255764496

255764496

excinuclease ABC subunit C

GeneID in NCBI database:8209596Locus tag:CLIBASIA_02430
Protein GI in NCBI database:255764496Protein Accession:YP_003065012.2
Gene range:-(682088, 683938)Protein Length:616aa
Gene description:excinuclease ABC subunit C
COG prediction:[L] Nuclease subunit of the excinuclease complex
KEGG prediction:uvrC; excinuclease ABC subunit C; K03703 excinuclease ABC subunit C
SEED prediction:Excinuclease ABC subunit C
Pathway involved in KEGG:Nucleotide excision repair [PATH:las03420]
Subsystem involved in SEED:DNA repair, UvrABC system
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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------
MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTPT
ccHHHccccccEEEEEcccccEEEEEcHHHHHHHHHHHHccccccHHHHHHHHHHHEEEEEEEccHHHHHHHHHHHHHHHccHHHHHccccccccEEEEEccccccEEEEEccccccccEEEcccccHHHHHHHHHHHHHHcccccccccccccccccccEEEcccccccccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEEEccEEEEEEEEEEccEEEccccEEEEccccccHHHHHHHHHHHHHcccccccEEEcccccccHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccccccEEEEEEEEccccccccccEEEEcccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEEEEccHHHHHHHHHHHHHccccccccEEEEEcccccccccEEEEcccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccHHHHHHccHHHHHHcccccHHHHHHHHHHHccccccccc
cccccccccccEEEEEcccccEEEEccHHHHHHHHHHHcccccccHHHHHHHHHHcccEEEEcccHHHHHHHHHHHHHHHcccccEEEcccccccEEEEccccccHHHHHHccccccccccccccccHHHHHHHHHHHHHHcccccccccHccccccccHHEEEccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHccccHccccEEEEEEccccEEEEEEEEEcccEcccccccccccccccHHHHHHHHHHHHHHccccccEEEEccccccHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEcccccccccEEEEEEEcccccccHHHHEEEEcccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccEEEEEccHHHHHHHHHHHHHcccccccEEEEEEcccccccccEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHccccccHHHHHHHHHHHccHHHHHHccHHHHHccccccHHHHHHHHHHHHHccccccc
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
MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENIllseeaeetslleisFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTPT
**SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHI*******YNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSH***************DFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQL****************SFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHR*************INGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY************
*********PGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAIT**********YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH********
*SS*QMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNF**KKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN******
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MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTPT
MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTPT
MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHTPT

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
254780572192 hypothetical protein CLIBASIA_02295 [Candidatus Li 0.024
>gi|254780572|ref|YP_003064985.1| hypothetical protein CLIBASIA_02295 [Candidatus Liberibacter asiaticus str. psy62] Length = 192 Back     alignment
 Score = 32.3 bits (72), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 12/99 (12%)

Query: 6   MPECPGVYQMLDI-----AGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQI-NNIR 59
           MP    V+ +L+I     AG+ L+   AY++ ++I++   S+ +TH +T       N++R
Sbjct: 29  MPYFMLVFAILEISLSFTAGQ-LFESAAYDVARKIRTGEISSKNTHSLTEFRRVFCNDLR 87

Query: 60  FTVTCTEVEA-----LLLEANMIKRLKPRFNILLRDDKS 93
               C+E E      L L+   IK L+     + R DKS
Sbjct: 88  VLFNCSENEIGRPYDLYLDVKQIKSLQEITETVPRKDKS 126

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
315121799615 excinuclease ABC subunit C [Candidatus Liberibacter sol 1 0.0
222148164690 excinuclease ABC subunit C [Agrobacterium vitis S4] Len 1 0.0
227821493673 excinuclease ABC subunit C [Sinorhizobium fredii NGR234 1 0.0
150396006674 excinuclease ABC subunit C [Sinorhizobium medicae WSM41 1 0.0
327193359679 excinuclease ABC protein, C subunit [Rhizobium etli CNP 1 0.0
307317729674 excinuclease ABC, C subunit [Sinorhizobium meliloti AK8 1 0.0
307300995674 excinuclease ABC, C subunit [Sinorhizobium meliloti BL2 1 0.0
15964924674 excinuclease ABC subunit C [Sinorhizobium meliloti 1021 1 0.0
209548689680 excinuclease ABC subunit C [Rhizobium leguminosarum bv. 1 0.0
119367493681 RecName: Full=UvrABC system protein C; Short=Protein uv 1 0.0
>gi|315121799|ref|YP_004062288.1| excinuclease ABC subunit C [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 615 Back     alignment and organism information
 Score = 1054 bits (2726), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 496/609 (81%), Positives = 556/609 (91%)

Query: 3   SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTV 62
           S+Q+PE PGVYQMLD AG+VLYVGKAYNLQKR+KSY   NNHTHRI  MI+Q  N+ FT 
Sbjct: 2   SKQIPESPGVYQMLDAAGKVLYVGKAYNLQKRVKSYTQLNNHTHRIMCMINQTRNLNFTT 61

Query: 63  TCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYF 122
           T TEVEALLLEA+MIKRLKPRFNILLRDDKSFPYI+ITD+HKIP+LYKHR    ++GSYF
Sbjct: 62  TRTEVEALLLEASMIKRLKPRFNILLRDDKSFPYIIITDEHKIPSLYKHRGPPVMKGSYF 121

Query: 123 GPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYME 182
           GPFASVDAVEKTINSLQR FFLRSC+D++F  RTRPCLLFQIKRCSGPCTGEIS+EKYME
Sbjct: 122 GPFASVDAVEKTINSLQRAFFLRSCSDNIFGCRTRPCLLFQIKRCSGPCTGEISAEKYME 181

Query: 183 FVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRM 242
           FV+EAK FLSG NH+LK KIA+ MN+ATL+EDYESAIIHRDRL ALSHIQNH++SI   M
Sbjct: 182 FVYEAKDFLSGRNHDLKRKIAQKMNKATLEEDYESAIIHRDRLVALSHIQNHSESINETM 241

Query: 243 DCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPEN 302
           DCFSLYH+KN+ACIQT FF FGQNRG+ TFFLKTD +STNAQI SYFLRQFY DKPCPE+
Sbjct: 242 DCFSLYHDKNIACIQTFFFRFGQNRGSYTFFLKTDPQSTNAQIFSYFLRQFYEDKPCPES 301

Query: 303 ILLSEEAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISH 362
           ILLSE+AEE+ LLEISF ++YG+KVKIT+PKQGEK+KIIEQALINA  SH QK++ EISH
Sbjct: 302 ILLSEKAEESQLLEISFCEKYGHKVKITIPKQGEKKKIIEQALINARNSHAQKIALEISH 361

Query: 363 QMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDV 422
           Q ++KDF +KFALP+IPKRIEIYDNSH+MGCSAVGCMVV GE+G +KNQYRKFNLHP+DV
Sbjct: 362 QAMIKDFAEKFALPYIPKRIEIYDNSHVMGCSAVGCMVVAGESGLIKNQYRKFNLHPDDV 421

Query: 423 KTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGV 482
           KTQDDCAMMR+VLERRFSQLIKNEEN NF PKKQEYSFPSWPDVVILDGG+GQLSAAQ V
Sbjct: 422 KTQDDCAMMRVVLERRFSQLIKNEENSNFPPKKQEYSFPSWPDVVILDGGRGQLSAAQSV 481

Query: 483 LKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAI 542
            KKLN+ENRITIISIAKG +R+AGMEKFFV+ G+ L+L+MRDP+LYFIQ+LRDEAHRFA+
Sbjct: 482 FKKLNIENRITIISIAKGQQRNAGMEKFFVENGKELMLHMRDPVLYFIQKLRDEAHRFAV 541

Query: 543 TTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACK 602
           TTHRKRRKKA+Y+PL+EINGIGPLRKR LLQSFGTVKMISRSSPETLAS EGISKKIACK
Sbjct: 542 TTHRKRRKKASYNPLEEINGIGPLRKRSLLQSFGTVKMISRSSPETLASTEGISKKIACK 601

Query: 603 IYNHFHKNT 611
           IY HFHKNT
Sbjct: 602 IYTHFHKNT 610


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148164|ref|YP_002549121.1| excinuclease ABC subunit C [Agrobacterium vitis S4] Length = 690 Back     alignment and organism information
>gi|227821493|ref|YP_002825463.1| excinuclease ABC subunit C [Sinorhizobium fredii NGR234] Length = 673 Back     alignment and organism information
>gi|150396006|ref|YP_001326473.1| excinuclease ABC subunit C [Sinorhizobium medicae WSM419] Length = 674 Back     alignment and organism information
>gi|327193359|gb|EGE60262.1| excinuclease ABC protein, C subunit [Rhizobium etli CNPAF512] Length = 679 Back     alignment and organism information
>gi|307317729|ref|ZP_07597167.1| excinuclease ABC, C subunit [Sinorhizobium meliloti AK83] Length = 674 Back     alignment and organism information
>gi|307300995|ref|ZP_07580764.1| excinuclease ABC, C subunit [Sinorhizobium meliloti BL225C] Length = 674 Back     alignment and organism information
>gi|15964924|ref|NP_385277.1| excinuclease ABC subunit C [Sinorhizobium meliloti 1021] Length = 674 Back     alignment and organism information
>gi|209548689|ref|YP_002280606.1| excinuclease ABC subunit C [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 680 Back     alignment and organism information
>gi|119367493|sp|Q8UGA9|UVRC_AGRT5 RecName: Full=UvrABC system protein C; Short=Protein uvrC; AltName: Full=Excinuclease ABC subunit C Length = 681 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
PRK00558598 PRK00558, uvrC, excinuclease ABC subunit C; Validated 0.0
TIGR00194574 TIGR00194, uvrC, excinuclease ABC, C subunit 1e-126
PRK14671621 PRK14671, uvrC, excinuclease ABC subunit C; Provisional 1e-93
PRK14669624 PRK14669, uvrC, excinuclease ABC subunit C; Provisional 1e-91
PRK14668577 PRK14668, uvrC, excinuclease ABC subunit C; Provisional 7e-88
PRK14667567 PRK14667, uvrC, excinuclease ABC subunit C; Provisional 2e-65
PRK14670574 PRK14670, uvrC, excinuclease ABC subunit C; Provisional 2e-59
COG0322581 COG0322, UvrC, Nuclease subunit of the excinuclease com 1e-147
PRK12306519 PRK12306, uvrC, excinuclease ABC subunit C; Reviewed 1e-96
PRK14666694 PRK14666, uvrC, excinuclease ABC subunit C; Provisional 5e-49
PRK07883557 PRK07883, PRK07883, hypothetical protein; Validated 4e-45
pfam08459154 pfam08459, UvrC_HhH_N, UvrC Helix-hairpin-helix N-termi 4e-47
PRK14672691 PRK14672, uvrC, excinuclease ABC subunit C; Provisional 7e-34
PRK14666694 PRK14666, uvrC, excinuclease ABC subunit C; Provisional 9e-31
PRK14672691 PRK14672, uvrC, excinuclease ABC subunit C; Provisional 5e-27
PRK10545286 PRK10545, PRK10545, nucleotide excision repair endonucl 4e-15
smart0046584 smart00465, GIYc, GIY-YIG type nucleases (URI domain) 1e-10
pfam0154177 pfam01541, GIY-YIG, GIY-YIG catalytic domain 1e-05
COG1948254 COG1948, MUS81, ERCC4-type nuclease [DNA replication, r 2e-05
PRK13766773 PRK13766, PRK13766, Hef nuclease; Provisional 7e-05
TIGR00575652 TIGR00575, dnlj, DNA ligase, NAD-dependent 1e-04
COG0272667 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT d 0.002
PRK07956665 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validate 0.003
>gnl|CDD|179065 PRK00558, uvrC, excinuclease ABC subunit C; Validated Back     alignment and domain information
>gnl|CDD|161756 TIGR00194, uvrC, excinuclease ABC, C subunit Back     alignment and domain information
>gnl|CDD|184786 PRK14671, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|173132 PRK14669, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|184785 PRK14668, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|184784 PRK14667, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|173133 PRK14670, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|30670 COG0322, UvrC, Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|183423 PRK12306, uvrC, excinuclease ABC subunit C; Reviewed Back     alignment and domain information
>gnl|CDD|173129 PRK14666, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|181157 PRK07883, PRK07883, hypothetical protein; Validated Back     alignment and domain information
>gnl|CDD|149497 pfam08459, UvrC_HhH_N, UvrC Helix-hairpin-helix N-terminal Back     alignment and domain information
>gnl|CDD|173135 PRK14672, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|173129 PRK14666, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|173135 PRK14672, uvrC, excinuclease ABC subunit C; Provisional Back     alignment and domain information
>gnl|CDD|182535 PRK10545, PRK10545, nucleotide excision repair endonuclease; Provisional Back     alignment and domain information
>gnl|CDD|128741 smart00465, GIYc, GIY-YIG type nucleases (URI domain) Back     alignment and domain information
>gnl|CDD|144946 pfam01541, GIY-YIG, GIY-YIG catalytic domain Back     alignment and domain information
>gnl|CDD|32131 COG1948, MUS81, ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional Back     alignment and domain information
>gnl|CDD|161936 TIGR00575, dnlj, DNA ligase, NAD-dependent Back     alignment and domain information
>gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|181181 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 616 excinuclease ABC subunit C [Candidatus Liberibacter asi
PRK00558609 uvrC excinuclease ABC subunit C; Validated 100.0
COG0322581 UvrC Nuclease subunit of the excinuclease complex [DNA 100.0
TIGR00194601 uvrC excinuclease ABC, C subunit; InterPro: IPR004791 E 100.0
PRK12306519 uvrC excinuclease ABC subunit C; Reviewed 100.0
PRK07883575 hypothetical protein; Validated 100.0
pfam08459154 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal. This do 100.0
PRK10545286 nucleotide excision repair endonuclease; Provisional 100.0
LOAD_uvrC_endov123 consensus 100.0
pfam04493205 Endonuclease_5 Endonuclease V. Endonuclease V is specif 97.42
COG1515212 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA r 97.34
cd06559208 Endonuclease_V Endonuclease_V, a DNA repair enzyme that 96.89
PRK11617223 endonuclease V; Provisional 96.58
cd04657426 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-lik 96.53
KOG4417261 consensus 94.96
cd02826393 Piwi-like Piwi-like: PIWI domain. Domain found in prote 92.23
pfam02171296 Piwi Piwi domain. This domain is found in the protein P 90.41
cd04658448 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piw 90.08
smart0046584 GIYc GIY-YIG type nucleases (URI domain). 99.71
pfam0154177 GIY-YIG GIY-YIG catalytic domain. This domain called GI 99.36
pfam09517170 RE_Eco29kI Eco29kI restriction endonuclease. This famil 95.48
PRK0032986 GIY-YIG nuclease superfamily protein; Validated 93.9
COG3680259 Uncharacterized protein conserved in bacteria [Function 90.58
PRK13766764 Hef nuclease; Provisional 99.08
KOG2841254 consensus 98.63
TIGR00575 706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 98.57
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 98.38
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 98.29
TIGR02236 333 recomb_radA DNA repair and recombination protein RadA; 98.03
PRK01172674 ski2-like helicase; Provisional 97.84
PRK13482352 DNA integrity scanning protein DisA; Provisional 97.61
PRK02362736 ski2-like helicase; Provisional 97.59
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 97.54
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 97.49
COG0632201 RuvA Holliday junction resolvasome, DNA-binding subunit 97.44
PRK13901196 ruvA Holliday junction DNA helicase motor protein; Prov 97.32
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 97.29
COG1623349 Predicted nucleic-acid-binding protein (contains the HH 96.94
PRK09482256 xni exonuclease IX; Provisional 96.93
TIGR00596939 rad1 DNA repair protein (rad1); InterPro: IPR006167 All 96.91
smart00475259 53EXOc 5'-3' exonuclease. 96.83
pfam01367100 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold. 96.82
KOG0442892 consensus 96.55
cd00008240 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease dom 96.42
PRK12766 238 50S ribosomal protein L32e; Provisional 96.07
TIGR00608 223 radc DNA repair protein RadC; InterPro: IPR001405 RadC 95.74
COG1555149 ComEA DNA uptake protein and related DNA-binding protei 95.43
TIGR0042670 TIGR00426 competence protein ComEA helix-hairpin-helix 95.42
pfam0063330 HHH Helix-hairpin-helix motif. The helix-hairpin-helix 95.22
cd0008075 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) mo 95.15
PTZ00217394 flap endonuclease-1; Provisional 95.15
cd00128316 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPG 94.7
PRK03980295 flap endonuclease-1; Provisional 94.27
PRK07956 668 ligA NAD-dependent DNA ligase LigA; Validated 94.22
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 94.18
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 93.66
smart00483334 POLXc DNA polymerase X family. includes vertebrate poly 93.59
cd01703 394 Pol_iota Pol iota is member of the DNA polymerase Y-fam 93.45
TIGR03674338 fen_arch flap structure-specific endonuclease. Endonucl 93.44
PRK07220740 DNA topoisomerase I; Validated 93.02
COG1555149 ComEA DNA uptake protein and related DNA-binding protei 91.84
TIGR00375384 TIGR00375 conserved hypothetical protein TIGR00375; Int 90.92
KOG2093 1016 consensus 90.16
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recombinati 98.6
PRK07997 928 consensus 97.21
PRK07456 975 consensus 97.11
PRK06887 954 consensus 97.04
PRK08835 931 consensus 97.0
TIGR00593 1005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 96.94
PRK05797 869 consensus 96.93
PRK08786 927 consensus 96.84
PRK07300 880 consensus 96.78
PRK08434 887 consensus 96.78
PRK07556 977 consensus 96.7
PRK05755 889 DNA polymerase I; Provisional 96.67
PRK08928 861 consensus 96.66
PRK07625 922 consensus 96.62
PRK05929 870 consensus 96.6
PRK08076 877 consensus 96.56
PRK07898 902 consensus 96.56
PRK12311332 rpsB 30S ribosomal protein S2; Provisional 91.83
TIGR00631667 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 A 98.11
pfam0215136 UVR UvrB/uvrC motif. 97.69
PRK04301318 radA DNA repair and recombination protein RadA; Validat 96.83
COG3880176 Modulator of heat shock repressor CtsR, McsA [Signal tr 96.79
smart00483334 POLXc DNA polymerase X family. includes vertebrate poly 96.4
PRK01216351 DNA polymerase IV; Validated 95.7
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 95.41
PRK03352345 DNA polymerase IV; Validated 95.07
COG1796326 POL4 DNA polymerase IV (family X) [DNA replication, rec 94.77
cd01701405 Pol_zeta Pol_zeta, a member of the Y-family of DNA poly 94.72
PRK03103410 DNA polymerase IV; Reviewed 92.73
PRK03858398 DNA polymerase IV; Validated 92.35
PRK00254717 ski2-like helicase; Provisional 98.1
TIGR00084217 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR 97.46
COG0272 667 Lig NAD-dependent DNA ligase (contains BRCT domain type 92.82
PRK05298657 excinuclease ABC subunit B; Provisional 97.72
COG0556663 UvrB Helicase subunit of the DNA excision repair comple 97.6
PRK08609570 hypothetical protein; Provisional 97.26
TIGR01448 769 recD_rel helicase, RecD/TraA family; InterPro: IPR00634 96.66
PRK00024224 radC DNA repair protein RadC; Reviewed 96.29
PRK08609570 hypothetical protein; Provisional 96.13
cd01700344 Pol_V Pol V was discovered in Escherichia coli as Umuc 93.57
PRK02406355 DNA polymerase IV; Validated 94.85
PRK03348456 DNA polymerase IV; Provisional 93.96
COG0258310 Exo 5'-3' exonuclease (including N-terminal domain of P 94.71
PRK10430239 DNA-binding transcriptional activator DcuR; Provisional 94.26
PRK01810410 DNA polymerase IV; Validated 94.22
PRK02794417 DNA polymerase IV; Provisional 93.91
cd01702358 Pol_eta Pol eta is member of the DNA polimerase Y-famil 93.19
cd00424341 Pol_Y Y-family of DNA polymerases. Pol_Y's can transver 92.93
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1, RAD 91.07
cd00141307 NT_POLXc Nucleotidyltransferase (NT) domain of family X 90.15
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00194 uvrC excinuclease ABC, C subunit; InterPro: IPR004791 Excinuclease ABC complex is involved in DNA replication, recombination and repair Back     alignment and domain information
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>pfam08459 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal Back     alignment and domain information
>PRK10545 nucleotide excision repair endonuclease; Provisional Back     alignment and domain information
>LOAD_uvrC_endov consensus Back     alignment and domain information
>pfam04493 Endonuclease_5 Endonuclease V Back     alignment and domain information
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases Back     alignment and domain information
>PRK11617 endonuclease V; Provisional Back     alignment and domain information
>cd04657 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-like subfamily Back     alignment and domain information
>KOG4417 consensus Back     alignment and domain information
>cd02826 Piwi-like Piwi-like: PIWI domain Back     alignment and domain information
>pfam02171 Piwi Piwi domain Back     alignment and domain information
>cd04658 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes Back     alignment and domain information
>smart00465 GIYc GIY-YIG type nucleases (URI domain) Back     alignment and domain information
>pfam01541 GIY-YIG GIY-YIG catalytic domain Back     alignment and domain information
>pfam09517 RE_Eco29kI Eco29kI restriction endonuclease Back     alignment and domain information
>PRK00329 GIY-YIG nuclease superfamily protein; Validated Back     alignment and domain information
>COG3680 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>KOG2841 consensus Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO) Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PRK02362 ski2-like helicase; Provisional Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional Back     alignment and domain information
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA Back     alignment and domain information
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only] Back     alignment and domain information
>PRK09482 xni exonuclease IX; Provisional Back     alignment and domain information
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167 All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues Back     alignment and domain information
>smart00475 53EXOc 5'-3' exonuclease Back     alignment and domain information
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold Back     alignment and domain information
>KOG0442 consensus Back     alignment and domain information
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes Back     alignment and domain information
>PRK12766 50S ribosomal protein L32e; Provisional Back     alignment and domain information
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae Back     alignment and domain information
>pfam00633 HHH Helix-hairpin-helix motif Back     alignment and domain information
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif Back     alignment and domain information
>PTZ00217 flap endonuclease-1; Provisional Back     alignment and domain information
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases Back     alignment and domain information
>PRK03980 flap endonuclease-1; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B Back     alignment and domain information
>TIGR03674 fen_arch flap structure-specific endonuclease Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287 This family of conserved hypothetical proteins has no known function Back     alignment and domain information
>KOG2093 consensus Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK12311 rpsB 30S ribosomal protein S2; Provisional Back     alignment and domain information
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage Back     alignment and domain information
>pfam02151 UVR UvrB/uvrC motif Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms] Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK01216 DNA polymerase IV; Validated Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information
>PRK03352 DNA polymerase IV; Validated Back     alignment and domain information
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases Back     alignment and domain information
>PRK03103 DNA polymerase IV; Reviewed Back     alignment and domain information
>PRK03858 DNA polymerase IV; Validated Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK05298 excinuclease ABC subunit B; Provisional Back     alignment and domain information
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO Back     alignment and domain information
>PRK00024 radC DNA repair protein RadC; Reviewed Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV Back     alignment and domain information
>PRK02406 DNA polymerase IV; Validated Back     alignment and domain information
>PRK03348 DNA polymerase IV; Provisional Back     alignment and domain information
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional Back     alignment and domain information
>PRK01810 DNA polymerase IV; Validated Back     alignment and domain information
>PRK02794 DNA polymerase IV; Provisional Back     alignment and domain information
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family Back     alignment and domain information
>cd00424 Pol_Y Y-family of DNA polymerases Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
3c65_A226 Crystal Structure Of Bacillus Stearothermophilus Uv 1e-56
2nrt_A220 Crystal Structure Of The C-Terminal Half Of Uvrc Le 2e-48
1yd6_A99 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 1e-38
1ycz_A96 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 2e-24
1yd2_A96 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 3e-23
1yd4_A96 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 4e-23
1yd3_A96 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 4e-23
1yd5_A96 Crystal Structure Of The Giy-Yig N-Terminal Endonuc 6e-23
2nrr_A159 Crystal Structure Of The C-Terminal Rnaseh Endonucl 1e-26
1kft_A78 Solution Structure Of The C-Terminal Domain Of Uvrc 4e-16
1x2i_A75 Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF 3e-07
2bgw_A219 Xpf From Aeropyrum Pernix, Complex With Dna Length 9e-07
2bhn_A214 Xpf From Aeropyrum Pernix Length = 214 1e-06
2owo_A671 Last Stop On The Road To Repair: Structure Of E.Col 1e-05
2zj2_A720 Archaeal Dna Helicase Hjm Apo State In Form 1 Lengt 2e-04
1pzn_A 349 Rad51 (Rada) Length = 349 6e-04
1z00_A89 Solution Structure Of The C-Terminal Domain Of Ercc 6e-04
2a1j_B91 Crystal Structure Of The Complex Between The C-Term 6e-04
3c1y_A377 Structure Of Bacterial Dna Damage Sensor Protein Wi 0.002
>gi|195927400|pdb|3C65|A Chain A, Crystal Structure Of Bacillus Stearothermophilus Uvrc 5' Endonuclease Domain Length = 226 Back     alignment and structure
 Score =  225 bits (574), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 78/235 (33%), Positives = 124/235 (52%), Gaps = 22/235 (9%)

Query: 377 HIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLE 436
             P+RIE +DNS+I G   V  +VV  +    K +YRK+ +    V   +D    R V+ 
Sbjct: 12  PAPRRIEAFDNSNIYGADPVSALVVFLDGKPAKKEYRKYKVKT--VAGPNDYETXREVVR 69

Query: 437 RRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLK-KLNVENRITII 495
           RR+++++K                   PD++I+DGGKG LSA + VL+ +L ++  + + 
Sbjct: 70  RRYTRVLKEG--------------LPLPDLIIIDGGKGHLSAVRDVLENELGLD--VPLA 113

Query: 496 SIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAA-Y 554
            +AK  K     E       + + L+ +    Y +QR++DE HRFA+  HRK R+K   +
Sbjct: 114 GLAKDEKHRTS-ELLAGDPPDVVPLDRQSQEFYLLQRIQDEVHRFAVXFHRKTRQKTMFH 172

Query: 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609
           S LD+I G+G  RK+ LL  FG+VK +  ++ E L     I + +A KIY   H+
Sbjct: 173 SVLDDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKLHE 226


>gi|126031198|pdb|2NRT|A Chain A, Crystal Structure Of The C-Terminal Half Of Uvrc Length = 220 Back     alignment and structure
>gi|61680598|pdb|1YD6|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Bacillus Caldotenax Length = 99 Back     alignment and structure
>gi|61680591|pdb|1YCZ|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Thermotoga Maritima Length = 96 Back     alignment and structure
>gi|61680594|pdb|1YD2|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Thermotoga Maritima: Point Mutant Y19f Bound To The Catalytic Divalent Cation Length = 96 Back     alignment and structure
>gi|61680596|pdb|1YD4|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Thermotoga Maritima: Point Mutant Y29f Bound To Its Catalytic Divalent Cation Length = 96 Back     alignment and structure
>gi|61680595|pdb|1YD3|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Thermotoga Maritima: Point Mutant Y43f Bound To Its Catalytic Divalent Cation Length = 96 Back     alignment and structure
>gi|61680597|pdb|1YD5|A Chain A, Crystal Structure Of The Giy-Yig N-Terminal Endonuclease Domain Of Uvrc From Thermotoga Maritima: Point Mutant N88a Bound To Its Catalytic Divalent Cation Length = 96 Back     alignment and structure
>gi|126031195|pdb|2NRR|A Chain A, Crystal Structure Of The C-Terminal Rnaseh Endonuclase Domain Of Uvrc Length = 159 Back     alignment and structure
>gi|27065203|pdb|1KFT|A Chain A, Solution Structure Of The C-Terminal Domain Of Uvrc From E- Coli Length = 78 Back     alignment and structure
>gi|78100875|pdb|1X2I|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM Pyrococcus Furiosus, Helix-Hairpin-Helix Domain Length = 75 Back     alignment and structure
>gi|61680877|pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna Length = 219 Back     alignment and structure
>gi|61680885|pdb|2BHN|A Chain A, Xpf From Aeropyrum Pernix Length = 214 Back     alignment and structure
gi|149242732|pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna Ligase Bound To Nicked Dna-Adenylate Length = 671 Back     alignment and structure
gi|223365750|pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1 Length = 720 Back     alignment and structure
>gi|34809805|pdb|1PZN|A Chain A, Rad51 (Rada) Length = 349 Back     alignment and structure
>gi|85544011|pdb|1Z00|A Chain A, Solution Structure Of The C-Terminal Domain Of Ercc1 Complexed With The C-Terminal Domain Of Xpf Length = 89 Back     alignment and structure
>gi|73536055|pdb|2A1J|B Chain B, Crystal Structure Of The Complex Between The C-Terminal Domains Of Human Xpf And Ercc1 Length = 91 Back     alignment and structure
>gi|187609352|pdb|3C1Y|A Chain A, Structure Of Bacterial Dna Damage Sensor Protein With Co- Purified And Co-Crystallized Ligand Length = 377 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucleotide 2e-34
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse H, h 6e-34
2nrr_A159 Uvrabc system protein C; UVRC, endonuclase, NER, hydrol 2e-28
2wsh_A143 Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacte 1e-22
1yd6_A99 UVRC; DNA binding protein; 2.00A {Bacillus caldotenax} 5e-20
1yd0_A96 Uvrabc system protein C; DNA binding protein; 1.50A {Th 1e-19
1mk0_A97 Intron-associated endonuclease 1; alpha/beta fold, cata 6e-14
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 4e-15
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 3e-10
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 1e-09
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 2e-07
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein-prote 2e-07
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 3e-07
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 2e-06
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 6e-06
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 9e-04
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 0.002
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Length = 226 Back     alignment and structure
 Score =  142 bits (359), Expect = 2e-34
 Identities = 65/232 (28%), Positives = 108/232 (46%), Gaps = 20/232 (8%)

Query: 379 PKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERR 438
           P+RIE +DNS+I G   V  +VV  +    K +YRK+ +             MR V+ RR
Sbjct: 14  PRRIEAFDNSNIYGADPVSALVVFLDGKPAKKEYRKYKVKTVAGPNDY--ETMREVVRRR 71

Query: 439 FSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIA 498
           +++++K                      +I+  G     +A   + +  +   + +  +A
Sbjct: 72  YTRVLKEGLP---------------LPDLIIIDGGKGHLSAVRDVLENELGLDVPLAGLA 116

Query: 499 KGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAAY-SPL 557
           K  K             + + L+ +    Y +QR++DE HRFA+  HRK R+K  + S L
Sbjct: 117 KDEKHRTSELLAG-DPPDVVPLDRQSQEFYLLQRIQDEVHRFAVMFHRKTRQKTMFHSVL 175

Query: 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609
           D+I G+G  RK+ LL  FG+VK +  ++ E L     I + +A KIY   H+
Sbjct: 176 DDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIYEKLHE 226


>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Length = 220 Back     alignment and structure
>2nrr_A Uvrabc system protein C; UVRC, endonuclase, NER, hydrolase; 1.20A {Thermotoga maritima} Length = 159 Back     alignment and structure
>2wsh_A Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacteria phage T4} Length = 143 Back     alignment and structure
>1yd6_A UVRC; DNA binding protein; 2.00A {Bacillus caldotenax} Length = 99 Back     alignment and structure
>1yd0_A Uvrabc system protein C; DNA binding protein; 1.50A {Thermotoga maritima} PDB: 1ycz_A 1yd1_A 1yd4_A 1yd3_A 1yd2_A 1yd5_A Length = 96 Back     alignment and structure
>1mk0_A Intron-associated endonuclease 1; alpha/beta fold, catalytic domain, DNA-binding surface, hydrolase; HET: CIT; 1.60A {Enterobacteria phage T4} SCOP: d.226.1.1 PDB: 1ln0_A Length = 97 Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Length = 78 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Length = 84 Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 63 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Length = 219 Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Length = 241 Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Length = 75 Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Length = 91 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Length = 89 Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Length = 667 Back     alignment and structure
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Length = 720 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target616 excinuclease ABC subunit C [Candidatus Liberibacter asi
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucleotide 100.0
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse H, h 100.0
2nrr_A159 Uvrabc system protein C; UVRC, endonuclase, NER, hydrol 100.0
1yd6_A99 UVRC; DNA binding protein; 2.00A {Bacillus caldotenax} 99.96
1yd0_A96 Uvrabc system protein C; DNA binding protein; 1.50A {Th 99.95
2wsh_A143 Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacte 99.92
1mk0_A97 Intron-associated endonuclease 1; alpha/beta fold, cata 98.66
3mx1_A235 ECO29KIR; type II restriction endonuclease, GIY-YIG end 94.13
1zg2_A107 Hypothetical UPF0213 protein BH0048; BHR2, structure, a 93.93
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 99.55
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 99.28
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 99.26
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 99.14
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 99.12
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 99.1
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 98.89
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 98.36
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 98.21
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein-prote 98.17
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 98.16
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, DNA re 98.08
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligomeric c 97.7
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; reco 97.6
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-binding, DN 97.53
2ziu_A311 MUS81 protein; helix-hairpin-helix, alternative splicin 97.34
3bz1_U104 Photosystem II 12 kDa extrinsic protein; electron trans 96.84
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynthesis 96.83
1b22_A114 DNA repair protein RAD51; DNA binding, riken structural 96.79
2p6r_A702 Afuhel308 helicase; protein-DNA complex, SF2 helicase, 96.32
2zix_A307 Crossover junction endonuclease MUS81; helix-hairpin-he 96.2
2duy_A75 Competence protein comea-related protein; helix-hairpin 95.68
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA binding do 95.6
3mr3_A 435 DNA polymerase ETA; POL ETA, polymerase, thymine dimer, 95.44
1exn_A290 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enteroba 95.34
2va8_A715 SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP 95.32
2izo_A346 FEN1, flap structure-specific endonuclease; hydrolase, 94.82
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 94.6
3gqc_A 504 DNA repair protein REV1; protein-DNA complex, alternati 94.46
2owo_A 671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 94.21
1ul1_X379 Flap endonuclease-1; protein complex, DNA-binding prote 93.89
1rxw_A336 Flap structure-specific endonuclease; helical clamp, he 93.33
2ziu_B341 Crossover junction endonuclease EME1; helix-hairpin-hel 92.98
2aq4_A 434 DNA repair protein REV1; polymerase, PAD, N-digit, G-lo 92.62
1b43_A340 Protein (FEN-1); nuclease, DNA repair, DNA replication, 92.55
1wcn_A70 Transcription elongation protein NUSA; RNA-binding prot 92.2
2i5h_A205 Hypothetical protein AF1531; PFAM:DUF655, PSI-2, struct 90.12
1e52_A63 Excinuclease ABC subunit; DNA excision repair, UVRB, DN 98.2
2ihm_A360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 96.14
2w36_A225 Endonuclease V; hypoxanthine, endonuclease, endonucleas 97.48
3ga2_A246 Endonuclease V; alpha-beta protein, structural genomics 96.85
3ho1_A685 Argonaute; argonaute, protein-DNA-RNA complex, plasmid; 96.72
3goc_A237 Endonuclease V; alpha-beta protein, structural genomics 96.41
1u04_A771 Argonaute, hypothetical protein PF0537; RNAI, silencing 96.14
2qh9_A184 UPF0215 protein AF_1433; structural genomics, PSI-2, MC 95.03
1c4o_A664 DNA nucleotide excision repair enzyme UVRB; uvrabc, hel 97.04
2d7d_A661 Uvrabc system protein B; helicase, protein-DNA-ADP tern 93.47
1jms_A381 Terminal deoxynucleotidyltransferase; polymerase; 2.36A 96.42
2fmp_A335 DNA polymerase beta; nucleotidyl transferase, transfera 95.62
2bcq_A335 DNA polymerase lambda; misalignment, extrahelical, muta 95.3
3osn_A420 DNA polymerase IOTA; hoogsteen base PAIR, protein-DNA c 94.39
3lda_A400 DNA repair protein RAD51; DNA binding protein, ATP-bind 93.86
3bq0_A354 POL IV, DBH, DNA polymerase IV; Y-family, lesion bypass 93.44
3oqg_A180 HPY188I; endonuclease-DNA complex, restriction enzyme, 96.36
2w9m_A578 Polymerase X; SAXS, DNA repair, DNA polymerase, DNA rep 95.82
3im1_A328 Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase 91.09
2q0z_X339 Protein Pro2281; SEC63, SEC, NESG, HR1979, structural g 90.55
3maj_A382 DNA processing chain A; MCSG, PSI-2, structural genomic 95.33
2edu_A98 Kinesin-like protein KIF22; kinesin-like DNA binding do 93.46
1a76_A326 Flap endonuclease-1 protein; 5'-3' EXO/endo nuclease, D 92.14
2duy_A75 Competence protein comea-related protein; helix-hairpin 92.07
3bz1_U104 Photosystem II 12 kDa extrinsic protein; electron trans 90.11
3mfi_A 520 DNA polymerase ETA; DNA damage, DNA repair, DNA replica 91.97
1s5l_U134 Photosystem II 12 kDa extrinsic protein; photosynthesis 90.41
1t94_A 459 Polymerase (DNA directed) kappa; replication, DNA repai 90.82
1jms_A381 Terminal deoxynucleotidyltransferase; polymerase; 2.36A 90.33
2ihm_A360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 90.31
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=561.92  Aligned_cols=224  Identities=35%  Similarity=0.609  Sum_probs=207.9

Q ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99998751566435169997074437754048888851687280323211024444554116899899999999775313
Q gi|255764496|r  366 LKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKN  445 (616)
Q Consensus       366 l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~  445 (616)
                      +.+|++.|+|+. |+|||||||||++|+++|||||||++|+|.|+.||+|||++  +.++|||+||+||++|||+++.++
T Consensus         2 ~~~L~~~L~l~~-p~rIE~fDiSh~~G~~~V~s~Vvf~~g~~~K~~YR~f~ik~--~~~~DDy~~m~Evl~Rr~~r~~~~   78 (226)
T 3c65_A            2 SHMLGERLGIPA-PRRIEAFDNSNIYGADPVSALVVFLDGKPAKKEYRKYKVKT--VAGPNDYETMREVVRRRYTRVLKE   78 (226)
T ss_dssp             HHHHHHHHTSCC-CSEEEEEEEEESSSSSCEEEEEEEETTEECGGGCEEEECCC--CCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCC-CCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             789999858499-88799997876589885599999978953867660226567--889974999999999987776631


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCH
Q ss_conf             11123333333345457984899809858999999999975887787189997187767663489817983488579989
Q gi|255764496|r  446 EENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDP  525 (616)
Q Consensus       446 ~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~  525 (616)
                      +.              ++|||||||||+||||+|.++|++.+.. .|||+||||+++|++. +.+++..++++.|+++++
T Consensus        79 ~~--------------~~PDLilIDGGkgQl~~a~~~l~~~~~~-~i~ii~iaK~~~~~~~-~~~~~~~~~~i~l~~~s~  142 (226)
T 3c65_A           79 GL--------------PLPDLIIIDGGKGHLSAVRDVLENELGL-DVPLAGLAKDEKHRTS-ELLAGDPPDVVPLDRQSQ  142 (226)
T ss_dssp             TC--------------CCCSEEEESSCHHHHHHHHHHHHHTSCC-CCCEEEC--------C-CCEETTTTEECCCCTTSH
T ss_pred             CC--------------CCCCEEEECCCHHHHHHHHHHHHHHCCC-CCCEEEECCCCCCCCC-CCCCCCCCCCEECCCCCH
T ss_conf             89--------------9999899789889999999999974788-8544430245211343-220158754230687888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH
Q ss_conf             999999887877887889899864321-4771004888798999999998088898993898888627899989999999
Q gi|255764496|r  526 ILYFIQRLRDEAHRFAITTHRKRRKKA-AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY  604 (616)
Q Consensus       526 ~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~  604 (616)
                      +|+|||+||||||||||+|||++|+|. +.|.||+||||||+|+++||+||||+++|++||.|||++| |||+++|++||
T Consensus       143 ~l~lLq~iRDEaHRFAi~~hRk~r~k~~~~S~Ld~I~GIG~~~~~~Ll~~Fgs~~~i~~As~eeL~~v-gI~~~~A~~I~  221 (226)
T 3c65_A          143 EFYLLQRIQDEVHRFAVMFHRKTRQKTMFHSVLDDIPGVGEKRKKALLNYFGSVKKMKEATVEELQRA-NIPRAVAEKIY  221 (226)
T ss_dssp             HHHHHHHHHHHHHHHTTC--------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHC-CCCHHHHHHHH
T ss_conf             99999999999999999999998740320371102688699999999998189999973899999876-99999999999


Q ss_pred             HHHCC
Q ss_conf             98547
Q gi|255764496|r  605 NHFHK  609 (616)
Q Consensus       605 ~~l~~  609 (616)
                      ++||+
T Consensus       222 ~~l~e  226 (226)
T 3c65_A          222 EKLHE  226 (226)
T ss_dssp             -----
T ss_pred             HHHCC
T ss_conf             99629



>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>2nrr_A Uvrabc system protein C; UVRC, endonuclase, NER, hydrolase; 1.20A {Thermotoga maritima} Back     alignment and structure
>1yd6_A UVRC; DNA binding protein; 2.00A {Bacillus caldotenax} Back     alignment and structure
>1yd0_A Uvrabc system protein C; DNA binding protein; 1.50A {Thermotoga maritima} PDB: 1ycz_A 1yd1_A 1yd4_A 1yd3_A 1yd2_A 1yd5_A Back     alignment and structure
>2wsh_A Endonuclease II; GIY-YIG, hydrolase; 1.90A {Enterobacteria phage T4} Back     alignment and structure
>1mk0_A Intron-associated endonuclease 1; alpha/beta fold, catalytic domain, DNA-binding surface, hydrolase; HET: CIT; 1.60A {Enterobacteria phage T4} SCOP: d.226.1.1 PDB: 1ln0_A Back     alignment and structure
>3mx1_A ECO29KIR; type II restriction endonuclease, GIY-YIG endonuclease, HYDR; 2.30A {Escherichia coli} PDB: 3mx4_A* 3nic_A* Back     alignment and structure
>1zg2_A Hypothetical UPF0213 protein BH0048; BHR2, structure, autostructure, northeast structural genomics consortium, PSI; NMR {Bacillus halodurans} Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>2ziu_A MUS81 protein; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Danio rerio} PDB: 2ziv_A 2ziw_A Back     alignment and structure
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>1s5l_U Photosystem II 12 kDa extrinsic protein; photosynthesis, oxygen-evolving, tetra- manganese, membrane; HET: CL1 PHO HEM PL9 LMT BCR; 3.50A {Thermosynechococcus elongatus} Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Back     alignment and structure
>2zix_A Crossover junction endonuclease MUS81; helix-hairpin-helix, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium, metal-binding, nucleus; 3.50A {Homo sapiens} Back     alignment and structure
>2duy_A Competence protein comea-related protein; helix-hairpin-helix, structural genomics, NPPSFA; 1.75A {Thermus thermophilus HB8} SCOP: a.60.2.7 Back     alignment and structure
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix turn helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.60.2.7 Back     alignment and structure
>3mr3_A DNA polymerase ETA; POL ETA, polymerase, thymine dimer, CPD, XPV, xeroderma PIGM variant, DNA damage; HET: DNA TTD DZ4; 1.75A {Homo sapiens} PDB: 3mr2_A* 3mr5_A* 3mr6_A* Back     alignment and structure
>1exn_A 5'-exonuclease, 5'-nuclease; hydrolase; 2.50A {Enterobacteria phage T5} SCOP: a.60.7.1 c.120.1.2 PDB: 1ut5_A 1ut8_A 1xo1_A Back     alignment and structure
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-binding, nucleotide-binding; 2.30A {Sulfolobus solfataricus} Back     alignment and structure
>2izo_A FEN1, flap structure-specific endonuclease; hydrolase, DNA repair, DNA-binding, endonuclease, metal-binding, excision repair, DNA replication, PCNA; HET: DNA; 2.9A {Sulfolobus solfataricus} Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>3gqc_A DNA repair protein REV1; protein-DNA complex, alternative splicing, DNA damage, DNA repair, DNA synthesis; HET: DNA DOC DCP; 2.50A {Homo sapiens} Back     alignment and structure
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A {Homo sapiens} SCOP: a.60.7.1 c.120.1.2 Back     alignment and structure
>1rxw_A Flap structure-specific endonuclease; helical clamp, helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase/DNA complex; 2.00A {Archaeoglobus fulgidus} SCOP: a.60.7.1 c.120.1.2 PDB: 1rxv_A Back     alignment and structure
>2ziu_B Crossover junction endonuclease EME1; helix-hairpin-helix, alternative splicing, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; 2.70A {Homo sapiens} PDB: 2ziw_B 2zix_B 2ziv_B Back     alignment and structure
>2aq4_A DNA repair protein REV1; polymerase, PAD, N-digit, G-loop, transferase; HET: DNA DOC DCP; 2.32A {Saccharomyces cerevisiae} PDB: 3bjy_A* Back     alignment and structure
>1b43_A Protein (FEN-1); nuclease, DNA repair, DNA replication, transferase; 2.00A {Pyrococcus furiosus} SCOP: a.60.7.1 c.120.1.2 PDB: 1mc8_A Back     alignment and structure
>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>2i5h_A Hypothetical protein AF1531; PFAM:DUF655, PSI-2, structural genomics, protein structure initiative; 1.74A {Archaeoglobus fulgidus} SCOP: e.71.1.1 Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>2w36_A Endonuclease V; hypoxanthine, endonuclease, endonucleasev, hydrolase, inosine, DNA damage, DNA repair; HET: BRU; 2.10A {Thermotoga maritima} PDB: 2w35_A 3hd0_A Back     alignment and structure
>3ga2_A Endonuclease V; alpha-beta protein, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Bacillus subtilis} Back     alignment and structure
>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, plasmid; 2.60A {Thermus thermophilus HB27} PDB: 3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A 3hjf_A Back     alignment and structure
>3goc_A Endonuclease V; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; HET: YES; 1.60A {Streptomyces aver