254781170

254781170

deoxyribodipyrimidine photolyase

GeneID in NCBI database:8210195Locus tag:CLIBASIA_05385
Protein GI in NCBI database:254781170Protein Accession:YP_003065583.1
Gene range:+(1166037, 1167488)Protein Length:483aa
Gene description:deoxyribodipyrimidine photolyase
COG prediction:[L] Deoxyribodipyrimidine photolyase
KEGG prediction:deoxyribodipyrimidine photolyase (EC:4.1.99.3); K01669 deoxyribodipyrimidine photo-lyase [EC:4.1.99.3]
SEED prediction:Deoxyribodipyrimidine photolyase (EC 4.1.99.3)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:DNA repair, bacterial photolyase
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
TOPPRED2 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---
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
cccccccccEEEEEcccccccccHHHHHHHHHccccEEEEEEEcHHHHccccccHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHcccEEEEEcccEEEcHHHHHcccccccccHHHHHHHHHHHcccccccccccccccccccccccccccHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHcccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHcHHHHHcccccHHHHcccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccHHHHHHHHccccccccccccccHHHHHHHHccccHHHHHHHHHHHcccHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHcccc
cccccccccEEEEEHHcccccccHHHHHHHHcccccEEEEEEEcHHHcccccccHHHHHHHHHHHHHHHHHHHHccccEEEEEccccccHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHccEEEEccccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccHHHcccccHHHHccccccHHHHHHHHHHHHHcHHHHHHHHccccccccccccHHHHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHccccccccccccHHHccccccccHHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHccccccccHHHHHHHcccccHHHHHHcccHccccccccccHcccccccEcccccccccccHHHHHHHHHHHHHHHHHHHcc
MKATTAMSVHLVWLRndlritdnkALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKgivfqyhqcsnfddsiEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVIcksfddsvllppgsilNHALQMYKVYTPFRKALIQNLVQAdlrslpvpairltgpvtpsniprffdypfqaidpmfpigEQNALHILRKFCKEKVYYYVEqrdipaiqgtsqlspylsigvlsprqcWNRLKEEFVDLLikpksgafsWLNELIWREFYRHLMAFypsvcmgkpfipwtekiewnkdsHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSqlldgdlasnnggwqwaastgndsvpyfrifnptiqgkrfdpqgtfirhwlpelnnvptqyihaphswldkndlslnyplpivdhkkaCHHTLNQYYAAKKQSLL
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICksfddsvllpPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIpaiqgtsqlspYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
******M****VWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADL*SL***************IPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEE************FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK****
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
***TTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQ***
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MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL
MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSLL

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
315122561477 deoxyribodipyrimidine photolyase [Candidatus Liberibact 1 0.0
157369495476 deoxyribodipyrimidine photolyase [Serratia proteamacula 1 0.0
270263757476 deoxyribodipyrimidine photolyase [Serratia odorifera 4R 1 0.0
320539319475 putative deoxyribodipyrimidine photolyase, FAD-binding 1 0.0
293397249476 deoxyribodipyrimidine photolyase [Serratia odorifera DS 1 1e-176
322833858476 Deoxyribodipyrimidine photo-lyase [Rahnella sp. Y9602] 1 1e-171
238797755481 Deoxyribodipyrimidine photo-lyase [Yersinia mollaretii 1 1e-168
253687618497 Deoxyribodipyrimidine photo-lyase [Pectobacterium carot 1 1e-168
238756042479 Deoxyribodipyrimidine photo-lyase [Yersinia ruckeri ATC 1 1e-167
238786314481 Deoxyribodipyrimidine photo-lyase [Yersinia bercovieri 1 1e-167
>gi|315122561|ref|YP_004063050.1| deoxyribodipyrimidine photolyase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 477 Back     alignment and organism information
 Score =  786 bits (2029), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/476 (76%), Positives = 414/476 (86%)

Query: 7   MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLL 66
           MSVHLVWLRNDLRITDNKALYAAC N +AKVIAVFIATP+QW QHG+SARQ+ FIYA+LL
Sbjct: 1   MSVHLVWLRNDLRITDNKALYAACKNPNAKVIAVFIATPQQWNQHGMSARQATFIYATLL 60

Query: 67  QVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKR 126
           QVQ+SLS++GIV QYHQCS+FDD+I+WLD YC +++VT+LFYNRQYEINE RRD+ LE+R
Sbjct: 61  QVQQSLSKRGIVLQYHQCSHFDDAIKWLDVYCQEKKVTELFYNRQYEINEHRRDQELERR 120

Query: 127 LQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTG 186
           L++RVIC+ FDDSVLLPPG I N A +MYK+YTPFRK  IQNL Q+DLRS+P P IR TG
Sbjct: 121 LKNRVICRGFDDSVLLPPGKIFNRACEMYKIYTPFRKEFIQNLTQSDLRSVPAPTIRQTG 180

Query: 187 PVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLS 246
           PV  + +P +FDYPFQ +DP+FPIGE NAL ILRKFCKEKV YYVEQRDIPAIQGTS LS
Sbjct: 181 PVILTKVPLYFDYPFQEVDPIFPIGEYNALQILRKFCKEKVQYYVEQRDIPAIQGTSHLS 240

Query: 247 PYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKP 306
           PYLSIG LSPRQCWNRL  EF D+LIK  SGAFSWLNELIWREFY HL+ FYPS+C GKP
Sbjct: 241 PYLSIGALSPRQCWNRLNVEFSDVLIKTNSGAFSWLNELIWREFYHHLIVFYPSLCTGKP 300

Query: 307 FIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLL 366
           FI WT+KIEWN D   L+ WKQG TGFP++DAAMRQLNT+GWMHNRLRMITASFLVKDLL
Sbjct: 301 FIQWTDKIEWNNDPRALEVWKQGNTGFPLVDAAMRQLNTMGWMHNRLRMITASFLVKDLL 360

Query: 367 VDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIR 426
           +DWRIGE+YFMSQLLDG+LASNNGGWQWAASTG+DSVPYFRIFNPT QGKRFDP+G FIR
Sbjct: 361 IDWRIGEKYFMSQLLDGNLASNNGGWQWAASTGHDSVPYFRIFNPTTQGKRFDPKGIFIR 420

Query: 427 HWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSL 482
            WLPEL NVP QYIH PH+W+D  +    YP PIVDHK+A  HT+++Y  A+KQS+
Sbjct: 421 QWLPELKNVPDQYIHTPHNWIDNKNTIHPYPHPIVDHKQARQHTISKYSIAQKQSI 476


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|157369495|ref|YP_001477484.1| deoxyribodipyrimidine photolyase [Serratia proteamaculans 568] Length = 476 Back     alignment and organism information
>gi|270263757|ref|ZP_06192026.1| deoxyribodipyrimidine photolyase [Serratia odorifera 4Rx13] Length = 476 Back     alignment and organism information
>gi|320539319|ref|ZP_08038988.1| putative deoxyribodipyrimidine photolyase, FAD-binding [Serratia symbiotica str. Tucson] Length = 475 Back     alignment and organism information
>gi|293397249|ref|ZP_06641522.1| deoxyribodipyrimidine photolyase [Serratia odorifera DSM 4582] Length = 476 Back     alignment and organism information
>gi|322833858|ref|YP_004213885.1| Deoxyribodipyrimidine photo-lyase [Rahnella sp. Y9602] Length = 476 Back     alignment and organism information
>gi|238797755|ref|ZP_04641249.1| Deoxyribodipyrimidine photo-lyase [Yersinia mollaretii ATCC 43969] Length = 481 Back     alignment and organism information
>gi|253687618|ref|YP_003016808.1| Deoxyribodipyrimidine photo-lyase [Pectobacterium carotovorum subsp. carotovorum PC1] Length = 497 Back     alignment and organism information
>gi|238756042|ref|ZP_04617366.1| Deoxyribodipyrimidine photo-lyase [Yersinia ruckeri ATCC 29473] Length = 479 Back     alignment and organism information
>gi|238786314|ref|ZP_04630253.1| Deoxyribodipyrimidine photo-lyase [Yersinia bercovieri ATCC 43970] Length = 481 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
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
PRK10674472 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; P 0.0
TIGR03556471 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo 1e-86
KOG0133531 KOG0133, KOG0133, KOG0133, Deoxyribodipyrimidine photol 6e-63
TIGR02766475 TIGR02766, crypt_chrom_pln, cryptochrome, plant family 1e-54
COG0415461 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA re 1e-138
pfam03441275 pfam03441, FAD_binding_7, FAD binding domain of DNA pho 1e-105
TIGR02765429 TIGR02765, crypto_DASH, cryptochrome, DASH family 6e-58
pfam00875164 pfam00875, DNA_photolyase, DNA photolyase 3e-38
>gnl|CDD|182638 PRK10674, PRK10674, deoxyribodipyrimidine photolyase; Provisional Back     alignment and domain information
>gnl|CDD|132595 TIGR03556, photolyase_8HDF, deoxyribodipyrimidine photo-lyase, 8-HDF type Back     alignment and domain information
>gnl|CDD|35355 KOG0133, KOG0133, KOG0133, Deoxyribodipyrimidine photolyase/cryptochrome [Replication, recombination and repair, Signal transduction mechanisms] Back     alignment and domain information
>gnl|CDD|131813 TIGR02766, crypt_chrom_pln, cryptochrome, plant family Back     alignment and domain information
>gnl|CDD|30764 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|146197 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase Back     alignment and domain information
>gnl|CDD|163007 TIGR02765, crypto_DASH, cryptochrome, DASH family Back     alignment and domain information
>gnl|CDD|144461 pfam00875, DNA_photolyase, DNA photolyase Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
PRK10674472 deoxyribodipyrimidine photolyase; Provisional 100.0
TIGR03556471 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HD 100.0
COG0415461 PhrB Deoxyribodipyrimidine photolyase [DNA replication, 100.0
KOG0133531 consensus 100.0
TIGR02766481 crypt_chrom_pln cryptochrome, plant family; InterPro: I 100.0
TIGR02765529 crypto_DASH cryptochrome, DASH family; InterPro: IPR014 100.0
TIGR00591471 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008 100.0
COG3046505 Uncharacterized protein related to deoxyribodipyrimidin 99.92
pfam03441275 FAD_binding_7 FAD binding domain of DNA photolyase. 100.0
pfam00875164 DNA_photolyase DNA photolyase. This domain binds a ligh 100.0
pfam04244223 DPRP Deoxyribodipyrimidine photo-lyase-related protein. 97.41
KOG0133531 consensus 91.96
>PRK10674 deoxyribodipyrimidine photolyase; Provisional Back     alignment and domain information
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type Back     alignment and domain information
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG0133 consensus Back     alignment and domain information
>TIGR02766 crypt_chrom_pln cryptochrome, plant family; InterPro: IPR014134 At least five major families of cryptochromes and photolyases share FAD cofactor binding, sequence homologues, and the ability to react to short wavelengths of visible light Back     alignment and domain information
>TIGR02765 crypto_DASH cryptochrome, DASH family; InterPro: IPR014133 Photolyases and cryptochromes are related flavoproteins Back     alignment and domain information
>TIGR00591 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008148 Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme Back     alignment and domain information
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only] Back     alignment and domain information
>pfam03441 FAD_binding_7 FAD binding domain of DNA photolyase Back     alignment and domain information
>pfam00875 DNA_photolyase DNA photolyase Back     alignment and domain information
>pfam04244 DPRP Deoxyribodipyrimidine photo-lyase-related protein Back     alignment and domain information
>KOG0133 consensus 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
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
1dnp_A471 Structure Of Deoxyribodipyrimidine Photolyase Lengt 1e-101
1u3c_A509 Crystal Structure Of The Phr Domain Of Cryptochrome 8e-72
1owl_A484 Structure Of Apophotolyase From Anacystis Nidulans 1e-70
1tez_A474 Complex Between Dna And The Dna Photolyase From Ana 1e-70
3fy4_A537 (6-4) Photolyase Crystal Structure Length = 537 1e-69
1np7_A489 Crystal Structure Analysis Of Synechocystis Sp. Pcc 3e-68
3cvw_A543 Drosophila Melanogaster (6-4) Photolyase H365n Muta 5e-68
3cvx_A543 Drosophila Melanogaster (6-4) Photolyase H369m Muta 7e-68
3cvu_A543 Drosophila Melanogaster (6-4) Photolyase Bound To D 9e-68
2e0i_A440 Crystal Structure Of Archaeal Photolyase From Sulfo 2e-65
2j4d_A525 Cryptochrome 3 From Arabidopsis Thaliana Length = 5 8e-59
2ijg_X526 Crystal Structure Of Cryptochrome 3 From Arabidopsi 1e-58
2vtb_B525 Structure Of Cryptochrome 3 - Dna Complex Length = 2e-56
1iqr_A420 Crystal Structure Of Dna Photolyase From Thermus Th 5e-50
>gi|1827916|pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase Length = 471 Back     alignment and structure
 Score =  373 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 244/472 (51%), Positives = 325/472 (68%), Gaps = 3/472 (0%)

Query: 8   SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQ 67
           + HLVW R DLR+ DN AL AAC NS A+V+A++IATP QW  H +S RQ+  I A L  
Sbjct: 1   TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNG 60

Query: 68  VQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL 127
           +Q +L++KGI   + +  +F  S+E +   C +  VT LFYN QYE+NE  RD  +E+ L
Sbjct: 61  LQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERAL 120

Query: 128 QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGP 187
           ++  +C+ FDDSV+LPPG+++    +MYKV+TPF+ A ++ L +     +  P +R +G 
Sbjct: 121 RNV-VCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGS 179

Query: 188 VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSP 247
           + PS                FP+ E+ A+  LR+FC+     Y +QRD PA++GTS+LS 
Sbjct: 180 IEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSA 239

Query: 248 YLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPF 307
            L+ G LSPRQC +RL  E    L         WLNELIWREFYRHL+ ++PS+C  +PF
Sbjct: 240 SLATGGLSPRQCLHRLLAEQPQALDGGAGSV--WLNELIWREFYRHLITYHPSLCKHRPF 297

Query: 308 IPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLV 367
           I WT++++W  +   LQAW++G TG+PI+DAAMRQLN+ GWMHNRLRMITASFLVKDLL+
Sbjct: 298 IAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLI 357

Query: 368 DWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRH 427
           DWR GE YFMSQL+DGDLA+NNGGWQWAASTG D+ PYFRIFNPT QG++FD +G FIR 
Sbjct: 358 DWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQ 417

Query: 428 WLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479
           WLPEL +VP + +H P  W  K  ++L+YP PIV+HK+A   TL  Y AA+K
Sbjct: 418 WLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 469


>gi|52695977|pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From Arabidopsis Thaliana Length = 509 Back     alignment and structure
gi|48425154|pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans Length = 484 Back     alignment and structure
>gi|58176791|pdb|1TEZ|A Chain A, Complex Between Dna And The Dna Photolyase From Anacystis Nidulans Length = 474 Back     alignment and structure
>gi|228312124|pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure Length = 537 Back     alignment and structure
gi|28374085|pdb|1NP7|A Chain A, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803 Cryptochrome Length = 489 Back     alignment and structure
>gi|261278633|pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant Bound To Ds Dna With A T-T (6-4) Photolesion And Cofactor F0 Length = 543 Back     alignment and structure
>gi|261278636|pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543 Back     alignment and structure
>gi|211939158|pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543 Back     alignment and structure
>gi|119389332|pdb|2E0I|A Chain A, Crystal Structure Of Archaeal Photolyase From Sulfolobus Tokodaii With Two Fad Molecules: Implication Of A Novel Light-Harvesting Cofactor Length = 440 Back     alignment and structure
>gi|150261312|pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana Length = 525 Back     alignment and structure
gi|119390180|pdb|2IJG|X Chain X, Crystal Structure Of Cryptochrome 3 From Arabidopsis Thaliana Length = 526 Back     alignment and structure
>gi|238828068|pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex Length = 525 Back     alignment and structure
gi|17942830|pdb|1IQR|A Chain A, Crystal Structure Of Dna Photolyase From Thermus Thermophilus Length = 420 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
2wq7_A543 RE11660P; lyase-DNA complex, DNA repair, DNA lesion, ly 1e-108
1owl_A484 Photolyase, deoxyribodipyrimidine photolyase; DNA repai 2e-98
1dnp_A471 DNA photolyase; DNA repair, electron transfer, excitati 1e-94
1np7_A489 DNA photolyase; protein with FAD cofactor; HET: DNA FAD 8e-93
2j4d_A525 Cryptochrome 3, cryptochrome DASH; DNA-binding protein, 2e-74
1u3d_A509 Cryptochrome 1 apoprotein; photolyase, AMPPNP, signalin 1e-68
2e0i_A440 432AA long hypothetical deoxyribodipyrimidine photolyas 2e-68
3fy4_A537 6-4 photolyase; DNA repair, clock cryptochrome; HET: ME 1e-65
2j07_A420 Deoxyribodipyrimidine photo-lyase; chromophore, DNA bin 8e-61
>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Length = 543 Back     alignment and structure
 Score =  386 bits (993), Expect = e-108
 Identities = 131/510 (25%), Positives = 206/510 (40%), Gaps = 38/510 (7%)

Query: 1   MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAK-----VIAVFIATPEQWRQHGISA 55
           M +  +  VH  W R  LR+ DN AL      ++A      V  +FI  P       + A
Sbjct: 24  MDSQRSTLVH--WFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGA 81

Query: 56  RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115
            +  F+  +L  +   L +        +        E         RV  L +    E  
Sbjct: 82  NRWRFLQQTLEDLDNQLRKLNSRLFVVRG----KPAEVFPRIFKSWRVEMLTFETDIEPY 137

Query: 116 EVRRDKLLEKRL-QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADL 174
            V RD  ++K      V  ++     +  P  ++   L    +       +++ L    +
Sbjct: 138 SVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKV 197

Query: 175 RSLPVPAIRLTGP------------VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKF 222
             +P     +  P                 + +    P +     FP GE  AL  + + 
Sbjct: 198 LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEES 257

Query: 223 CKEKVYYYVEQRDIPAI----QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGA 278
            K++++    ++   A       T+ LSPYL  G LS R    +LKE  +    K     
Sbjct: 258 LKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE-IIKRQPKHSQPP 316

Query: 279 FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDA 338
            S + +L+WREFY  + A  P+         +  +I W +    L+AW  G TG+P IDA
Sbjct: 317 VSLIGQLMWREFYYTVAAAEPN-FDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDA 375

Query: 339 AMRQLNTIGWMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAAS 397
            MRQL   GW+H+  R   A FL + DL + W  G+  F   LLD D A N G W W ++
Sbjct: 376 IMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSA 435

Query: 398 TGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------D 451
           +      YFR+++P   GK+ DPQG +IR ++PEL+  P   I+ P      +       
Sbjct: 436 SAFFH-QYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCV 494

Query: 452 LSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481
           L  +YP  IV H+      + +  AA K +
Sbjct: 495 LGTDYPHRIVKHEVVHKENIKRMGAAYKVN 524


>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A* Length = 484 Back     alignment and structure
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1 Length = 471 Back     alignment and structure
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1 Length = 489 Back     alignment and structure
>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Length = 525 Back     alignment and structure
>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A* Length = 509 Back     alignment and structure
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Length = 440 Back     alignment and structure
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Length = 537 Back     alignment and structure
>2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A* Length = 420 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
1dnp_A471 DNA photolyase; DNA repair, electron transfer, excitati 100.0
1u3d_A509 Cryptochrome 1 apoprotein; photolyase, AMPPNP, signalin 100.0
2wq7_A543 RE11660P; lyase-DNA complex, DNA repair, DNA lesion, ly 100.0
3fy4_A537 6-4 photolyase; DNA repair, clock cryptochrome; HET: ME 100.0
1np7_A489 DNA photolyase; protein with FAD cofactor; HET: DNA FAD 100.0
1owl_A484 Photolyase, deoxyribodipyrimidine photolyase; DNA repai 100.0
2j4d_A525 Cryptochrome 3, cryptochrome DASH; DNA-binding protein, 100.0
2e0i_A440 432AA long hypothetical deoxyribodipyrimidine photolyas 100.0
2j07_A420 Deoxyribodipyrimidine photo-lyase; chromophore, DNA bin 100.0
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1 Back     alignment and structure
Probab=100.00  E-value=0  Score=1033.16  Aligned_cols=469  Identities=52%  Similarity=0.975  Sum_probs=423.7

Q ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEEEECHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC
Q ss_conf             42688835867556778999999957982999997383784788899899999999999999999975980999965753
Q gi|254781170|r    8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQYHQCSNF   87 (483)
Q Consensus         8 ~~~IvWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~~~~~Fl~esL~~L~~~L~~~g~~L~v~~~~~~   87 (483)
                      |++||||||||||+||+||.+|++.++.+|+||||+||.+++.++.|.+|++|+++||.+|+++|+++|++|+++.++..
T Consensus         1 ~t~ivWfRrDLRl~DN~aL~~A~~~~~~~vlpvyi~dp~~~~~~~~~~r~~~Fl~esL~~L~~~L~~~g~~L~i~~g~~~   80 (471)
T 1dnp_A            1 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDF   80 (471)
T ss_dssp             CEEEEECSSCCCSTTCHHHHHHSSSTTSEEEEEEEECHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHTTCCEEEEECSSH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             91999849994543689999999759996899999880564289978999999999999999999978997799976753


Q ss_pred             CCHHHHHHHHHHHCCCCCEEEECCCCCHHHHCCHHHHHHHHHCCCCEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             50899999999870976142100111001100102688875200000022343455576002378644321014799886
Q gi|254781170|r   88 DDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQ  167 (483)
Q Consensus        88 g~~~~~L~~l~~~~~i~~v~~n~~~~~~~~~rd~~i~~~l~~~~~~~~~~~~~l~~p~~i~~~~~~~~~vftpf~k~~~~  167 (483)
                      +.++++|.+++++++|+.|++++++++++..||..|...++ ++.++.++++++++++.+.+..++++++||||+++|.+
T Consensus        81 ~~~~~il~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~~~-~~~~~~~~~~~l~~~~~i~~~~~~~~~~ft~f~k~~~~  159 (471)
T 1dnp_A           81 VASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALR-NVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLK  159 (471)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEECCCSHHHHHHHHHHHHHCT-TSEEEEECCSSSSCTTSSCCTTSCCCSSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHC-CCEEEECCCCEEECCCEEECCCCCCCCCCCHHHHHHHH
T ss_conf             15899999999975960999705412147789999998622-83378458837843412431577663000188999988


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCC
Q ss_conf             3156632212455445677667555753234764-345546888764333221111111011012026865456665446
Q gi|254781170|r  168 NLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPF-QAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLS  246 (483)
Q Consensus       168 ~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tSrLS  246 (483)
                      .+........+.|.........+..... .+.+. ......++|||++|+++|++|+++++.+|.+.||.|+.++||+||
T Consensus       160 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ge~~A~~~L~~Fl~~r~~~Y~~~r~~P~~~~tSrLS  238 (471)
T 1dnp_A          160 RLREGMPECVAAPKVRSSGSIEPSPSIT-LNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLS  238 (471)
T ss_dssp             HHHTCCCCCCCCCCCCTTCCCCCCCCCC-CCSCCCCCCTTTSCCSHHHHHHHHHHHHHTHHHHHHHHTTCTTSCCSCCCH
T ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             6542256666776433310147886434-367644532025884268999999999986666778752375447887658


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHHHHHH
Q ss_conf             11114648799999999998643111234772001023202468887888633578886153011012000104678998
Q gi|254781170|r  247 PYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAW  326 (483)
Q Consensus       247 PyL~~G~IS~R~v~~~~~~~~~~~~~~~~~~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~~~aW  326 (483)
                      |||+|||||||+|++++.+.....  ..+.+...|++||+|||||+++++++|..+...++.+.++.++|+.|++.|++|
T Consensus       239 PyL~~G~IS~R~v~~~~~~~~~~~--~~~~~~~~~~~eL~WRe~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W  316 (471)
T 1dnp_A          239 ASLATGGLSPRQCLHRLLAEQPQA--LDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAW  316 (471)
T ss_dssp             HHHHHTSSCHHHHHHHHHHHCGGG--GGTSTTHHHHHHHHHHHHHHHHHHHCGGGGGTCCSSGGGGGSCCCCCHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCHHHHHCCCCCCHHHHHHH
T ss_conf             788708677999999999971012--221107888888888999999999785154421220343320124685888876


Q ss_pred             HHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCC
Q ss_conf             72278886889999999971676358999999999984104700223347766413311147456100201278984702
Q gi|254781170|r  327 KQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYF  406 (483)
Q Consensus       327 ~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~  406 (483)
                      ++|+||||+||||||||++|||||||||||||||||++|+||||+|++||+++|||||||||+|||||+||||+|++|||
T Consensus       317 ~~G~TG~PlvDA~MrqL~~tG~mhnr~Rm~~asfl~~~L~i~Wr~g~~~f~~~llD~d~~~n~~~wq~~ag~g~~~~~~~  396 (471)
T 1dnp_A          317 QEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYF  396 (471)
T ss_dssp             HHTCSSCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTSCCCHHHHHHHHHTTCTTCCHHHHHHHHHHHTTCSTTCCCTT
T ss_pred             HCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCC
T ss_conf             42898972899999997866788859999999999856898868889999988147880007589999847588899865


Q ss_pred             CCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHHHCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             20464589887248997833008243279977804955401312578999976318999999999999999640
Q gi|254781170|r  407 RIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQ  480 (483)
Q Consensus       407 Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~ih~p~~~~~~~~~~~~YP~pivd~~~~~~~a~~~~~~~~k~  480 (483)
                      |||||++||++|||+|+|||||||||+++|+++||+||+++..+.++.|||+|||||+++|++|+++|+++||+
T Consensus       397 R~~np~~q~~~~Dp~g~yir~wvPeL~~~p~~~ih~pw~~~~~~~~~~~Yp~Pivd~~~~~~~~~~~~~~~rk~  470 (471)
T 1dnp_A          397 RIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARKG  470 (471)
T ss_dssp             CCCCHHHHHHHHTTTCHHHHHHCGGGTTSCTTGGGSHHHHHHTTTCCCSSCCCSSCHHHHHHHHHHHHHHHTCC
T ss_pred             EEECHHHHHHHHCCCCCCHHHHCHHHHCCCHHHHCCHHHCCHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             01089899998698976488859663179977837931161430867899866688999999999999998566



>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP: a.99.1.1 c.28.1.1 PDB: 1u3c_A* Back     alignment and structure
>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Back     alignment and structure
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Back     alignment and structure
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1 Back     alignment and structure
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A* Back     alignment and structure
>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Back     alignment and structure
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Back     alignment and structure
>2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB: 1iqu_A* 1iqr_A* 2j08_A* 2j09_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
d1dnpa1269 a.99.1.1 (A:201-469) C-terminal domain of DNA photolyas 2e-62
d1u3da1300 a.99.1.1 (A:198-497) Cryptochrome C-terminal domain {Th 3e-46
d1owla1271 a.99.1.1 (A:205-475) C-terminal domain of DNA photolyas 2e-42
d2j07a1234 a.99.1.1 (A:172-405) C-terminal domain of DNA photolyas 3e-41
d1np7a1279 a.99.1.1 (A:205-483) Cryptochrome C-terminal domain {Sy 9e-40
d1dnpa2200 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [Ta 7e-29
d1u3da2185 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidop 3e-19
d1owla2202 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elonga 1e-17
d1np7a2204 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 4e-17
d2j07a2170 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus 6e-16
>d1dnpa1 a.99.1.1 (A:201-469) C-terminal domain of DNA photolyase {Escherichia coli [TaxId: 562]} Length = 269 Back     information, alignment and structure

class: All alpha proteins
fold: Cryptochrome/photolyase FAD-binding domain
superfamily: Cryptochrome/photolyase FAD-binding domain
family: Cryptochrome/photolyase FAD-binding domain
domain: C-terminal domain of DNA photolyase
species: Escherichia coli [TaxId: 562]
 Score =  234 bits (596), Expect = 2e-62
 Identities = 161/271 (59%), Positives = 203/271 (74%), Gaps = 2/271 (0%)

Query: 209 PIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFV 268
           P+ E+ A+  LR+FC+     Y +QRD PA++GTS+LS  L+ G LSPRQC +RL  E  
Sbjct: 1   PVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQP 60

Query: 269 DLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQ 328
                       WLNELIWREFYRHL+ ++PS+C  +PFI WT++++W  +   LQAW++
Sbjct: 61  Q--ALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQE 118

Query: 329 GYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASN 388
           G TG+PI+DAAMRQLN+ GWMHNRLRMITASFLVKDLL+DWR GE YFMSQL+DGDLA+N
Sbjct: 119 GKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAAN 178

Query: 389 NGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLD 448
           NGGWQWAASTG D+ PYFRIFNPT QG++FD +G FIR WLPEL +VP + +H P  W  
Sbjct: 179 NGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQ 238

Query: 449 KNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479
           K  ++L+YP PIV+HK+A   TL  Y AA+K
Sbjct: 239 KAGVTLDYPQPIVEHKEARVQTLAAYEAARK 269


>d1u3da1 a.99.1.1 (A:198-497) Cryptochrome C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 300 Back     information, alignment and structure
>d1owla1 a.99.1.1 (A:205-475) C-terminal domain of DNA photolyase {Synechococcus elongatus [TaxId: 32046]} Length = 271 Back     information, alignment and structure
>d2j07a1 a.99.1.1 (A:172-405) C-terminal domain of DNA photolyase {Thermus thermophilus [TaxId: 274]} Length = 234 Back     information, alignment and structure
>d1np7a1 a.99.1.1 (A:205-483) Cryptochrome C-terminal domain {Synechocystis sp., pcc 6803 [TaxId: 1143]} Length = 279 Back     information, alignment and structure
>d1dnpa2 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [TaxId: 562]} Length = 200 Back     information, alignment and structure
>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 185 Back     information, alignment and structure
>d1owla2 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elongatus [TaxId: 32046]} Length = 202 Back     information, alignment and structure
>d1np7a2 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143]} Length = 204 Back     information, alignment and structure
>d2j07a2 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus [TaxId: 274]} Length = 170 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
d1u3da1300 Cryptochrome C-terminal domain {Thale cress (Arabidopsi 100.0
d1dnpa1269 C-terminal domain of DNA photolyase {Escherichia coli [ 100.0
d1owla1271 C-terminal domain of DNA photolyase {Synechococcus elon 100.0
d1np7a1279 Cryptochrome C-terminal domain {Synechocystis sp., pcc 100.0
d2j07a1234 C-terminal domain of DNA photolyase {Thermus thermophil 100.0
d1dnpa2200 DNA photolyase {Escherichia coli [TaxId: 562]} 100.0
d1np7a2204 Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143] 100.0
d1u3da2185 Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId 100.0
d1owla2202 DNA photolyase {Synechococcus elongatus [TaxId: 32046]} 100.0
d2j07a2170 DNA photolyase {Thermus thermophilus [TaxId: 274]} 100.0
>d1u3da1 a.99.1.1 (A:198-497) Cryptochrome C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
class: All alpha proteins
fold: Cryptochrome/photolyase FAD-binding domain
superfamily: Cryptochrome/photolyase FAD-binding domain
family: Cryptochrome/photolyase FAD-binding domain
domain: Cryptochrome C-terminal domain
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]
Probab=100.00  E-value=0  Score=701.13  Aligned_cols=275  Identities=33%  Similarity=0.590  Sum_probs=252.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHH----CCCCCCCCH
Q ss_conf             5546888764333221111111011012026865456665446111146487999999999986431----112347720
Q gi|254781170|r  204 IDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDL----LIKPKSGAF  279 (483)
Q Consensus       204 ~~~~~~gGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tSrLSPyL~~G~IS~R~v~~~~~~~~~~~----~~~~~~~~~  279 (483)
                      ....|++||++|+++|++||++++.+|.++||.|+.++||+|||||+|||||||+|+++++......    ......+.+
T Consensus        12 ~~~~W~pGe~~A~~~L~~Fl~~~l~~Y~~~Rn~p~~~~tSrLSPyL~~G~IS~ReV~~~v~~~~~~~~~~~~~~~~~~~~   91 (300)
T d1u3da1          12 LARAWSPGWSNGDKALTTFINGPLLEYSKNRRKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVN   91 (300)
T ss_dssp             HHHHCCCSHHHHHHHHHHHHTTGGGGTTTTTTCSSSTTSCCCHHHHHTTSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             83768866999999999999803777756348988668751468782898879999999998877665411344545599


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             01023202468887888633578886153011012000104678998722788868899999999716763589999999
Q gi|254781170|r  280 SWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITAS  359 (483)
Q Consensus       280 ~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~vaS  359 (483)
                      .|++||+||||++++++++|.... .++.+.++.++|..|++.|++|++|+||||+||||||||++||||||||||||||
T Consensus        92 ~fi~eL~wRef~~~~~~~~~~~~~-~~~~~~~~~~~~~~d~~~~~~w~~G~TG~p~vDA~mr~L~~tG~mhnr~Rm~vaS  170 (300)
T d1u3da1          92 LFLKSIGLREYSRYISFNHPYSHE-RPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSS  170 (300)
T ss_dssp             HHHHHHHHHHHHHHHHHSSTTTTT-SCSCCTTTTCCCCCCHHHHHHHHHTCSSCHHHHHHHHHHHHHSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-CCHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_conf             999998888889999985456540-2122210012223687888888850255349999999998611147789999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCCHHH
Q ss_conf             99984104700223347766413311147456100201278984702204645898872489978330082432799778
Q gi|254781170|r  360 FLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQY  439 (483)
Q Consensus       360 fl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p~~~  439 (483)
                      |||++|+||||.|++||+++|||||||+|++||||+||+|+|++||+|||||++|+++|||+|+|||||||||+++|+++
T Consensus       171 fl~~~L~i~W~~ga~~f~~~l~D~d~a~n~~~wq~~ag~g~~~~~~~ri~np~~q~~~~Dp~g~fir~wvPEL~~~p~~~  250 (300)
T d1u3da1         171 FFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGYKFDPNGEYVRRWLPELSRLPTDW  250 (300)
T ss_dssp             HHHHTSCCCHHHHHHHHHHHCTTCCHHHHHHHHHHHHTCSTTCCCSSCCCCHHHHHHHHCTTSHHHHHHCGGGTTCCHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHCCCCCCHHHHHHHHCCCCHHHHHHCHHHHCCCHHH
T ss_conf             99987164432579999998725442058899999983150011101344288999883675327988682411499787


Q ss_pred             HCCHHHHHH------HCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             049554013------1257899997631899999999999999964
Q gi|254781170|r  440 IHAPHSWLD------KNDLSLNYPLPIVDHKKACHHTLNQYYAAKK  479 (483)
Q Consensus       440 ih~p~~~~~------~~~~~~~YP~pivd~~~~~~~a~~~~~~~~k  479 (483)
                      ||+||+++.      .+.+|.+||.||||++++|++|+++++++.+
T Consensus       251 ih~Pw~~~~~~~~~~~~~~g~~Yp~pivd~~~~~~r~~~~~~~~~~  296 (300)
T d1u3da1         251 IHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMWQ  296 (300)
T ss_dssp             HTCTTTSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHHHHH
T ss_pred             HCCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             4795428888998809866889972228889999999999999987



>d1dnpa1 a.99.1.1 (A:201-469) C-terminal domain of DNA photolyase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1owla1 a.99.1.1 (A:205-475) C-terminal domain of DNA photolyase {Synechococcus elongatus [TaxId: 32046]} Back     information, alignment and structure
>d1np7a1 a.99.1.1 (A:205-483) Cryptochrome C-terminal domain {Synechocystis sp., pcc 6803 [TaxId: 1143]} Back     information, alignment and structure
>d2j07a1 a.99.1.1 (A:172-405) C-terminal domain of DNA photolyase {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1dnpa2 c.28.1.1 (A:1-200) DNA photolyase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1np7a2 c.28.1.1 (A:1-204) Cryptochrome {Synechocystis sp., pcc 6803 [TaxId: 1143]} Back     information, alignment and structure
>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1owla2 c.28.1.1 (A:3-204) DNA photolyase {Synechococcus elongatus [TaxId: 32046]} Back     information, alignment and structure
>d2j07a2 c.28.1.1 (A:2-171) DNA photolyase {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 483 deoxyribodipyrimidine photolyase [Candidatus Liber
2j4d_A_317-525209 (A:317-525) Cryptochrome 3, cryptochrome DASH; DNA 6e-55
1dnp_A_264-426163 (A:264-426) DNA photolyase; DNA repair, electron t 2e-52
2j07_A_222-395174 (A:222-395) Deoxyribodipyrimidine photo-lyase; chr 7e-52
1u3d_A_318-446129 (A:318-446) Cryptochrome 1 apoprotein; photolyase, 2e-41
1owl_A_308-448141 (A:308-448) Photolyase, deoxyribodipyrimidine phot 2e-40
1np7_A_314-441128 (A:314-441) DNA photolyase; protein with FAD cofac 7e-40
2e0i_A_268-406139 (A:268-406) 432AA long hypothetical deoxyribodipyr 1e-39
2wq7_A_347-475129 (A:347-475) RE11660P; lyase-DNA complex, DNA repai 4e-38
3fy4_A_323-451129 (A:323-451) 6-4 photolyase; DNA repair, clock cryp 6e-38
1u3d_A_1-259259 (A:1-259) Cryptochrome 1 apoprotein; photolyase, A 2e-40
1dnp_A_1-140140 (A:1-140) DNA photolyase; DNA repair, electron tra 4e-32
2j07_A_1-149149 (A:1-149) Deoxyribodipyrimidine photo-lyase; chrom 6e-26
1np7_A_1-146146 (A:1-146) DNA photolyase; protein with FAD cofacto 2e-25
2j4d_A_34-183150 (A:34-183) Cryptochrome 3, cryptochrome DASH; DNA- 5e-25
2wq7_A_1-163163 (A:1-163) RE11660P; lyase-DNA complex, DNA repair, 5e-24
3fy4_A_1-142142 (A:1-142) 6-4 photolyase; DNA repair, clock crypto 1e-22
2e0i_A_1-132132 (A:1-132) 432AA long hypothetical deoxyribodipyrim 3e-22
1owl_A_1-196196 (A:1-196) Photolyase, deoxyribodipyrimidine photol 4e-29
1np7_A_147-313167 (A:147-313) DNA photolyase; protein with FAD cofac 3e-28
2e0i_A_133-267135 (A:133-267) 432AA long hypothetical deoxyribodipyr 9e-26
1owl_A_197-307111 (A:197-307) Photolyase, deoxyribodipyrimidine phot 2e-23
2j4d_A_1-33_184-316166 (A:1-33,A:184-316) Cryptochrome 3, cryptochrome DA 2e-21
1dnp_A_184-26380 (A:184-263) DNA photolyase; DNA repair, electron t 2e-14
3fy4_A_196-29095 (A:196-290) 6-4 photolyase; DNA repair, clock cryp 4e-14
2wq7_A_220-31394 (A:220-313) RE11660P; lyase-DNA complex, DNA repai 1e-12
3fy4_A_452-53786 (A:452-537) 6-4 photolyase; DNA repair, clock cryp 1e-04
>2j4d_A (A:317-525) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*Length = 209 Back     alignment and structure
 Score =  209 bits (533), Expect = 6e-55
 Identities = 65/208 (31%), Positives = 108/208 (51%), Gaps = 4/208 (1%)

Query: 276 SGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPI 335
           +  +  L ELIWR+++R L     +        P   + +W++D  L ++W+   TG+P+
Sbjct: 1   NSTYWVLFELIWRDYFRFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPL 59

Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395
           IDA M++L+T G+M NR R I  SFLV+D+ +DWR+G E+F + LLD D  SN G W + 
Sbjct: 60  IDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 119

Query: 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLN 455
           A  GND     R F+   Q + +DP+G ++  WL +L  +P +  H P   +  + +   
Sbjct: 120 AGVGNDP-REDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPL 178

Query: 456 --YPLPIVDHKKACHHTLNQYYAAKKQS 481
                P+    K+       +   + + 
Sbjct: 179 KHGNGPMAGGSKSGGGFRGSHSGRRSRH 206


>1dnp_A (A:264-426) DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli}Length = 163 Back     alignment and structure
>2j07_A (A:222-395) Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus}Length = 174 Back     alignment and structure
>1u3d_A (A:318-446) Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana}Length = 129 Back     alignment and structure
>1owl_A (A:308-448) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301}Length = 141 Back     alignment and structure
>1np7_A (A:314-441) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP}Length = 128 Back     alignment and structure
>2e0i_A (A:268-406) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str}Length = 139 Back     alignment and structure
>2wq7_A (A:347-475) RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*Length = 129 Back     alignment and structure
>3fy4_A (A:323-451) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}Length = 129 Back     alignment and structure
>1u3d_A (A:1-259) Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana}Length = 259 Back     alignment and structure
>1dnp_A (A:1-140) DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli}Length = 140 Back     alignment and structure
>2j07_A (A:1-149) Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus}Length = 149 Back     alignment and structure
>1np7_A (A:1-146) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP}Length = 146 Back     alignment and structure
>2j4d_A (A:34-183) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*Length = 150 Back     alignment and structure
>2wq7_A (A:1-163) RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*Length = 163 Back     alignment and structure
>3fy4_A (A:1-142) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}Length = 142 Back     alignment and structure
>2e0i_A (A:1-132) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str}Length = 132 Back     alignment and structure
>1owl_A (A:1-196) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301}Length = 196 Back     alignment and structure
>1np7_A (A:147-313) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP}Length = 167 Back     alignment and structure
>2e0i_A (A:133-267) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str}Length = 135 Back     alignment and structure
>1owl_A (A:197-307) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301}Length = 111 Back     alignment and structure
>2j4d_A (A:1-33,A:184-316) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B*Length = 166 Back     alignment and structure
>1dnp_A (A:184-263) DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli}Length = 80 Back     alignment and structure
>3fy4_A (A:196-290) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}Length = 95 Back     alignment and structure
>2wq7_A (A:220-313) RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*Length = 94 Back     alignment and structure
>3fy4_A (A:452-537) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}Length = 86 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target483 deoxyribodipyrimidine photolyase [Candidatus Liberibact
2j4d_A_317-525209 Cryptochrome 3, cryptochrome DASH; DNA-binding pro 100.0
2j07_A_222-395174 Deoxyribodipyrimidine photo-lyase; chromophore, DN 100.0
1dnp_A_264-426163 DNA photolyase; DNA repair, electron transfer, exc 100.0
1u3d_A_1-259259 Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig 100.0
1owl_A_308-448141 Photolyase, deoxyribodipyrimidine photolyase; DNA 100.0
2e0i_A_268-406139 432AA long hypothetical deoxyribodipyrimidine phot 100.0
1u3d_A_318-446129 Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig 100.0
1np7_A_314-441128 DNA photolyase; protein with FAD cofactor; HET: DN 100.0
2wq7_A_347-475129 RE11660P; lyase-DNA complex, DNA repair, DNA lesio 100.0
3fy4_A_323-451129 6-4 photolyase; DNA repair, clock cryptochrome; HE 100.0
1owl_A_1-196196 Photolyase, deoxyribodipyrimidine photolyase; DNA 100.0
2j07_A_1-149149 Deoxyribodipyrimidine photo-lyase; chromophore, DN 100.0
1dnp_A_1-140140 DNA photolyase; DNA repair, electron transfer, exc 99.97
1np7_A_1-146146 DNA photolyase; protein with FAD cofactor; HET: DN 99.97
2j4d_A_34-183150 Cryptochrome 3, cryptochrome DASH; DNA-binding pro 99.97
3fy4_A_1-142142 6-4 photolyase; DNA repair, clock cryptochrome; HE 99.97
2wq7_A_1-163163 RE11660P; lyase-DNA complex, DNA repair, DNA lesio 99.96
2e0i_A_1-132132 432AA long hypothetical deoxyribodipyrimidine phot 99.96
1np7_A_147-313167 DNA photolyase; protein with FAD cofactor; HET: DN 99.97
2e0i_A_133-267135 432AA long hypothetical deoxyribodipyrimidine phot 99.96
1owl_A_197-307111 Photolyase, deoxyribodipyrimidine photolyase; DNA 99.92
2j4d_A_1-33_184-316166 Cryptochrome 3, cryptochrome DASH; DNA-binding pro 99.9
3fy4_A_196-29095 6-4 photolyase; DNA repair, clock cryptochrome; HE 99.71
1dnp_A_184-26380 DNA photolyase; DNA repair, electron transfer, exc 99.71
2wq7_A_220-31394 RE11660P; lyase-DNA complex, DNA repair, DNA lesio 99.69
3fy4_A_452-53786 6-4 photolyase; DNA repair, clock cryptochrome; HE 99.08
2wq7_A_164-219_314-34689 RE11660P; lyase-DNA complex, DNA repair, DNA lesio 93.09
3fy4_A_143-195_291-32285 6-4 photolyase; DNA repair, clock cryptochrome; HE 90.26
>2j4d_A (A:317-525) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Back     alignment and structure
Probab=100.00  E-value=0  Score=495.34  Aligned_cols=203  Identities=32%  Similarity=0.589  Sum_probs=193.7

Q ss_pred             CCHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHCCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             72001023202468887888633578886153011012000104678998722788868899999999716763589999
Q gi|254781170|r  277 GAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMI  356 (483)
Q Consensus       277 ~~~~fl~eL~WRef~~~~~~~~P~~~~~~~~~~~~~~~~w~~~~~~~~aW~~G~TG~PlVDA~MR~L~~tG~mhnr~Rm~  356 (483)
                      |+++|++||+||||++++++++|++.. .++.+.++.++|+++++.|++|++|+||+|+||||||||++|||||||+|||
T Consensus         2 ~~e~f~~eL~wRe~~~~~~~~~p~~~~-~~~~~~~~~~~~~~~~~~~~~w~~G~TG~p~vDAamr~L~~tG~lhn~~Rm~   80 (209)
T 2j4d_A            2 STYWVLFELIWRDYFRFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQI   80 (209)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHGGGGT-STTTTTTCCCCCBCCHHHHHHHHTTCSSCHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCHHH-HCCCCCCCCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             337898999998886689871761232-0222100122212231123432311368818999999999863557799999


Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHCCCHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCCCEEHCCCHHHHCCC
Q ss_conf             99999984104700223347766413311147456100201278984702204645898872489978330082432799
Q gi|254781170|r  357 TASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVP  436 (483)
Q Consensus       357 vaSfl~~~L~idWr~g~~~f~~~llD~d~~~n~~~wq~~a~~G~d~~~~~Ri~np~~q~~~~Dp~g~~ir~wvPeL~~~p  436 (483)
                      ||||||+.|++||+.|++||+++|||||+++|+|||||+||+|+|+.+ +|+|||++|++++||+|+|||+|||||+++|
T Consensus        81 vasfl~~~l~~~w~~g~~~f~~~liD~d~a~n~~~wq~~aG~~~~~~~-~r~~~p~~q~~~~Dp~g~yi~~w~pel~~~p  159 (209)
T 2j4d_A           81 VCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPRE-DRYFSIPKQAQNYDPEGEYVAFWLQQLRRLP  159 (209)
T ss_dssp             HHHHHHHTSCBCHHHHHHHHHHHCTTCCHHHHHHHHHHHHTCSSCGGG-CCCCCHHHHHHHHCTTCHHHHHHSGGGTTSC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHCHHHHHHHHCCCCCCCC-CCCCCHHHHHHHHCCCCCCHHHHCHHHHCCC
T ss_conf             999989871668778999999873686443188887898657889998-5046988999985999756687488753699


Q ss_pred             HHHHCCHHHHHHHCC--CCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             778049554013125--789999763189999999999999996400
Q gi|254781170|r  437 TQYIHAPHSWLDKND--LSLNYPLPIVDHKKACHHTLNQYYAAKKQS  481 (483)
Q Consensus       437 ~~~ih~p~~~~~~~~--~~~~YP~pivd~~~~~~~a~~~~~~~~k~~  481 (483)
                      .++||+||.++....  .+.+||.||||++++|++++++|+++|++.
T Consensus       160 ~~~i~~p~~~~~~~~~~~~~~yp~pivd~~~~~~~~~~~~~~~~~~~  206 (209)
T 2j4d_A          160 KEKRHWPGRLMYMDTVVPLKHGNGPMAGGSKSGGGFRGSHSGRRSRH  206 (209)
T ss_dssp             TTTTTSCHHHHTCCCSSCCSCCC------------------------
T ss_pred             HHHHCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHC
T ss_conf             88806976588443415767796233189999999998888887503



>2j07_A (A:222-395) Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} Back     alignment and structure
>1dnp_A (A:264-426) DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} Back     alignment and structure
>1u3d_A (A:1-259) Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} Back     alignment and structure
>1owl_A (A:308-448) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} Back     alignment and structure
>2e0i_A (A:268-406) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Back     alignment and structure
>1u3d_A (A:318-446) Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} Back     alignment and structure
>1np7_A (A:314-441) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} Back     alignment and structure
>2wq7_A (A:347-475) RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Back     alignment and structure
>3fy4_A (A:323-451) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Back     alignment and structure
>1owl_A (A:1-196) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} Back     alignment and structure
>2j07_A (A:1-149) Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} Back     alignment and structure
>1dnp_A (A:1-140) DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} Back     alignment and structure
>1np7_A (A:1-146) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} Back     alignment and structure
>2j4d_A (A:34-183) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Back     alignment and structure
>3fy4_A (A:1-142) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Back     alignment and structure
>2wq7_A (A:1-163) RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET: TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A* 2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A* Back     alignment and structure
>2e0i_A (A:1-132) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Back     alignment and structure
>1np7_A (A:147-313) DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} Back     alignment and structure
>2e0i_A (A:133-267) 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Back     alignment and structure
>1owl_A (A:197-307) Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} Back     alignment and structure
>2j4d_A (A:1-33,A:184-316) Cryptochrome 3, cryptochrome DASH; DNA-binding protein, flavoprotein, FAD, mitochondrion, plastid, chromophore, chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana} PDB: 2vtb_A* 2ijg_X* 2vtb_B* Back     alignment and structure
>3fy4_A (A:196-290) 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Back     alignment and structure