein	0.520	0.508	0.264	0.00046

TAIR|locus:2094593 XRCC4 "homolog of X-ray repair cross complementing 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 670 (240.9 bits), Expect = 7.4e-66, P = 7.4e-66
 Identities = 141/254 (55%), Positives = 173/254 (68%)

Query:     2 ETRQTCLKLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPV 61
             +T+ TCL+LEI  A DPIFVKGTW  S FD+S+TDG ++W+CNA+EE+V +RAA WDQPV
Sbjct:    22 KTKHTCLRLEISGA-DPIFVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQWDQPV 80

Query:    62 TEYIKLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKVPA 121
             +EY+KLAE+YLGFQQP  VY F+DA +G KRLSWTFEKEGTKLEWRWKC P+ +SKK+  
Sbjct:    81 SEYLKLAEQYLGFQQPNSVYSFSDALEGSKRLSWTFEKEGTKLEWRWKCKPSDDSKKITV 140

Query:   122 GILDFLMDANIRLS----------------AEKCLAQSERFKNEKLEFESAIYAKFLGVL 165
             GILDFLM+ANIRLS                AE+CLAQ E+  +EK EFESA YAKFL VL
Sbjct:   141 GILDFLMEANIRLSEEVVNKTRSFEKMRSEAERCLAQGEKLCDEKTEFESATYAKFLSVL 200

Query:   166 NSKKSKLRELQDKLSKQAVMGDLQQXXXXXXXXXXXXXXXXXXXKSEEEPAKDITSTSIG 225
             N+KK+KLR L+DK     V+ + +                    KSEEE +K  TS    
Sbjct:   201 NAKKAKLRALRDKEDSVRVVEEEESTDKAESFESGRSDDE----KSEEEASKKATS---- 252

Query:   226 VPASRARGRKRISR 239
                S+ARG KR +R
Sbjct:   253 ---SKARGGKRAAR 263

GO:0003677 "DNA binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0006310 "DNA recombination" evidence=IEA

GO:0008152 "metabolic process" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0008022 "protein C-terminus binding" evidence=IPI

TAIR|locus:2197679 AT1G61410 [Arabidopsis thaliana (taxid:3702)]

 Score = 151 (58.2 bits), Expect = 7.4e-11, P = 7.4e-11
 Identities = 43/109 (39%), Positives = 60/109 (55%)

Query:   132 IRLSAEKCLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKL-SKQAVMGDLQQ 190
             ++  AE+CLAQ E+  +EK EFE+A YAKFL VLN+KK+KLR ++DK  S +AV     +
Sbjct:    21 MKSEAERCLAQGEKLCDEKTEFENATYAKFLSVLNAKKAKLRAVRDKEDSVRAV-----E 75

Query:   191 XXXXXXXXXXXXXXXXXXXKSEEEPAKDITSTSIGVPASRARGRKRISR 239
                                +S EE ++  TS       S+ARG KR +R
Sbjct:    76 EEESTYKAESFESGRSDDEQSGEEASEKATS-------SKARGGKRAAR 117

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

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

GO:0006310 "DNA recombination" evidence=IEA

UNIPROTKB|Q13426 XRCC4 "DNA repair protein XRCC4" [Homo sapiens (taxid:9606)]

 Score = 81 (33.6 bits), Expect = 0.00016, Sum P(2) = 0.00016
 Identities = 38/140 (27%), Positives = 66/140 (47%)

Query:    20 FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
             F++ +W    +S F +++TDG +AW    SE ++   A        +Y+ +L +  L   
Sbjct:    19 FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78

Query:    76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKV--PAGILDFLMDANIR 133
              P  VY F  + + C    + FEK    + +R   G   N +KV  PA ++  L+   + 
Sbjct:    79 GPADVYTFNFSKESCY---FFFEKNLKDVSFR--LGSF-NLEKVENPAEVIRELICYCLD 132

Query:   134 LSAEKCLAQSERFK--NEKL 151
               AE   A++E  +  NE+L
Sbjct:   133 TIAEN-QAKNEHLQKENERL 151

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0002328 "pro-B cell differentiation" evidence=IEA

GO:0007417 "central nervous system development" evidence=IEA

GO:0010332 "response to gamma radiation" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

GO:0033152 "immunoglobulin V(D)J recombination" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0048146 "positive regulation of fibroblast proliferation" evidence=IEA

GO:0050769 "positive regulation of neurogenesis" evidence=IEA

GO:0071285 "cellular response to lithium ion" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA;NAS

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

GO:0005829 "cytosol" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0000793 "condensed chromosome" evidence=IDA

GO:0006302 "double-strand break repair" evidence=IDA;TAS

GO:0016874 "ligase activity" evidence=IDA

GO:0032807 "DNA ligase IV complex" evidence=IDA

GO:0010165 "response to X-ray" evidence=IDA

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0051351 "positive regulation of ligase activity" evidence=IDA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IDA

GO:0070419 "nonhomologous end joining complex" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

UNIPROTKB|F1REZ3 XRCC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 82 (33.9 bits), Expect = 0.00046, Sum P(2) = 0.00046
 Identities = 37/140 (26%), Positives = 68/140 (48%)

Query:    20 FVKGTWFQ---SHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
             F++  W +   S F +++TDG +AW+   SE ++   A        +Y+ +L +  +   
Sbjct:    19 FLQVAWEKTLGSGFVITLTDGQSAWIGTVSESEISQEADDMALEKEKYVDELRKALVSGA 78

Query:    76 QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKCGPAPNSKKV--PAGILDFLMDANIR 133
              P   Y F  + D C+   ++FEK    + +R   G   N +KV  PA ++  L+   + 
Sbjct:    79 GPTDTYKFNFSKDSCQ---FSFEKNLKDVSFR--LGSF-NLEKVANPAEVIRELICYCLD 132

Query:   134 LSAEKCLAQSERFK--NEKL 151
               +EK  A++E  +  NE+L
Sbjct:   133 TISEK-QAKNEHLQKENERL 151

GO:0051351 "positive regulation of ligase activity" evidence=IEA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IEA

GO:0050769 "positive regulation of neurogenesis" evidence=IEA

GO:0048146 "positive regulation of fibroblast proliferation" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0043524 "negative regulation of neuron apoptotic process" evidence=IEA

GO:0033152 "immunoglobulin V(D)J recombination" evidence=IEA

GO:0033077 "T cell differentiation in thymus" evidence=IEA

GO:0032807 "DNA ligase IV complex" evidence=IEA

GO:0010332 "response to gamma radiation" evidence=IEA

GO:0010165 "response to X-ray" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0007417 "central nervous system development" evidence=IEA

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

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

GO:0005829 "cytosol" evidence=IEA

GO:0002328 "pro-B cell differentiation" evidence=IEA

GO:0001701 "in utero embryonic development" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

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)
Q682V0	XRCC4_ARATH	No assigned EC number	0.6062	0.9333	0.8484	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

No EC number assignment, probably not an enzyme!

---

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	Length	Definition	E-value
Query	240
pfam06632	331	pfam06632, XRCC4, DNA double-strand break repair a	3e-09

>gnl|CDD|148314 pfam06632, XRCC4, DNA double-strand break repair and V(D)J recombination protein XRCC4

 Score = 56.0 bits (135), Expect = 3e-09
 Identities = 61/258 (23%), Positives = 109/258 (42%), Gaps = 38/258 (14%)

Query: 4   RQTCLKLEIPHATDPIFVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQP 60
            +  L  E P+     F++  W     S F +++TDG +AW    SE  +   A      
Sbjct: 6   SRISLSSE-PNII--YFLQVAWEKTLGSGFVITLTDGHSAWTGEVSESDISQEADDMAME 62

Query: 61  VTEYI-KLAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNS 116
             +Y+ +L +  +    P   Y F  + +      +++EK    + +R   +K    PN 
Sbjct: 63  REKYVDELRKALVSGAGPAGEYTFNFSKESLH---FSYEKNLKDVSFRLGSFKLEKVPNP 119

Query: 117 KKVPAGILDFLMDANIRLSA---------EKCL-------AQSERFKNEKLEFESAIYAK 160
            +V   ++ + +D    L A         E+ L        + E+  + K   E+ +Y +
Sbjct: 120 AEVIRELICYCLDTIAELQAKNEHLQKENERLLRDWNDIQGRFEKCVSGKEALETDLYKR 179

Query: 161 FLGVLNSKKSKLRELQDKLSK-QAVMGDLQQEEEEST------DETESFDEGTDDDKSEE 213
           F+ VLN KK+K+R L   LS+ Q +   ++Q++E S       DE   +D  TD++  +E
Sbjct: 180 FILVLNEKKAKIRSLHKLLSEAQELEKSIKQKKETSACSDKTPDEDSKYDGSTDEE--QE 237

Query: 214 EPAKDITSTSIGVPASRA 231
            P K   S    V    +
Sbjct: 238 APPKPSESMPAAVSKDDS 255

This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks. Length = 331

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	240
PF06632	342	XRCC4: DNA double-strand break repair and V(D)J re	100.0
PF09302	171	XLF: XLF (XRCC4-like factor); InterPro: IPR015381	94.95
PF15384	197	DUF4610: Domain of unknown function (DUF4610)	92.97

>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants

Probab=100.00  E-value=4.1e-52  Score=386.11  Aligned_cols=212  Identities=35%  Similarity=0.539  Sum_probs=162.6

Q ss_pred             ceeEEeecCCCCCc-EEEEEEEe---CCeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHhc-CCCCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTWF---QSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLG-FQQPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w~---~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL~-~~~p~~   79 (240)
                      ++|.||+++++|+. |||+|+|.   |+||.|++|||++||+|+|++.+|+.+|++|+|+.++|+++|++||+ +++|++
T Consensus         3 ~~~~~i~~~s~p~~~yfL~~~W~~~~~~~F~i~lTDG~saW~g~vs~~ei~~~A~~~~~~~~eYv~~l~kaL~~~~~~~~   82 (342)
T PF06632_consen    3 RKVRRIHISSEPDSIYFLQVSWEKDLGSGFDITLTDGQSAWSGTVSEEEIRQRAKDWDMEVEEYVQELKKALTGQQQPSS   82 (342)
T ss_dssp             EEEEEEEETTSCSSEEEEEEEESSSGGGEEEEEEESSSSEEEEEEEHHHHHHHHHHTTS-HHHHHHHHHHHHTSSSSSSS
T ss_pred             ceeeeeecCCCCCceEEEEEEeccCCCCceEEEEecCCCceeeecCHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCC
Confidence            68999999999988 99999994   47999999999999999999999999999999999999999999995 668999


Q ss_pred             eeeEEe--cCCCCceEEEEEEeeceeEEEEEe---eecCCCCcchHHHHHHHHhhHhhhhh--------------H--HH
Q 047048           80 VYGFTD--AADGCKRLSWTFEKEGTKLEWRWK---CGPAPNSKKVPAGILDFLMDANIRLS--------------A--EK  138 (240)
Q Consensus        80 ~y~~~~--~~~~~~~l~~t~eK~~~~I~~rl~---l~~~~d~~e~~~eL~d~l~~~n~~L~--------------~--E~  138 (240)
                      .|.|++  ..+++..|+|||+|++++|+||||   |..+++|.++|++||+||++.+.+|.              .  ++
T Consensus        83 ~y~f~~~~~~~~~~~l~~t~~K~~~~it~rLGsv~L~~~~~p~e~i~el~d~~l~~~~~l~~~~~~L~~enerL~~e~~~  162 (342)
T PF06632_consen   83 EYSFDLTEDRESNKSLSFTIEKRLKDITFRLGSVKLKQVDNPAEVIRELFDWCLDANSRLQAENEHLQKENERLESEANK  162 (342)
T ss_dssp             EEEEEE-----ETTTTEEEEEEEESSEEEEEEEEE-EE-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cceEEEeeccCCCceEEEEEEEecCCceEEEeeEECCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999988  344667899999999999999975   55688998889999999866444442              2  37


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHHHHHHHHhhhcccchhhhcc------cccCCCC--CCCCCCcc
Q 047048          139 CLAQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQDKLSKQAVMGDLQQEEEES------TDETESF--DEGTDDDK  210 (240)
Q Consensus       139 l~~qlEe~v~~K~e~E~~Ly~KFv~vLNEKK~KIRelq~~L~~~~~~~~~~~~e~~~------~~~~~~~--~~~~~~~~  210 (240)
                      |++|||+||++|++||.+||+||++||||||+|||+||++|..++...+.++.+.+.      ..+.++-  +++|+|++
T Consensus       163 ~~~qlE~~v~~K~~~E~~L~~KF~~vLNeKK~KIR~lq~~L~~~~~~~~~~~~~~~~~~~~d~~~~~e~~~D~g~Stdee  242 (342)
T PF06632_consen  163 LLKQLEKFVNAKEEHEEDLYAKFVLVLNEKKAKIRELQRLLASAKEEEKSPKQEREDSASSDKSPDEESEYDYGESTDEE  242 (342)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhccccchhhhhcccccccCCcccccccccccccccc
Confidence            899999999999999999999999999999999999999999999988776644332      1222332  23677777


Q ss_pred             ccCCcc
Q 047048          211 SEEEPA  216 (240)
Q Consensus       211 ~~~~~~  216 (240)
                      ++.++.
T Consensus       243 ~e~~~~  248 (342)
T PF06632_consen  243 SENPPS  248 (342)
T ss_dssp             ------
T ss_pred             cccccc
Confidence            766643

XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.

>PF09302 XLF: XLF (XRCC4-like factor); InterPro: IPR015381 XLF (also called Cernunnos) interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining

Probab=94.95  E-value=0.31  Score=40.90  Aligned_cols=126  Identities=17%  Similarity=0.266  Sum_probs=71.2

Q ss_pred             eeEEeecCCCCCcEEEEEEEeCCeeE----EEEecCCc--ceEEeecHHHHHHHhhccCCCHH----HHHHHHHHHhc--
Q 047048            6 TCLKLEIPHATDPIFVKGTWFQSHFD----LSITDGLN--AWLCNASEEQVKDRAALWDQPVT----EYIKLAERYLG--   73 (240)
Q Consensus         6 t~~Ri~~~~~~~~~~lkv~w~~s~f~----L~~TDG~~--~w~g~vs~~~i~~rA~~~~~s~e----ey~~~l~~aL~--   73 (240)
                      ..+.|..+.+  ++++++....++..    |.+||-.+  .|+-.++...|..||+..+.+.+    .+...|...+.  
T Consensus         4 ~~~~i~~~~~--~~l~~~~~~~~sy~~~~~i~ltDl~~~~vw~E~l~~~~i~~ra~~~n~~i~~~~~~~~~lL~~i~~~~   81 (171)
T PF09302_consen    4 KPLPISGSGG--PLLAKYEFTSSSYEDLFQIHLTDLANKQVWSERLDRNDIIQRAKELNTRIDPSPEQFRVLLDKILEAL   81 (171)
T ss_dssp             EEEEBSSSE----EEEEEEEETTEEE---TCEEE-SSTTTCCCCCCCHHHHHHHCCCCCTCCCCHCCCCHCCCHHHHCHC
T ss_pred             EEEecCCccc--hheEEEEcCCCCccceeEEEEeccccceeeEEecCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhc
Confidence            3444444333  56666666656655    99999998  99999999999999987765444    55555544442  


Q ss_pred             -CCCCCceeeEEecCC-CCceEEEEEEeece-eEEEEEeeecCCCCcchHHHHHHHHhhHhhhh
Q 047048           74 -FQQPGCVYGFTDAAD-GCKRLSWTFEKEGT-KLEWRWKCGPAPNSKKVPAGILDFLMDANIRL  134 (240)
Q Consensus        74 -~~~p~~~y~~~~~~~-~~~~l~~t~eK~~~-~I~~rl~l~~~~d~~e~~~eL~d~l~~~n~~L  134 (240)
                       ....+....+...+. ++..++++++-.+. .+.|.+.|.+.+.. .+..+|+-.+......+
T Consensus        82 ~~~~~~~~~~L~~~~~~~~l~l~~~~~l~~~~p~~w~~~L~~~~~~-~~~~~L~~Pll~~~~~l  144 (171)
T PF09302_consen   82 DSGSRSTSVTLSNEKKDDSLILSLKSKLPGPLPLKWDFHLTKQPPS-QFLSHLNSPLLRMSSAL  144 (171)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCEEEETTE-EEEEEEEEEE--HH-HHHHHTHHHHHHHHHHH
T ss_pred             cCCCCCcEEEEEecCCCCceEEEEEEEcCCCCCcccceeeecCcHH-HHHHHHHHHHHHHHHHH
Confidence             222333344432222 33345555544443 56777777765543 45566666665544443

It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated downregulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining []. XLF is homologous to the yeast non-homologous end-joining factor Nej1 []. ; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z56_A 3RWR_D 3Q4F_A 3SR2_H 2R9A_A 2QM4_C.

>PF15384 DUF4610: Domain of unknown function (DUF4610)

Probab=92.97  E-value=1  Score=39.59  Aligned_cols=94  Identities=15%  Similarity=0.151  Sum_probs=63.6

Q ss_pred             CCCcEEEEEEEeC------CeeEEEEecCCcceEEeecHHHHH-HHhhccCCCHHHHHHHHHHHhcCCCCCceeeEEecC
Q 047048           15 ATDPIFVKGTWFQ------SHFDLSITDGLNAWLCNASEEQVK-DRAALWDQPVTEYIKLAERYLGFQQPGCVYGFTDAA   87 (240)
Q Consensus        15 ~~~~~~lkv~w~~------s~f~L~~TDG~~~w~g~vs~~~i~-~rA~~~~~s~eey~~~l~~aL~~~~p~~~y~~~~~~   87 (240)
                      ++..|+.++.-.+      ..|.|.+|||...|...++.+.+. .+|..---+.+.|+...+.|+.++.    .++....
T Consensus        11 ~~~ryvCyce~~~~~~~~~g~~~i~vTDg~dvW~t~~t~dsL~~~k~~~~L~~~Edy~~rfR~Ac~~~~----vtvtlqe   86 (197)
T PF15384_consen   11 GPPRYVCYCEGEGSGDGDAGVWNIYVTDGADVWSTCFTPDSLAALKARFGLSSAEDYFSRFRAACEQQA----VTVTLQE   86 (197)
T ss_pred             CCCcEEEEEeCCCCCCCCCCeeEEEecccHHhhhhccCHHHHHHHHhhcccchHHHHHHHHHHHhhcCe----eEEEEec
Confidence            4344777766663      249999999999999999999976 5787766678899999999994332    1233223


Q ss_pred             CCCceEEEEEEeeceeEEEEEeeecCCCCc
Q 047048           88 DGCKRLSWTFEKEGTKLEWRWKCGPAPNSK  117 (240)
Q Consensus        88 ~~~~~l~~t~eK~~~~I~~rl~l~~~~d~~  117 (240)
                      +   +.++|+-.....|++.|  .++++++
T Consensus        87 d---~a~Ltls~g~s~L~~dL--~k~p~~E  111 (197)
T PF15384_consen   87 D---RASLTLSGGPSALTFDL--SKVPAPE  111 (197)
T ss_pred             C---eEEEEecCCCccceEEh--hhCCCch
Confidence            3   35666655555666554  4555553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	240
3ii6_A	203	Structure Of Human Xrcc4 In Complex With The Tandem		2e-06
1fu1_A	203	Crystal Structure Of Human Xrcc4 Length = 203		3e-05
1ik9_A	213	Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex		3e-05

>pdb|3II6|A Chain A, Structure Of Human Xrcc4 In Complex With The Tandem Brct Domains Of Dna Ligaseiv. Length = 203

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 83/187 (44%), Gaps = 26/187 (13%)
Query: 20  FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
           F++ +W    +S F +++TDG +AW    SE ++   A   +    +Y+ +L +  L   
Sbjct: 19  FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMEMEKGKYVGELRKALLSGA 78
Query: 76  QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
            P  VY F  + + C    + FEK    + +R   +      N  +V   ++ + +D   
Sbjct: 79  GPADVYTFNFSKESC---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTTA 135
Query: 133 RLSAEKCLAQSE-------------RFK---NEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
              A+    Q E             RF+   + K   E+ +Y +F+ VLN KK+K+R L 
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKLSKQA 183
           +KL   A
Sbjct: 196 NKLLNAA 202

>pdb|1FU1|A Chain A, Crystal Structure Of Human Xrcc4 Length = 203

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 46/187 (24%), Positives = 81/187 (43%), Gaps = 26/187 (13%)
Query: 20  FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
           F++ +W    +S F +++TDG +AW    SE ++   A        +Y+ +L +  L   
Sbjct: 19  FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78
Query: 76  QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
            P  VY F  + +      + FEK    + +R   +      N  +V   ++ + +D   
Sbjct: 79  GPADVYTFNFSKESX---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIXYXLDTTA 135
Query: 133 RLSAEKCLAQSE-------------RFK---NEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
              A+    Q E             RF+   + K   E+ +Y +F+ VLN KK+K+R L 
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKXVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKLSKQA 183
           +KL   A
Sbjct: 196 NKLLNAA 202

>pdb|1IK9|A Chain A, Crystal Structure Of A Xrcc4-Dna Ligase Iv Complex Length = 213

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/183 (24%), Positives = 83/183 (45%), Gaps = 26/183 (14%)
Query: 20  FVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYI-KLAERYLGFQ 75
           F++ +W    +S F +++TDG +AW    SE ++   A        +Y+ +L +  L   
Sbjct: 19  FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 78
Query: 76  QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWRWKC-------GPAPNSKKVPAGILDFLM 128
            P  VY F  + +      + FEK    + +R           PA   +++ A  LD + 
Sbjct: 79  GPADVYTFNFSKESA---YFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIA 135
Query: 129 -----DANIRLSAEKCL-------AQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQ 176
                + +++   E+ L        + E+  + K   E+ +Y +F+ VLN KK+K+R L 
Sbjct: 136 ENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLH 195
Query: 177 DKL 179
           +KL
Sbjct: 196 NKL 198

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	240
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	9e-34
3mud_A	175	DNA repair protein XRCC4, tropomyosin alpha-1 CHA;	1e-21
3q4f_C	186	DNA repair protein XRCC4; DSB repair, nuclear, rec	2e-15

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A* Length = 213

 Score =  120 bits (301), Expect = 9e-34
 Identities = 46/213 (21%), Positives = 85/213 (39%), Gaps = 29/213 (13%)

Query: 4   RQTCLKLEIPHATDPIFVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQP 60
            +  L  E    +   F++ +W    +S F +++TDG +AW    SE ++   A      
Sbjct: 6   SRIHLVSE---PSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAME 62

Query: 61  VTEYIK-LAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNS 116
             +Y+  L +  L    P  VY F  + +      + FEK    + +R   +      N 
Sbjct: 63  KGKYVGELRKALLSGAGPADVYTFNFSKESAY---FFFEKNLKDVSFRLGSFNLEKVENP 119

Query: 117 KKVPAGILDFLMDANIRLSA----------------EKCLAQSERFKNEKLEFESAIYAK 160
            +V   ++ + +D      A                     + E+  + K   E+ +Y +
Sbjct: 120 AEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKR 179

Query: 161 FLGVLNSKKSKLRELQDKLSKQAVMGDLQQEEE 193
           F+ VLN KK+K+R L +KL   A   +   ++E
Sbjct: 180 FILVLNEKKTKIRSLHNKLLNAAQEREKDIKQE 212

>3mud_A DNA repair protein XRCC4, tropomyosin alpha-1 CHA; tropomysoin, overlap complex, coiled-coils, contractIle PROT; HET: DNA; 2.20A {Homo sapiens} PDB: 3sr2_A* Length = 175

 Score = 87.1 bits (215), Expect = 1e-21
 Identities = 30/158 (18%), Positives = 60/158 (37%), Gaps = 16/158 (10%)

Query: 4   RQTCLKLEIPHATDPIFVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQP 60
            +  L  E    +   F++ +W    +S F +++TDG +AW    SE ++   A      
Sbjct: 9   SRIHLVSEP---SITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAME 65

Query: 61  VTEYIK-LAERYLGFQQPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNS 116
             +Y+  L +  L    P  VY F  + + C    + FEK    + +R   +      N 
Sbjct: 66  KGKYVGELRKALLSGAGPADVYTFNFSKESCY---FFFEKNLKDVSFRLGSFNLEKVENP 122

Query: 117 KKVPAGILDFLMDANIRLSAEKCLAQSERFKNEKLEFE 154
            +V   ++ + +D   +        + +       + E
Sbjct: 123 AEVIRELICYCLDTTAKNEKSIDDLEEK---VAHAKEE 157

>3q4f_C DNA repair protein XRCC4; DSB repair, nuclear, recombination-recombination complex, DN protein-protein binding complex; HET: DNA; 5.50A {Homo sapiens} Length = 186

 Score = 71.3 bits (174), Expect = 2e-15
 Identities = 32/142 (22%), Positives = 59/142 (41%), Gaps = 13/142 (9%)

Query: 20  FVKGTWFQ---SHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIK-LAERYLGFQ 75
           F++ +W +   S F +++TDG +AW    SE ++   A        +Y+  L +  L   
Sbjct: 48  FLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGA 107

Query: 76  QPGCVYGFTDAADGCKRLSWTFEKEGTKLEWR---WKCGPAPNSKKVPAGILDFLMDANI 132
            P  VY F  + + C    +  EK    + +R   +      N  +V   ++ + +D   
Sbjct: 108 GPADVYTFNFSKESC-YFFF--EKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIA 164

Query: 133 RLSAEKCLAQSERFKNEKLEFE 154
              A+    Q E   NE+L  +
Sbjct: 165 ENQAKNEHLQKE---NERLLRD 183

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	240
1ik9_A	213	DNA repair protein XRCC4; DNA END joining, double-	100.0
3w03_C	184	DNA repair protein XRCC4; coiled-coil, NHEJ, DSBS	99.98
3q4f_C	186	DNA repair protein XRCC4; DSB repair, nuclear, rec	99.96
3mud_A	175	DNA repair protein XRCC4, tropomyosin alpha-1 CHA;	99.96
1z56_A	246	Ligase interacting factor 1; DNA repair, BRCT, NHE	99.9
2qm4_A	235	Non-homologous END-joining factor 1; XRCC4 like fa	97.32

>1ik9_A DNA repair protein XRCC4; DNA END joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil; HET: DNA; 2.30A {Homo sapiens} SCOP: b.59.1.1 h.1.11.1 PDB: 3ii6_A* 1fu1_A* 3rwr_A*

Probab=100.00  E-value=7e-51  Score=355.56  Aligned_cols=183  Identities=22%  Similarity=0.346  Sum_probs=161.9

Q ss_pred             ceeEEeecCCCCCc-EEEEEEEeC---CeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHhcCC-CCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTWFQ---SHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYLGFQ-QPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w~~---s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL~~~-~p~~   79 (240)
                      ++|+||+++++|+. |||+|+|.+   ++|.|++|||++||+|+|++++|..+|++|+|++++|+++|++||+++ +|++
T Consensus         3 ~~v~ri~~s~~~~~~~~l~~~w~~~~~~~f~l~~TdG~~~w~g~v~~~~i~~rAk~~~~~~eey~~~l~~aL~~~~~p~~   82 (213)
T 1ik9_A            3 RKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPAD   82 (213)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEESSCGGGEEEEEEECSSCEEEEEEEHHHHHHHHHHTTCCHHHHHHHHHHHHCC----CC
T ss_pred             ceeEEeeecCCCCCeEEEEEEEcCCCCCceEEEEecCCCceEEEecHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCCCc
Confidence            68999999998755 999999965   689999999999999999999999999999999999999999999888 9999


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEE---eeecCCCCcchHHHHHHHHhhH-------hhhhhH---------HHHH
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRW---KCGPAPNSKKVPAGILDFLMDA-------NIRLSA---------EKCL  140 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl---~l~~~~d~~e~~~eL~d~l~~~-------n~~L~~---------E~l~  140 (240)
                      .|.|+..++   .++|||+|.+++|+|||   +|.+++||.+++++|||||+.+       |.+|+.         ++++
T Consensus        83 ~~~~~~~~~---~l~~t~rK~~~~I~~rLGsi~L~~~~d~~e~i~elfd~~~~~~~~~~~~~~~L~~e~~~l~~~~~~l~  159 (213)
T 1ik9_A           83 VYTFNFSKE---SAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQ  159 (213)
T ss_dssp             CEEEEEETT---TTEEEEEEECSSCEEEEEEEECEECSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cceeeecCc---eeEEEEEEecCceEEEEEEEEeecCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999987664   38999999999999995   5667899999889999998665       555542         3789


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhchhHHHHHHH-HHHHHHhhhcccch
Q 047048          141 AQSERFKNEKLEFESAIYAKFLGVLNSKKSKLRELQ-DKLSKQAVMGDLQQ  190 (240)
Q Consensus       141 ~qlEe~v~~K~e~E~~Ly~KFv~vLNEKK~KIRelq-~~L~~~~~~~~~~~  190 (240)
                      +|||+||++|++||.+||+||++||||||+|||+|| ++|+.++++++..+
T Consensus       160 ~qlE~~v~~K~~~E~~L~~KF~~lLNeKK~KIR~lq~~Ll~~~~~~~~~~~  210 (213)
T 1ik9_A          160 GRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIK  210 (213)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhhhhh
Confidence            999999999999999999999999999999999999 88888888877654

>3w03_C DNA repair protein XRCC4; coiled-coil, NHEJ, DSBS repair, KU70/80, DNA-PKCS, DNA ligas binding protein; HET: DNA; 8.49A {Homo sapiens}

Probab=99.98  E-value=2.2e-31  Score=227.33  Aligned_cols=146  Identities=20%  Similarity=0.321  Sum_probs=130.2

Q ss_pred             ceeEEeecCCCCCc-EEEEEEE---eCCeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHh-cCCCCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTW---FQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYL-GFQQPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w---~~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL-~~~~p~~   79 (240)
                      ++|.||+++++|+. |||+|+|   +|++|.|++|||.++|+|+|++++|.++|++|+|+.++|+++|++|| ++++|++
T Consensus        23 ~~~~~i~~~s~p~~~yflk~~W~~~l~sgF~L~LTDG~sAW~G~vSe~~I~~~A~~~~m~~e~Yv~eL~kAl~~~~~~~~  102 (184)
T 3w03_C           23 RKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPAD  102 (184)
T ss_dssp             EEEEEECBTTCTTSCEEEEEEESSCGGGEEEEEEECSSCEEEEEEEHHHHHHHHHHTTCCHHHHHHHHHHHHSSCCCSSC
T ss_pred             cceEEEEecCCCCceEEEEEEeccCCCCceEEEEECCCceeeEEcCHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCc
Confidence            58999999999998 9999999   67899999999999999999999999999999999999999999999 5888999


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEE---eeecCCCCcchHHHHHHHHhhHhhhhhH--HHHHHHHHHHHHHHHHH
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRW---KCGPAPNSKKVPAGILDFLMDANIRLSA--EKCLAQSERFKNEKLEF  153 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl---~l~~~~d~~e~~~eL~d~l~~~n~~L~~--E~l~~qlEe~v~~K~e~  153 (240)
                      .|.|+++++.   ++|+|+|.+.+|.|+|   +|.+++||.+++++||+||++.+.+|+.  +.++++.|++-.+-+..
T Consensus       103 ~Y~f~~s~e~---~~fs~eK~l~di~frLGSv~L~~v~~p~e~i~elid~~ld~~~~L~~~n~~LqkeNeRL~~E~n~~  178 (184)
T 3w03_C          103 VYTFNFSKES---CYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDV  178 (184)
T ss_dssp             CEEEEECTTT---CEEEEEEEETTEEEEEEEEECEECSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEecCccc---eEEEeeeccCceEEEEeeeeeeECCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999988764   8899999999999995   6778999999999999999998888874  35667776666555443

>3q4f_C DNA repair protein XRCC4; DSB repair, nuclear, recombination-recombination complex, DN protein-protein binding complex; HET: DNA; 5.50A {Homo sapiens}

Probab=99.96  E-value=5.4e-29  Score=210.52  Aligned_cols=141  Identities=21%  Similarity=0.317  Sum_probs=124.2

Q ss_pred             ceeEEeecCCCCCc-EEEEEEEe---CCeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHh-cCCCCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTWF---QSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYL-GFQQPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w~---~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL-~~~~p~~   79 (240)
                      ++|.||+++++|+. |||+|+|.   |+||.|++|||+++|+|+|++++|.+.|++++|..+.|+++|++|| ++..|+.
T Consensus        32 ~~v~~i~~~sep~~~yfLqvsW~~~lgsGF~i~LTDGqSaW~G~VS~~~Is~eAd~m~Me~e~YV~eL~KALv~~~~~~~  111 (186)
T 3q4f_C           32 RKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPAD  111 (186)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEESSCGGGEEEEEEECSSCEEEEEEEHHHHHHHHHHTTCCHHHHHHHHHHHHSSCCCSSC
T ss_pred             hhhhheeecCCCCccEEEEEEeccCCCcceEEEEeCCcceeeeEECHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCc
Confidence            47999999999888 99999994   5789999999999999999999999999999999999999999999 6778999


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEEe---eecCCCCcchHHHHHHHHhhHhhhhhH--HHHHHHHHHHHH
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRWK---CGPAPNSKKVPAGILDFLMDANIRLSA--EKCLAQSERFKN  148 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl~---l~~~~d~~e~~~eL~d~l~~~n~~L~~--E~l~~qlEe~v~  148 (240)
                      .|.|+.++++   ++|+|+|.+++|+|+||   |.+++||.+++++||+||.+.-..|.+  +.|+++.+++.+
T Consensus       112 ~y~F~~S~e~---~~Fs~eK~LkdvsF~LGSv~L~~V~nPaE~irELi~~~L~~i~~L~a~N~hLqkENeRL~~  182 (186)
T 3q4f_C          112 VYTFNFSKES---CYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAKNEHLQKENERLLR  182 (186)
T ss_dssp             CEEEEECTTT---CEEEEEEECSSCEEEEEEEECEECSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEEeccce---eEEEEEEEecCcEEEEeeEEeeeCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999885   78889999999999985   668999999999999998776555553  255666665544

>3mud_A DNA repair protein XRCC4, tropomyosin alpha-1 CHA; tropomysoin, overlap complex, coiled-coils, contractIle PROT; HET: DNA; 2.20A {Homo sapiens} PDB: 3sr2_A*

Probab=99.96  E-value=8.1e-28  Score=203.31  Aligned_cols=147  Identities=20%  Similarity=0.300  Sum_probs=127.0

Q ss_pred             ceeEEeecCCCCCc-EEEEEEEe---CCeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHh-cCCCCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTWF---QSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYL-GFQQPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w~---~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL-~~~~p~~   79 (240)
                      ++|.||+++++|+. |||+|+|.   |+||.|++|||+++|+|+|++++|.+.|++++|..+.|+++|++|| ++..|+.
T Consensus         6 ~~~~~i~~~s~p~~~yfL~v~w~~~l~~gf~i~ltDG~saW~g~Vs~~~i~~eA~~~~me~e~Yv~el~kAl~~~~~~~~   85 (175)
T 3mud_A            6 RKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPAD   85 (175)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEESSCGGGEEEEEEECSSCEEEEEEEHHHHHHHHHHTTCCHHHHHHHHHHHHTTCCCTTC
T ss_pred             hhhhheeecCCCCceEEEEEeccccCCcceEEEEeCCcceeeeeeCHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCc
Confidence            57999999999888 99999994   5789999999999999999999999999999999999999999999 6778999


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEEe---eecCCCCcchHHHHHHHHhhHhhhhh------HHHHHHHHHHHHHHH
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRWK---CGPAPNSKKVPAGILDFLMDANIRLS------AEKCLAQSERFKNEK  150 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl~---l~~~~d~~e~~~eL~d~l~~~n~~L~------~E~l~~qlEe~v~~K  150 (240)
                      .|.|++++++   .+++|+|.+.+++|+||   |.++++|.+++++||+++.+.-..|.      .+++...-+++...-
T Consensus        86 ~~~f~~s~e~---~~~syek~lk~vsfrLGs~~Lk~a~~paE~ireli~~AertV~kLqkeiD~LEDeL~~eKek~k~i~  162 (175)
T 3mud_A           86 VYTFNFSKES---CYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTTAKNEKSIDDLEEKVAHAKEENLNMH  162 (175)
T ss_dssp             CEEEEECTTT---CEEEEEEECSSCEEEEEEEECEECSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ceEEecChhH---HHHHHHHHHHHHHHHhcccccccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999885   77888999999999984   66899999999999999877666664      234555555555555


Q ss_pred             HHHH
Q 047048          151 LEFE  154 (240)
Q Consensus       151 ~e~E  154 (240)
                      .+++
T Consensus       163 ~eLD  166 (175)
T 3mud_A          163 QMLD  166 (175)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>1z56_A Ligase interacting factor 1; DNA repair, BRCT, NHEJ, XRCC4, DNA ligase, coiled-coil; HET: DNA; 3.92A {Saccharomyces cerevisiae}

Probab=99.90  E-value=4.1e-25  Score=193.85  Aligned_cols=147  Identities=14%  Similarity=0.159  Sum_probs=46.1

Q ss_pred             EEEEecCCcceEEeecHHHHH-HHhhcc-----CCCHHHHHHHHHHHhcCCCC------CceeeEEec-CCCCceEEEEE
Q 047048           31 DLSITDGLNAWLCNASEEQVK-DRAALW-----DQPVTEYIKLAERYLGFQQP------GCVYGFTDA-ADGCKRLSWTF   97 (240)
Q Consensus        31 ~L~~TDG~~~w~g~vs~~~i~-~rA~~~-----~~s~eey~~~l~~aL~~~~p------~~~y~~~~~-~~~~~~l~~t~   97 (240)
                      .|++|+|++||+|+  +..|. .|++++     .++.++|.++|+.+|++..+      ...|.=+.. ...+..+++|+
T Consensus        52 ~LvaTEGe~py~~s--~~~i~~LR~k~~~n~~~~~~~~eW~~iL~~l~~~k~~~~~l~~~~~~~~w~~~iev~~~~~itm  129 (246)
T 1z56_A           52 KMLVSEGTGIFSKS--SFGINDLRIFTGENIDEESKKYVWYELLKMLTGHKVYIASLDEKVVFTKWTCRMQDDEVWKVVM  129 (246)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hhhhcCCcCccccc--ccchhheeeecccccccccchHHHHHHHHHHhcCCccccchhccccccccccCceeCCEEEEEE
Confidence            38999999999999  55566 799999     99999999999998876532      222321111 12345689999


Q ss_pred             EeeceeEEEEEe-eecCCCCcchHHHHHHHHhhHhhhhh------------HHHHHHHHHHHHHHHHHHHHHHH------
Q 047048           98 EKEGTKLEWRWK-CGPAPNSKKVPAGILDFLMDANIRLS------------AEKCLAQSERFKNEKLEFESAIY------  158 (240)
Q Consensus        98 eK~~~~I~~rl~-l~~~~d~~e~~~eL~d~l~~~n~~L~------------~E~l~~qlEe~v~~K~e~E~~Ly------  158 (240)
                      |+++..|++||+ +.+.+++.+. ++||+|.....+.++            -..++.||++||.+|++|| +|+      
T Consensus       130 rkri~~Itqrlg~ltL~~~~~~e-IdLFewA~~L~q~i~~ln~k~~~~E~si~~L~~qLeElv~~k~~~d-qLi~~RD~~  207 (246)
T 1z56_A          130 ELESSAIIRKIAELTLHPVKKGE-IDLFEMADKLYKDICCVNDSYRNIKESDSSNRNRVEQLARERELLD-KLLETRDER  207 (246)
T ss_dssp             ------------------------------CTTSGGGTTHHHHHHHHTTTTTTHHHHHHHHTTTTHHHHH-HHHHHTTTH
T ss_pred             eehhhHHHhhheeEEeecCccch-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcch
Confidence            999999999997 6677777664 699999554444443            1378999999999999999 999      


Q ss_pred             --HHHHHHHhchhHHHHHHHHHHHH
Q 047048          159 --AKFLGVLNSKKSKLRELQDKLSK  181 (240)
Q Consensus       159 --~KFv~vLNEKK~KIRelq~~L~~  181 (240)
                        ++|++||||||+|||+||++|..
T Consensus       208 tR~~fv~LLNEKK~KIR~qqrlL~s  232 (246)
T 1z56_A          208 TRAMMVTLLNEKKKKIRELHEILRQ  232 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGTTTT
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHHH
Confidence              99999999999999999999865

>2qm4_A Non-homologous END-joining factor 1; XRCC4 like factor, homodimer, beta-sandwich, coiled-coil, recombination; HET: MSE; 2.30A {Homo sapiens} PDB: 3sr2_C* 2r9a_A 3q4f_E* 3rwr_D*

Probab=97.32  E-value=0.0094  Score=52.35  Aligned_cols=102  Identities=19%  Similarity=0.266  Sum_probs=69.2

Q ss_pred             EeecCCCCCcEEEEEEEeCCeeEEEEecCCcceEEeecHHHHHHHhhccCC----CHH----HHHHHHHHHh-cCCCCCc
Q 047048            9 KLEIPHATDPIFVKGTWFQSHFDLSITDGLNAWLCNASEEQVKDRAALWDQ----PVT----EYIKLAERYL-GFQQPGC   79 (240)
Q Consensus         9 Ri~~~~~~~~~~lkv~w~~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~----s~e----ey~~~l~~aL-~~~~p~~   79 (240)
                      +|+.++.  .||++.....+++.|.+||-.+.|+=+++...|-.||+....    +++    .|-..+..+| .+..|+ 
T Consensus        17 ~l~l~~~--~llvk~~ft~~sY~l~lTDL~~vW~E~l~~~~I~~Rak~lN~rl~i~~s~~~~~l~~ll~~aL~~~~~~~-   93 (235)
T 2qm4_A           17 WLQLAEN--SLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPS-   93 (235)
T ss_dssp             EEECSSS--EEEEEEEEETTEEEEEEECSSCEEEEEECHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHCSCSCC-
T ss_pred             EEeeCCC--CeEEEEEecCCcEEEEEEccchhceeecCHHHHHHHHHHhCcCCCCChhHhHHHHHHHHHHHHhcCCCCc-
Confidence            4555543  399999999999999999999999999999999999877665    554    4555566788 444444 


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEE--eeecCC
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRW--KCGPAP  114 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl--~l~~~~  114 (240)
                      ..+|.....+ ..|+++++-.+.++.|+|  .|.+.+
T Consensus        94 ~~sls~~~~~-~~L~L~~~~~L~~lPlkW~fhL~~~~  129 (235)
T 2qm4_A           94 EATFSCDCVA-DALILRVRSELSGLPFYWNFHCMLAS  129 (235)
T ss_dssp             CCEEEEEEET-TEEEEEEEEEETTEEEEEEEEEEECC
T ss_pred             ceEEEecCCC-CcEEEEEEEECCCCCEEEEEEEeeCC
Confidence            3344322111 236666655555566665  455554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	240
d1ik9a1	117	XRCC4, N-terminal domain {Human (Homo sapiens) [Ta	99.89

>d1ik9a1 b.59.1.1 (A:1-117) XRCC4, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: XRCC4, N-terminal domain
superfamily: XRCC4, N-terminal domain
family: XRCC4, N-terminal domain
domain: XRCC4, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.6e-23  Score=163.32  Aligned_cols=104  Identities=21%  Similarity=0.338  Sum_probs=92.2

Q ss_pred             ceeEEeecCCCCCc-EEEEEEEe---CCeeEEEEecCCcceEEeecHHHHHHHhhccCCCHHHHHHHHHHHh-cCCCCCc
Q 047048            5 QTCLKLEIPHATDP-IFVKGTWF---QSHFDLSITDGLNAWLCNASEEQVKDRAALWDQPVTEYIKLAERYL-GFQQPGC   79 (240)
Q Consensus         5 ~t~~Ri~~~~~~~~-~~lkv~w~---~s~f~L~~TDG~~~w~g~vs~~~i~~rA~~~~~s~eey~~~l~~aL-~~~~p~~   79 (240)
                      .++.||+.+++|+. |||+++|.   |++|.|++|||+++|+|+|++.+|.+.|++++|..+.|+++|++|| .+..++.
T Consensus         3 ~~v~~I~~~sep~~~YFL~vsw~~dlgsGf~l~LtDG~saW~G~Vse~dis~eA~~m~Me~e~Yv~el~kAl~~~~~~~~   82 (117)
T d1ik9a1           3 RKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPAD   82 (117)
T ss_dssp             EEEEEEEETTEEEEEEEEEEEESSCGGGEEEEEEECSSCEEEEEEEHHHHHHHHHHTTCCHHHHHHHHHHHHCC----CC
T ss_pred             ceEeEEEecCCCCceEEEEEEeeecCCCceEEEEeCCceeeeeEECHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCCCCc
Confidence            57999999999887 99999995   5789999999999999999999999999999999999999999999 4778888


Q ss_pred             eeeEEecCCCCceEEEEEEeeceeEEEEEeee
Q 047048           80 VYGFTDAADGCKRLSWTFEKEGTKLEWRWKCG  111 (240)
Q Consensus        80 ~y~~~~~~~~~~~l~~t~eK~~~~I~~rl~l~  111 (240)
                      .|.|+.+.+.   ++|+|+|.+.+|.|+||..
T Consensus        83 ~y~F~~s~~~---~~fs~kK~lkdv~FqLGs~  111 (117)
T d1ik9a1          83 VYTFNFSKES---AYFFFEKNLKDVSFRLGSF  111 (117)
T ss_dssp             CEEEEEETTT---TEEEEEEECSSCEEEEEEE
T ss_pred             ceEEEecccc---EEEEEEeeecceEEEEeeE
Confidence            9999998765   6888899999999999754