Citrus Sinensis ID: 036667

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKRLTDWLKDH
Secondary Structure (PSIPRED)
cccccccccccccHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHcccHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEEEccccccHHHHHHcccEEccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHccccccccccccccccccccHHHHHHccc
Coil and Loop (DISEMBL)
mpkeyiyepwtapltiqtrakciigrdypapvvshdsasKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKfegeenqesgrrQKQKRLTDWLKDH
Flexible Loop (DISEMBL)
mpkeyiyepwtapltIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAyalnqklngqvseddLKNLRRkfegeenqesgrrqkqkrltdwlkdh
Low Complexity Region (SEG)
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKRLTDWLKDH
Disordered region (IsUnstruct)
****YIYEPWTAPLTIQTRAKCIIGRDYPAPVV***************************************************************
Disordered Region (DISOPRED)
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEA***********************************************
Disordered Region (DISEMBL)
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAP***********KRKLGEAYALNQKLNGQVSEDDLKNLRRKF************************
Disordered Region (DISPRO)
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLN***************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKFEGEENQESGRRQKQKRLTDWLKDH
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	96	2.2.26 [Sep-21-2011]
O48652	556	(6-4)DNA photolyase OS=Ar	yes	no	0.927	0.160	0.629	2e-30
Q0E2Y1	551	(6-4)DNA photolyase OS=Or	yes	no	0.927	0.161	0.516	5e-19
Q49AN0	593	Cryptochrome-2 OS=Homo sa	yes	no	0.520	0.084	0.5	1e-08
Q9R194	592	Cryptochrome-2 OS=Mus mus	yes	no	0.520	0.084	0.48	1e-08
Q8QG60	582	Cryptochrome-2 OS=Gallus	no	no	0.520	0.085	0.48	2e-08
Q5IZC5	620	Cryptochrome-1 OS=Erithac	N/A	no	0.520	0.080	0.48	3e-08
Q6ZZY0	620	Cryptochrome-1 OS=Sylvia	N/A	no	0.520	0.080	0.48	3e-08
Q923I8	594	Cryptochrome-2 OS=Rattus	yes	no	0.520	0.084	0.46	4e-08
Q8QG61	621	Cryptochrome-1 OS=Gallus	no	no	0.520	0.080	0.44	6e-08
Q70AD6	587	Cryptochrome-1 OS=Spalax	N/A	no	0.520	0.085	0.46	1e-07

>sp|O48652|UVR3_ARATH (6-4)DNA photolyase OS=Arabidopsis thaliana GN=UVR3 PE=1 SV=2

 Score =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 79/89 (88%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 467 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 526

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK + +E++ES  R ++ +L
Sbjct: 527 DEENLRDLRRKLQKDEHEESKIRNQRPKL 555

Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products). Binds specifically to DNA containing 6-4 products and repairs these lesions in a visible light-dependent manner. Not required for repair of cyclobutane pyrimidine dimer (CPD).
Arabidopsis thaliana (taxid: 3702)
EC: 4EC: .EC: 1EC: .EC: 9EC: 9EC: .EC: 1EC: 3

>sp|Q0E2Y1|UVR3_ORYSJ (6-4)DNA photolyase OS=Oryza sativa subsp. japonica GN=UVR3 PE=3 SV=1

 Score = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/89 (51%), Positives = 59/89 (66%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAPL+IQ +A CIIG+DYP PVV H  ASKECK+ +GEAYA N+  + + 
Sbjct: 459 MPKEYIYEPWTAPLSIQKKANCIIGKDYPKPVVDHAIASKECKKMMGEAYASNRLDDDKP 518

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            +    N  R+     +Q +    K K+L
Sbjct: 519 DKGKSSNSSRRKLSAGSQVTPNSSKTKQL 547

Involved in repair of UV radiation-induced DNA damage. Catalyzes the photoreactivation of pyrimidine [6-4] pyrimidone photoproduct (6-4 products).

Oryza sativa subsp. japonica (taxid: 39947)

EC: 4

EC: .

EC: 1

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: 3

>sp|Q49AN0|CRY2_HUMAN Cryptochrome-2 OS=Homo sapiens GN=CRY2 PE=1 SV=2

 Score = 58.5 bits (140), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 32/50 (64%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P  YIYEPW AP +IQ  AKCIIG DYP P+V+H   S+    ++ + Y
Sbjct: 458 FPSRYIYEPWNAPESIQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIY 507

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Homo sapiens (taxid: 9606)

>sp|Q9R194|CRY2_MOUSE Cryptochrome-2 OS=Mus musculus GN=Cry2 PE=1 SV=1

 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 32/50 (64%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y
Sbjct: 457 FPSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIY 506

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Mus musculus (taxid: 10090)

>sp|Q8QG60|CRY2_CHICK Cryptochrome-2 OS=Gallus gallus GN=CRY2 PE=2 SV=2

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 32/50 (64%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y
Sbjct: 448 FPSRYIYEPWNAPESVQKAAKCIIGVDYPKPMVNHAETSRLNIERMKQIY 497

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Gallus gallus (taxid: 9031)

>sp|Q5IZC5|CRY1_ERIRU Cryptochrome-1 OS=Erithacus rubecula GN=CRY1 PE=2 SV=2

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 34/50 (68%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P +YIY+PW AP +IQ  AKCIIG +YP P+V+H  AS+    ++ + Y
Sbjct: 439 FPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIY 488

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Erithacus rubecula (taxid: 37610)

>sp|Q6ZZY0|CRY1_SYLBO Cryptochrome-1 OS=Sylvia borin GN=CRY1 PE=2 SV=1

 Score = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 34/50 (68%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P +YIY+PW AP +IQ  AKCIIG +YP P+V+H  AS+    ++ + Y
Sbjct: 439 FPAKYIYDPWNAPESIQKAAKCIIGVNYPKPMVNHAEASRLNIERMKQIY 488

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Sylvia borin (taxid: 73324)

>sp|Q923I8|CRY2_RAT Cryptochrome-2 OS=Rattus norvegicus GN=Cry2 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 31/50 (62%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P  YIYEPW AP ++Q  A CIIG DYP P+V+H   S+    ++ + Y
Sbjct: 457 FPSRYIYEPWNAPESVQKAANCIIGVDYPRPIVNHAETSRLNIERMKQIY 506

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Rattus norvegicus (taxid: 10116)

>sp|Q8QG61|CRY1_CHICK Cryptochrome-1 OS=Gallus gallus GN=CRY1 PE=2 SV=1

 Score = 56.2 bits (134), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P +YIY+PW AP ++Q  AKC+IG +YP P+V+H  AS+    ++ + Y
Sbjct: 439 FPAKYIYDPWNAPESVQKAAKCVIGVNYPKPMVNHAEASRLNIERMKQIY 488

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Gallus gallus (taxid: 9031)

>sp|Q70AD6|CRY1_SPAJD Cryptochrome-1 OS=Spalax judaei GN=CRY1 PE=2 SV=1

 Score = 55.5 bits (132), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 33/50 (66%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
            P +YIY+PW AP  IQ  AKC+IG +YP P+V+H  AS+    ++ + Y
Sbjct: 439 FPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIY 488

Blue light-dependent regulator of the circadian feedback loop. Inhibits CLOCK|NPAS2-ARNTL E box-mediated transcription. Acts, in conjunction with CRY2, in maintaining period length and circadian rhythmicity. Has no photolyase activity. Capable of translocating circadian clock core proteins such as PER proteins to the nucleus. May inhibit CLOCK|NPAS2-ARNTL transcriptional activity through stabilizing the unphosphorylated form of ARNTL.

Spalax judaei (taxid: 134510)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	96
317106754	536	JHL25H03.11 [Jatropha curcas]	0.916	0.164	0.752	3e-32
356526185	535	PREDICTED: (6-4)DNA photolyase-like [Gly	0.937	0.168	0.711	4e-32
255553063	537	DNA photolyase, putative [Ricinus commun	0.906	0.162	0.738	6e-32
224073768	540	predicted protein [Populus trichocarpa]	0.906	0.161	0.772	6e-31
147865945	633	hypothetical protein VITISV_029095 [Viti	0.927	0.140	0.685	3e-29
297834434	546	6-4 photolyase [Arabidopsis lyrata subsp	0.927	0.163	0.640	4e-29
297743390	538	unnamed protein product [Vitis vinifera]	0.937	0.167	0.677	5e-29
359483005	564	PREDICTED: (6-4)DNA photolyase [Vitis vi	0.937	0.159	0.677	6e-29
228312124	537	Chain A, (6-4) Photolyase Crystal Struct	0.927	0.165	0.629	1e-28
18400841	556	(6-4)DNA photolyase [Arabidopsis thalian	0.927	0.160	0.629	1e-28

>gi|317106754|dbj|BAJ53248.1| JHL25H03.11 [Jatropha curcas]

 Score =  142 bits (358), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 67/89 (75%), Positives = 80/89 (89%), Gaps = 1/89 (1%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKE+IYEPWTAPL++QT+AKCIIGRDYP PVVSHDSASKECKRKL EAYALNQKLNGQ+
Sbjct: 448 MPKEFIYEPWTAPLSVQTKAKCIIGRDYPKPVVSHDSASKECKRKLAEAYALNQKLNGQL 507

Query: 61  SEDDLKNLRRKFEGEENQESG-RRQKQKR 88
           +E+DL NL+RK + +++QE    RQKQK+
Sbjct: 508 TEEDLGNLKRKLQQDQDQERKITRQKQKK 536

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526185|ref|XP_003531700.1| PREDICTED: (6-4)DNA photolyase-like [Glycine max]

 Score =  141 bits (356), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 64/90 (71%), Positives = 79/90 (87%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MP+EYIYEPWTAP +IQT+A CIIG+DYP PVVSHDSASKEC+RK+GEAYALN++LNG V
Sbjct: 445 MPREYIYEPWTAPKSIQTKANCIIGKDYPMPVVSHDSASKECRRKMGEAYALNKELNGLV 504

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRLT 90
           SEDDLKNLRRK +  E QE+G ++ +++L 
Sbjct: 505 SEDDLKNLRRKLDESEGQEAGAKRYKQQLI 534

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553063|ref|XP_002517574.1| DNA photolyase, putative [Ricinus communis] gi|223543206|gb|EEF44738.1| DNA photolyase, putative [Ricinus communis]

 Score =  141 bits (355), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 65/88 (73%), Positives = 80/88 (90%), Gaps = 1/88 (1%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAPL++QT+AKCIIGRDYP PVV+HDSASKECK+KL E+YALNQKLNG++
Sbjct: 449 MPKEYIYEPWTAPLSVQTKAKCIIGRDYPKPVVAHDSASKECKKKLAESYALNQKLNGKL 508

Query: 61  SEDDLKNLRRKFEGEENQES-GRRQKQK 87
            E+DL+NLRRK E +++QE  G+RQ+ K
Sbjct: 509 GEEDLRNLRRKLEQDQDQEHKGKRQRLK 536

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073768|ref|XP_002304163.1| predicted protein [Populus trichocarpa] gi|222841595|gb|EEE79142.1| predicted protein [Populus trichocarpa]

 Score =  137 bits (346), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 68/88 (77%), Positives = 76/88 (86%), Gaps = 1/88 (1%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAP  IQ +AKCIIGRDYP PVV HDSASKECKRKL EAYALN+KLNGQ+
Sbjct: 448 MPKEYIYEPWTAPPGIQRKAKCIIGRDYPKPVVYHDSASKECKRKLAEAYALNKKLNGQL 507

Query: 61  SEDDLKNLRRKFEGEENQESG-RRQKQK 87
           S++DL NLRRK E +E+QE   RRQ+QK
Sbjct: 508 SQEDLDNLRRKLEQDEDQEPKIRRQRQK 535

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865945|emb|CAN80978.1| hypothetical protein VITISV_029095 [Vitis vinifera]

 Score =  132 bits (331), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 61/89 (68%), Positives = 74/89 (83%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAP +IQ +AKCIIG+DYP PVV HDSA KECKRKL EAYALN++L+G V
Sbjct: 543 MPKEYIYEPWTAPPSIQXKAKCIIGKDYPKPVVCHDSAXKECKRKLAEAYALNKRLDGSV 602

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
           +E+DLK LRRK E +EN ES   + +++L
Sbjct: 603 TEEDLKKLRRKLEEDENXESNTSRTRQKL 631

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297834434|ref|XP_002885099.1| 6-4 photolyase [Arabidopsis lyrata subsp. lyrata] gi|297330939|gb|EFH61358.1| 6-4 photolyase [Arabidopsis lyrata subsp. lyrata]

 Score =  132 bits (331), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 57/89 (64%), Positives = 79/89 (88%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 457 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 516

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK E +E++ES  R ++ +L
Sbjct: 517 DEENLRDLRRKLEKDEHEESKIRNQRPKL 545

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743390|emb|CBI36257.3| unnamed protein product [Vitis vinifera]

 Score =  131 bits (329), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 61/90 (67%), Positives = 74/90 (82%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAP +IQ +AKCIIG+DYP PVV HDSA KECKRKL EAYALN++L+G V
Sbjct: 448 MPKEYIYEPWTAPPSIQAKAKCIIGKDYPKPVVCHDSAIKECKRKLAEAYALNKRLDGSV 507

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRLT 90
           +E+DLK LRRK E +EN ES   + +++L 
Sbjct: 508 TEEDLKKLRRKLEEDENPESNTSRTRQKLI 537

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483005|ref|XP_002285327.2| PREDICTED: (6-4)DNA photolyase [Vitis vinifera]

 Score =  131 bits (329), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 61/90 (67%), Positives = 74/90 (82%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPKEYIYEPWTAP +IQ +AKCIIG+DYP PVV HDSA KECKRKL EAYALN++L+G V
Sbjct: 474 MPKEYIYEPWTAPPSIQAKAKCIIGKDYPKPVVCHDSAIKECKRKLAEAYALNKRLDGSV 533

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRLT 90
           +E+DLK LRRK E +EN ES   + +++L 
Sbjct: 534 TEEDLKKLRRKLEEDENPESNTSRTRQKLI 563

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|228312124|pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure gi|228312125|pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure gi|228312126|pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure gi|2804280|dbj|BAA24449.1| 6-4 photolyase [Arabidopsis thaliana] gi|3929918|dbj|BAA34711.1| 6-4 photolyase [Arabidopsis thaliana] gi|11994334|dbj|BAB02293.1| 6-4 photolyase [Arabidopsis thaliana]

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 79/89 (88%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 507

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK + +E++ES  R ++ +L
Sbjct: 508 DEENLRDLRRKLQKDEHEESKIRNQRPKL 536

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18400841|ref|NP_566520.1| (6-4)DNA photolyase [Arabidopsis thaliana] gi|306756349|sp|O48652.2|UVR3_ARATH RecName: Full=(6-4)DNA photolyase; AltName: Full=Protein UV repair defective 3 gi|332642182|gb|AEE75703.1| (6-4)DNA photolyase [Arabidopsis thaliana]

 Score =  130 bits (327), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 79/89 (88%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 467 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 526

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK + +E++ES  R ++ +L
Sbjct: 527 DEENLRDLRRKLQKDEHEESKIRNQRPKL 555

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	96
TAIR|locus:2093217	556	UVR3 "UV REPAIR DEFECTIVE 3" [	0.927	0.160	0.629	2e-29
UNIPROTKB|Q2TV23	529	LOC395100 "Cryptochrome-like p	0.927	0.168	0.373	7.7e-11
UNIPROTKB|F1P5X2	547	LOC395100 "Uncharacterized pro	0.927	0.162	0.373	8.1e-11
UNIPROTKB|F1N0J9	610	Bt.20450 "Uncharacterized prot	0.593	0.093	0.456	1.2e-10
ZFIN|ZDB-GENE-010426-7	582	cry4 "cryptochrome 4" [Danio r	0.979	0.161	0.366	1.9e-10
ZFIN|ZDB-GENE-010426-8	545	cry5 "cryptochrome 5" [Danio r	0.520	0.091	0.52	4.6e-10
UNIPROTKB|F1P3P5	531	CRY2 "Cryptochrome-2" [Gallus	0.593	0.107	0.438	1.1e-09
UNIPROTKB|F1NX44	537	CRY2 "Cryptochrome-2" [Gallus	0.593	0.106	0.438	1.2e-09
MGI|MGI:1270859	592	Cry2 "cryptochrome 2 (photolya	0.593	0.096	0.438	1.2e-09
UNIPROTKB|Q8QG60	582	CRY2 "Cryptochrome-2" [Gallus	0.593	0.097	0.438	1.5e-09

TAIR|locus:2093217 UVR3 "UV REPAIR DEFECTIVE 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 331 (121.6 bits), Expect = 2.0e-29, P = 2.0e-29
 Identities = 56/89 (62%), Positives = 79/89 (88%)

Query:     1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
             MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct:   467 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 526

Query:    61 SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
              E++L++LRRK + +E++ES  R ++ +L
Sbjct:   527 DEENLRDLRRKLQKDEHEESKIRNQRPKL 555

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006281 "DNA repair" evidence=IEA

GO:0009507 "chloroplast" evidence=ISM

GO:0003914 "DNA (6-4) photolyase activity" evidence=ISS;IDA

GO:0009411 "response to UV" evidence=IMP

UNIPROTKB|Q2TV23 LOC395100 "Cryptochrome-like protein" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 7.7e-11, P = 7.7e-11
 Identities = 34/91 (37%), Positives = 53/91 (58%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVS 61
             P +YIYEPWTA    Q +A CIIGRDYP P+V H  AS    + + +A     ++  Q++
Sbjct:   438 PSKYIYEPWTASEEEQKQAGCIIGRDYPFPMVDHKEASDHNLQLMKQAREEQHRI-AQLT 496

Query:    62 EDDLKN-LRRKFEGEENQESGRRQKQKRLTD 91
              DD  + +  K + + ++ES  + K  R+T+
Sbjct:   497 RDDADDPMEMKLKRDHSEESFTKTKAARMTE 527

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

UNIPROTKB|F1P5X2 LOC395100 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.1e-11, P = 8.1e-11
 Identities = 34/91 (37%), Positives = 53/91 (58%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVS 61
             P +YIYEPWTA    Q +A CIIGRDYP P+V H  AS    + + +A     ++  Q++
Sbjct:   456 PSKYIYEPWTASEEEQKQAGCIIGRDYPFPMVDHKEASDHNLQLMKQAREEQHRI-AQLT 514

Query:    62 EDDLKN-LRRKFEGEENQESGRRQKQKRLTD 91
              DD  + +  K + + ++ES  + K  R+T+
Sbjct:   515 RDDADDPMEMKLKRDHSEESFTKTKAARMTE 545

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

UNIPROTKB|F1N0J9 Bt.20450 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 145 (56.1 bits), Expect = 1.2e-10, Sum P(2) = 1.2e-10
 Identities = 26/57 (45%), Positives = 35/57 (61%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNG 58
             P  YIYEPW AP +IQ  AKC+IG DYP P+V+H  AS+    ++ + Y    +  G
Sbjct:   476 PSRYIYEPWNAPESIQKAAKCVIGVDYPRPIVNHAEASRLNIERMKQVYQQLSRYRG 532

GO:2000118 "regulation of sodium-dependent phosphate transport" evidence=IEA

GO:0042752 "regulation of circadian rhythm" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0003913 "DNA photolyase activity" evidence=IEA

ZFIN|ZDB-GENE-010426-7 cry4 "cryptochrome 4" [Danio rerio (taxid:7955)]

 Score = 157 (60.3 bits), Expect = 1.9e-10, P = 1.9e-10
 Identities = 37/101 (36%), Positives = 55/101 (54%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKE---CKRKLGEAYALNQKLNG 58
             P +YIYEPW AP  +Q  A CIIG+DYP P+VSH  AS+      R++        +L  
Sbjct:   461 PSQYIYEPWKAPEDVQLSAGCIIGKDYPRPIVSHIEASQRNLALMRQVRTEQQTTAELTR 520

Query:    59 QVSEDDLK-NLRRKFEGEEN--QESGRRQKQKRLTDWLKDH 96
              V++D ++  L+R+   EE   +E+  +   KR +    DH
Sbjct:   521 DVADDPMEAGLKRELREEEGLLEEAESQCTSKRFSG-SSDH 560

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0009881 "photoreceptor activity" evidence=IDA

ZFIN|ZDB-GENE-010426-8 cry5 "cryptochrome 5" [Danio rerio (taxid:7955)]

 Score = 153 (58.9 bits), Expect = 4.6e-10, P = 4.6e-10
 Identities = 26/50 (52%), Positives = 35/50 (70%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYA 51
             P EYIYEPW AP ++Q RA CI+G+DYP P+V H+   K+   ++  AYA
Sbjct:   465 PTEYIYEPWKAPRSVQERAGCIVGKDYPRPIVDHEVVHKKNILRMKAAYA 514

GO:0006281 "DNA repair" evidence=IEA;IDA

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0009416 "response to light stimulus" evidence=IDA

GO:0016829 "lyase activity" evidence=IEA

GO:0003914 "DNA (6-4) photolyase activity" evidence=IDA

UNIPROTKB|F1P3P5 CRY2 "Cryptochrome-2" [Gallus gallus (taxid:9031)]

 Score = 138 (53.6 bits), Expect = 1.1e-09, Sum P(2) = 1.1e-09
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNG 58
             P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y    +  G
Sbjct:   398 PSRYIYEPWNAPESVQKAAKCIIGVDYPKPMVNHAETSRLNIERMKQIYQQLSRYRG 454

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

GO:0042752 "regulation of circadian rhythm" evidence=IEA

GO:2000118 "regulation of sodium-dependent phosphate transport" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IEA

UNIPROTKB|F1NX44 CRY2 "Cryptochrome-2" [Gallus gallus (taxid:9031)]

 Score = 138 (53.6 bits), Expect = 1.2e-09, Sum P(2) = 1.2e-09
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNG 58
             P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y    +  G
Sbjct:   404 PSRYIYEPWNAPESVQKAAKCIIGVDYPKPMVNHAETSRLNIERMKQIYQQLSRYRG 460

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

MGI|MGI:1270859 Cry2 "cryptochrome 2 (photolyase-like)" [Mus musculus (taxid:10090)]

 Score = 140 (54.3 bits), Expect = 1.2e-09, Sum P(2) = 1.2e-09
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNG 58
             P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y    +  G
Sbjct:   458 PSRYIYEPWNAPESVQKAAKCIIGVDYPRPIVNHAETSRLNIERMKQIYQQLSRYRG 514

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO

GO:0003684 "damaged DNA binding" evidence=ISO

GO:0003697 "single-stranded DNA binding" evidence=ISO

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006281 "DNA repair" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006606 "protein import into nucleus" evidence=IPI

GO:0007623 "circadian rhythm" evidence=IMP

GO:0009881 "photoreceptor activity" evidence=IEA

GO:0016829 "lyase activity" evidence=IEA

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0019902 "phosphatase binding" evidence=ISO

GO:0032515 "negative regulation of phosphoprotein phosphatase activity" evidence=ISO

GO:0042752 "regulation of circadian rhythm" evidence=IMP

GO:0048511 "rhythmic process" evidence=IEA

GO:0050896 "response to stimulus" evidence=IEA

UNIPROTKB|Q8QG60 CRY2 "Cryptochrome-2" [Gallus gallus (taxid:9031)]

 Score = 138 (53.6 bits), Expect = 1.5e-09, Sum P(2) = 1.5e-09
 Identities = 25/57 (43%), Positives = 34/57 (59%)

Query:     2 PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNG 58
             P  YIYEPW AP ++Q  AKCIIG DYP P+V+H   S+    ++ + Y    +  G
Sbjct:   449 PSRYIYEPWNAPESVQKAAKCIIGVDYPKPMVNHAETSRLNIERMKQIYQQLSRYRG 505

GO:0003913 "DNA photolyase activity" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0009881 "photoreceptor activity" evidence=IEA

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0048511 "rhythmic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	96
pfam03441	276	pfam03441, FAD_binding_7, FAD binding domain of DN	9e-11
TIGR02766	475	TIGR02766, crypt_chrom_pln, cryptochrome, plant fa	2e-05
COG0415	461	COG0415, PhrB, Deoxyribodipyrimidine photolyase [D	0.003

>gnl|CDD|217559 pfam03441, FAD_binding_7, FAD binding domain of DNA photolyase

 Score = 55.7 bits (135), Expect = 9e-11
 Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY 50
           +P  YI+EPW AP  +Q  A C++G+DYP P+V H  A K        A 
Sbjct: 229 LPDRYIHEPWKAPRPVQ--AGCVLGKDYPKPIVDHKEARKRALDAYKAAR 276

Length = 276

>gnl|CDD|131813 TIGR02766, crypt_chrom_pln, cryptochrome, plant family

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKEC 42
           +P E+I+ PW AP ++   A   +G +YP P+V  D A +  
Sbjct: 429 LPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVGLDEA-RAR 469

At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light. Length = 475

>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 7/44 (15%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKR 44
           +P +YI+EPW          + ++G DYP P+V H  + ++   
Sbjct: 419 LPDKYIHEPWELS-------EVVLGVDYPKPIVDHKESREQALA 455

Length = 461

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
PF03441	277	FAD_binding_7: FAD binding domain of DNA photolyas	99.19
TIGR02766	475	crypt_chrom_pln cryptochrome, plant family. At lea	99.1
PRK10674	472	deoxyribodipyrimidine photolyase; Provisional	98.54
COG0415	461	PhrB Deoxyribodipyrimidine photolyase [DNA replica	98.45
KOG0133	531	consensus Deoxyribodipyrimidine photolyase/cryptoc	98.41
TIGR03556	471	photolyase_8HDF deoxyribodipyrimidine photo-lyase,	98.13

>PF03441 FAD_binding_7: FAD binding domain of DNA photolyase from Prosite

Probab=99.19  E-value=8.3e-12  Score=93.64  Aligned_cols=50  Identities=46%  Similarity=0.989  Sum_probs=44.0

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY   50 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~   50 (96)
                      ||.++||+||.++...+..++|.+|.+||.|||||+++|++|++++.++|
T Consensus       228 ~~~~~ih~p~~~~~~~~~~~~~~~~~~YP~pivd~~~~r~~~~~~~~~~~  277 (277)
T PF03441_consen  228 LPDEYIHEPWKAPPAVQKAAGCVLGNDYPKPIVDHKEARKRALKRYKAAY  277 (277)
T ss_dssp             STHHHHTSCHGSHHHHHHHCT-CTTTSSBTSSSHHHHHHHHHHHHHHHH-
T ss_pred             CChhheeChhccChHHHHHhCCccCCCCCcccCCHHHHHHHHHHHHHhcC
Confidence            58899999999999999999999999999999999999998877776654

; InterPro: IPR005101 This entry represents a multi-helical domain composed of two all-alpha subdomains that is found as the C-terminal domain in cryptochrome proteins, as well as at the N-terminal of DNA photolyase where it acts as a FAD-binding domain (the N-terminal of DNA photolyase binds a light-harvesting cofactor). Photolyases and cryptochromes are related flavoproteins that bind FAD. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes (CRY1 and CRY2) are blue light photoreceptors that mediate blue light-induced gene expression [, ]. DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [, ].; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 3ZXS_A 1DNP_A 2XRZ_B 2XRY_A 2VTB_A 2J4D_B 2IJG_X 3TVS_A 2E0I_D ....

>TIGR02766 crypt_chrom_pln cryptochrome, plant family

Probab=99.10  E-value=6.4e-11  Score=94.14  Aligned_cols=44  Identities=34%  Similarity=0.721  Sum_probs=39.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKR   44 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~   44 (96)
                      ||+++||+||+++..++...||.+|.+||.|||||+.+|++|+.
T Consensus       429 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~~~~  472 (475)
T TIGR02766       429 LPTEWIHHPWDAPESVLQAAGVELGSNYPLPIVGLDEARARLHE  472 (475)
T ss_pred             CCHHHhcCcccCCHHHHHHcCCccCCCCCcccCCHHHHHHHHHH
Confidence            68999999999998887788999999999999999999996653

At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.

>PRK10674 deoxyribodipyrimidine photolyase; Provisional

Probab=98.54  E-value=6.7e-08  Score=77.24  Aligned_cols=43  Identities=33%  Similarity=0.556  Sum_probs=32.6

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALN   53 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~   53 (96)
                      ||+++||+||+++..    .++  +.+||.|||||+.+|++|+    ++|+..
T Consensus       426 ~p~~~ih~Pw~~~~~----~~~--~~~YP~PiVd~~~~r~~~~----~~~~~~  468 (472)
T PRK10674        426 VPGKAIHQPWRWAEK----AGV--TLDYPQPIVDHKQARLATL----AAYEAA  468 (472)
T ss_pred             CCHHhhcCccccchh----cCC--CCCCCcCCcCHHHHHHHHH----HHHHHH
Confidence            689999999988732    244  3479999999999999654    555443

>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]

Probab=98.45  E-value=1e-07  Score=76.65  Aligned_cols=41  Identities=37%  Similarity=0.844  Sum_probs=34.0

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL   52 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~   52 (96)
                      ||.++||+||.++.       +.+|.+||.|||||..+|++|    +.+|+.
T Consensus       419 ~~~~~ih~p~~~~~-------~~~~~~YP~piVd~~~~r~~a----~~~y~~  459 (461)
T COG0415         419 LPDKYIHEPWELSE-------VVLGVDYPKPIVDHKESREQA----LAAYEA  459 (461)
T ss_pred             CChhhccChhhccc-------ccccCCCCccccccHHHHHHH----HHHHHh
Confidence            68899999999885       456889999999999999965    455654

>KOG0133 consensus Deoxyribodipyrimidine photolyase/cryptochrome [Replication, recombination and repair; Signal transduction mechanisms]

Probab=98.41  E-value=2.6e-07  Score=75.35  Aligned_cols=53  Identities=40%  Similarity=0.756  Sum_probs=47.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALN   53 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~   53 (96)
                      .|..+||.||.++..++..++|.+|.+||.|||++..+++.+.+++..+|+..
T Consensus       445 ~p~~~i~~pW~~p~~~~~~~~~~lg~~Yp~~iv~~~~a~k~~~e~~~~~~~~~  497 (531)
T KOG0133|consen  445 GPMHFIYEPWAAPEGVQTAAGELLGVDYPKPIVKLASAAKRNMEAMGCMWSIG  497 (531)
T ss_pred             CCcceeccCCCCcHHHhhhhhhhhhcccchhhhhhHHhhHhHHHHHHHHHhhc
Confidence            36789999999999999999999999999999999999999888888777643

>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type

Probab=98.13  E-value=2.3e-06  Score=68.48  Aligned_cols=41  Identities=20%  Similarity=0.397  Sum_probs=30.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL   52 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~   52 (96)
                      ||+++||+||..+. .+.      ..+||.|||||+.+|+    +++.+|+.
T Consensus       430 ~p~~~ih~p~~~~~-~~~------~~~YP~Pivd~~~~r~----~~~~~~~~  470 (471)
T TIGR03556       430 VDTKDLVTGKITPL-ERR------AVGYPLPIVDHNQQQQ----LFKQLYQQ  470 (471)
T ss_pred             CCHhhhcCcccCch-hhh------ccCCCCCCCCHHHHHH----HHHHHHhh
Confidence            68999999987662 222      2369999999999999    45666653

This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
3fy4_A	537	(6-4) Photolyase Crystal Structure Length = 537		2e-31
3cvu_A	543	Drosophila Melanogaster (6-4) Photolyase Bound To D		2e-07
3cvx_A	543	Drosophila Melanogaster (6-4) Photolyase H369m Muta		2e-07
3cvw_A	543	Drosophila Melanogaster (6-4) Photolyase H365n Muta		2e-07
1u3c_A	509	Crystal Structure Of The Phr Domain Of Cryptochrome		5e-04

>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure Length = 537

Iteration: 1
 Score =  130 bits (327), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 79/89 (88%)
Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 507
Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK + +E++ES  R ++ +L
Sbjct: 508 DEENLRDLRRKLQKDEHEESKIRNQRPKL 536

>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna With A T-T (6-4) Photolesion Length = 543

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2   PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
           P   IYEPW A L  Q    C++G DYP  +V H+   KE  +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527

>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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2   PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
           P   IYEPW A L  Q    C++G DYP  +V H+   KE  +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527

>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

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2   PKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKL 56
           P   IYEPW A L  Q    C++G DYP  +V H+   KE  +++G AY +N+++
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527

>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From Arabidopsis Thaliana Length = 509

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL 52
           +P ++I+ PW AP ++   A   +G +YP P+V  D A       L + + L
Sbjct: 443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMWQL 494

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	2e-27
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	3e-20
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	2e-17
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	3e-13
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	6e-10
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	8e-05
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	1e-04
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	5e-04

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Length = 537

 Score =  102 bits (257), Expect = 2e-27
 Identities = 56/89 (62%), Positives = 79/89 (88%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
           MPK+YIYEPWTAPL++QT+A CI+G+DYP P+V HDSASKECKRK+GEAYALN+K++G+V
Sbjct: 448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKV 507

Query: 61  SEDDLKNLRRKFEGEENQESGRRQKQKRL 89
            E++L++LRRK + +E++ES  R ++ +L
Sbjct: 508 DEENLRDLRRKLQKDEHEESKIRNQRPKL 536

>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

 Score = 82.7 bits (205), Expect = 3e-20
 Identities = 23/64 (35%), Positives = 35/64 (54%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQV 60
            P   IYEPW A L  Q    C++G DYP  +V H+   KE  +++G AY +N+++    
Sbjct: 472 YPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAYKVNREVRTGK 531

Query: 61  SEDD 64
            E+ 
Sbjct: 532 EEES 535

>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

 Score = 62.2 bits (152), Expect = 3e-13
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKL 46
           +P + I++PW    T Q +    +G DYP P V+    S E +RK+
Sbjct: 438 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFH-QSVEARRKI 482

>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

 Score = 53.0 bits (128), Expect = 6e-10
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYA 51
           +P ++I+ PW AP ++   A   +G +YP P+V  D A         EA +
Sbjct: 443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLH----EALS 489

>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 Length = 471

 Score = 38.7 bits (91), Expect = 8e-05
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 10/51 (19%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYA 51
           +P + ++EPW          K  +  DYP P+V H  A  +       AY 
Sbjct: 425 VPGKVVHEPWKWA------QKAGVTLDYPQPIVEHKEARVQTL----AAYE 465

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A* Length = 484

 Score = 37.9 bits (89), Expect = 1e-04
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 13/51 (25%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYA 51
           +  + +      P         I  R YPAP+V+H+   K+ K      Y 
Sbjct: 432 VHPKDLISGEITP---------IERRGYPAPIVNHNLRQKQFK----ALYN 469

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii} Length = 440

 Score = 36.4 bits (85), Expect = 5e-04
 Identities = 8/51 (15%), Positives = 14/51 (27%), Gaps = 15/51 (29%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYA 51
           +P   I+  +                 YP+P+V+        K      Y 
Sbjct: 391 VPPSIIHSIYKTK-----------VPGYPSPIVNWLERVNYVK----SEYK 426

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
3fy4_A	537	6-4 photolyase; DNA repair, clock cryptochrome; HE	99.62
1u3d_A	509	Cryptochrome 1 apoprotein; photolyase, AMPPNP, sig	99.21
2wq7_A	543	RE11660P; lyase-DNA complex, DNA repair, DNA lesio	99.17
3tvs_A	538	Cryptochrome-1; circadian clock light entrainment,	99.16
1np7_A	489	DNA photolyase; protein with FAD cofactor; HET: DN	99.09
1dnp_A	471	DNA photolyase; DNA repair, electron transfer, exc	98.62
2e0i_A	440	432AA long hypothetical deoxyribodipyrimidine PHO;	98.57
1owl_A	484	Photolyase, deoxyribodipyrimidine photolyase; DNA	98.46
2j4d_A	525	Cryptochrome 3, cryptochrome DASH; DNA-binding pro	98.21
2j07_A	420	Deoxyribodipyrimidine photo-lyase; flavoprotein, n	96.08

>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana}

Probab=99.62  E-value=7.5e-16  Score=123.39  Aligned_cols=80  Identities=68%  Similarity=1.272  Sum_probs=70.4

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhhhccCCccHHHHHHHhHhhccccccch
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQKLNGQVSEDDLKNLRRKFEGEENQES   80 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~   80 (96)
                      ||+++||+||.++..++..+||.+|.+||.|||||+++|++|++++.++|+..+..++.+...+.+.+++.++.....++
T Consensus       448 lp~~~Ih~Pw~~~~~~~~~~g~~~g~~YP~PIVdh~~ar~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  527 (537)
T 3fy4_A          448 MPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDGKVDEENLRDLRRKLQKDEHEES  527 (537)
T ss_dssp             CCTTTTTCGGGSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHTTC--
T ss_pred             CCHHhhCCcccCCHHHHHhcCCccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccccCCCCccc
Confidence            68999999999999888889999999999999999999999999999999999998888888888888887765544444

>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*

Probab=99.21  E-value=9.7e-12  Score=98.38  Aligned_cols=50  Identities=30%  Similarity=0.688  Sum_probs=42.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY   50 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~   50 (96)
                      +|+++||+||.++...+..++|.+|.+||.|||||+.+|++|++++..++
T Consensus       443 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~a~~~~~~~~  492 (509)
T 1u3d_A          443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMW  492 (509)
T ss_dssp             CCHHHHTCTTTSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHHHH
T ss_pred             cccccccCcccCChHHHHHhccccCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            58899999999998888888999999999999999999997654444433

>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*

Probab=99.17  E-value=1.5e-11  Score=98.17  Aligned_cols=50  Identities=42%  Similarity=0.859  Sum_probs=43.2

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAY   50 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~   50 (96)
                      +|+++||+||.++..++..++|.+|.+||.|||||+.+|++|++++..++
T Consensus       472 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~al~~~~~~~  521 (543)
T 2wq7_A          472 YPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAY  521 (543)
T ss_dssp             SCHHHHTSGGGSCHHHHHHTTCCBTTTBCCCSSCHHHHHHHHHHHHHHHH
T ss_pred             cccccccCcccCChHHHHhhcccccCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence            58899999999998888889999999999999999999997665554443

>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} SCOP: a.99.1.1 c.28.1.1

Probab=99.09  E-value=3.9e-11  Score=94.45  Aligned_cols=45  Identities=27%  Similarity=0.527  Sum_probs=40.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRK   45 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r   45 (96)
                      +|+++||+||.++..++..++|.+|.+||.|||||+++|++|+++
T Consensus       438 ~p~~~ih~pw~~~~~~~~~~~~~~g~~YP~PiVd~~~~r~~a~~~  482 (489)
T 1np7_A          438 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKI  482 (489)
T ss_dssp             CCSGGGGCGGGCCHHHHHHTTCCBTTTBCCCSSCHHHHHHHHHTC
T ss_pred             cCcccccCCccCCHHHHHHhccccCCCCCCCCCCHHHHHHHHHHH
Confidence            589999999999998888899999999999999999999976543

>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

Probab=98.62  E-value=1.1e-08  Score=80.38  Aligned_cols=44  Identities=32%  Similarity=0.647  Sum_probs=33.7

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQ   54 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~   54 (96)
                      +|+++||+||.+    +...+|.+  +||.|||||+++|++|    +++|+..+
T Consensus       425 ~p~~~ih~Pw~~----~~~~~~~~--~YP~PiVd~~~~r~~a----l~~~~~~~  468 (471)
T 1dnp_A          425 VPGKVVHEPWKW----AQKAGVTL--DYPQPIVEHKEARVQT----LAAYEAAR  468 (471)
T ss_dssp             SCTTGGGSHHHH----HHTTTCCC--SSCCCSSCHHHHHHHH----HHHHHHHT
T ss_pred             CChhhcCCchhh----HHhcCCCC--CCCCCCCCHHHHHHHH----HHHHHHhh
Confidence            589999999986    23456655  7999999999999965    55665543

>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD, DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}

Probab=98.57  E-value=2.2e-08  Score=78.33  Aligned_cols=39  Identities=18%  Similarity=0.278  Sum_probs=30.8

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQ   54 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~   54 (96)
                      +|+++||+||.+           +|.+||.|||||+++|++|    +++|+..+
T Consensus       391 ~p~~~ih~pw~~-----------~~~~YP~PiVd~~~~r~~a----~~~~~~~~  429 (440)
T 2e0i_A          391 VPPSIIHSIYKT-----------KVPGYPSPIVNWLERVNYV----KSEYKNVK  429 (440)
T ss_dssp             SCHHHHTTTTTS-----------CCTTSCCCSSCHHHHHHHH----HHHHHHC-
T ss_pred             cCcccccCchhh-----------cCCCCCCCCCCHHHHHHHH----HHHHHHHH
Confidence            588999999985           2678999999999999965    45565543

>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB: 1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*

Probab=98.46  E-value=8.7e-08  Score=75.40  Aligned_cols=39  Identities=23%  Similarity=0.422  Sum_probs=29.9

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGE   48 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~   48 (96)
                      +|+++||+||.++.    ..    | +||.|||||+.+|++|++++..
T Consensus       432 ~p~~~ih~Pw~~~~----~~----~-~YP~PiVd~~~~r~~a~~~~~~  470 (484)
T 1owl_A          432 VHPKDLISGEITPI----ER----R-GYPAPIVNHNLRQKQFKALYNQ  470 (484)
T ss_dssp             SCHHHHHHTCCCHH----HH----T-TSCCCSSCHHHHHHHHHHHHHH
T ss_pred             CChhhcCCcccchh----hh----c-CCCCCCCCHHHHHHHHHHHHHH
Confidence            58899999999832    12    3 7999999999999966544443

>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*

Probab=98.21  E-value=1.4e-07  Score=75.05  Aligned_cols=37  Identities=16%  Similarity=0.006  Sum_probs=21.5

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKEC   42 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a   42 (96)
                      +|+++||+||.++     ..+|.+|.+||.|||||..+|+++
T Consensus       474 ~p~~~ih~Pw~~~-----~~~~~~g~~Yp~Pi~~~~~~~~~~  510 (525)
T 2j4d_A          474 LPKEKRHWPGRLM-----YMDTVVPLKHGNGPMAGGSKSGGG  510 (525)
T ss_dssp             SCTTTTTSCHHHH-----TCCCSSCCSCCC------------
T ss_pred             CChhcccCCccCc-----ccccccCCCCCCCcccchhhhhcc
Confidence            5899999999863     357889999999999999999853

>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein, nucleotide-binding, DNA repair; 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*

Probab=96.08  E-value=0.0039  Score=48.08  Aligned_cols=22  Identities=18%  Similarity=0.028  Sum_probs=17.7

Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667           28 YPAPVVSHDSASKECKRKLGEAYALN   53 (96)
Q Consensus        28 YP~PIVDh~~ar~~a~~r~~~a~~~~   53 (96)
                      ||.|||||+.+|++|    +++|+..
T Consensus       396 YP~Pivd~~~~r~~a----~~~~~~~  417 (420)
T 2j07_A          396 PKDPVVDLEEARRRY----LRLARDL  417 (420)
T ss_dssp             CSSCSSCHHHHHHHH----HHHHHHH
T ss_pred             CCCCccCHHHHHHHH----HHHHHHh
Confidence            999999999999965    4555544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	96
d1u3da1	300	a.99.1.1 (A:198-497) Cryptochrome C-terminal domai	3e-11
d1np7a1	279	a.99.1.1 (A:205-483) Cryptochrome C-terminal domai	3e-10
d1dnpa1	269	a.99.1.1 (A:201-469) C-terminal domain of DNA phot	2e-07
d1owla1	271	a.99.1.1 (A:205-475) C-terminal domain of DNA phot	3e-05

>d1u3da1 a.99.1.1 (A:198-497) Cryptochrome C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 300

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]

 Score = 55.3 bits (132), Expect = 3e-11
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYAL 52
           +P ++I+ PW AP ++   A   +G +YP P+V  D A       L + + L
Sbjct: 246 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMWQL 297

>d1np7a1 a.99.1.1 (A:205-483) Cryptochrome C-terminal domain {Synechocystis sp., pcc 6803 [TaxId: 1143]} Length = 279

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: Synechocystis sp., pcc 6803 [TaxId: 1143]

 Score = 52.7 bits (125), Expect = 3e-10
 Identities = 12/44 (27%), Positives = 23/44 (52%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKR 44
           +P + I++PW    T Q +    +G DYP P V+   + +  ++
Sbjct: 234 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRK 277

>d1dnpa1 a.99.1.1 (A:201-469) C-terminal domain of DNA photolyase {Escherichia coli [TaxId: 562]} Length = 269

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 = 44.9 bits (105), Expect = 2e-07
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 6/49 (12%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEA 49
           +P + ++EPW          K  +  DYP P+V H  A  +       A
Sbjct: 225 VPGKVVHEPWKWA------QKAGVTLDYPQPIVEHKEARVQTLAAYEAA 267

>d1owla1 a.99.1.1 (A:205-475) C-terminal domain of DNA photolyase {Synechococcus elongatus [TaxId: 32046]} Length = 271

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: Synechococcus elongatus [TaxId: 32046]

 Score = 38.5 bits (88), Expect = 3e-05
 Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 9/48 (18%)

Query: 1   MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGE 48
           +  + +      P         I  R YPAP+V+H+   K+ K    +
Sbjct: 228 VHPKDLISGEITP---------IERRGYPAPIVNHNLRQKQFKALYNQ 266

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	96
d1u3da1	300	Cryptochrome C-terminal domain {Thale cress (Arabi	99.29
d1np7a1	279	Cryptochrome C-terminal domain {Synechocystis sp.,	99.17
d1dnpa1	269	C-terminal domain of DNA photolyase {Escherichia c	98.72
d1owla1	271	C-terminal domain of DNA photolyase {Synechococcus	98.39

>d1u3da1 a.99.1.1 (A:198-497) Cryptochrome C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

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=99.29  E-value=9.1e-13  Score=96.63  Aligned_cols=48  Identities=31%  Similarity=0.693  Sum_probs=42.1

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGE   48 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~   48 (96)
                      ||.++||+||.++..++...+|.+|.+||.||||++++|++|++++..
T Consensus       246 ~p~~~ih~Pw~~~~~~~~~~~~~~g~~Yp~pivd~~~~~~r~~~~~~~  293 (300)
T d1u3da1         246 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQ  293 (300)
T ss_dssp             CCHHHHTCTTTSCHHHHHHHTCCBTTTBCCCSSCHHHHHHHHHHHHHH
T ss_pred             CCHHHhCCcccCCHHHHHHcCCccCCCCCcccCCHHHHHHHHHHHHHH
Confidence            688999999999999999999999999999999999999965444333

>d1np7a1 a.99.1.1 (A:205-483) Cryptochrome C-terminal domain {Synechocystis sp., pcc 6803 [TaxId: 1143]}

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: Synechocystis sp., pcc 6803 [TaxId: 1143]

Probab=99.17  E-value=6.7e-12  Score=91.01  Aligned_cols=41  Identities=29%  Similarity=0.570  Sum_probs=38.5

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHH
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKE   41 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~   41 (96)
                      ||+++||+||+++..++..++|.+|.+||.||||++++++.
T Consensus       234 ~p~~~ih~pw~~~~~~~~~~~~~~~~~YP~Pivd~~~~~~~  274 (279)
T d1np7a1         234 LPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEA  274 (279)
T ss_dssp             CCSGGGGCGGGCCHHHHHHTTCCBTTTBCCCSSCHHHHHHH
T ss_pred             CCHHhhcChhhCCHHHHHHcCCCCCCCCCcccCCHHHHHHH
Confidence            68999999999999999999999999999999999998763

>d1dnpa1 a.99.1.1 (A:201-469) C-terminal domain of DNA photolyase {Escherichia coli [TaxId: 562]}

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]

Probab=98.72  E-value=1.7e-09  Score=77.60  Aligned_cols=43  Identities=33%  Similarity=0.587  Sum_probs=34.0

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALN   53 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~   53 (96)
                      +|+++||+||.++.      .|.++.+||.||||++++|++|    +++|+.+
T Consensus       225 ~p~~~ih~p~~~~~------~~~~~~~Yp~pivd~~~~r~~~----~~~~~~~  267 (269)
T d1dnpa1         225 VPGKVVHEPWKWAQ------KAGVTLDYPQPIVEHKEARVQT----LAAYEAA  267 (269)
T ss_dssp             SCTTGGGSHHHHHH------TTTCCCSSCCCSSCHHHHHHHH----HHHHHHH
T ss_pred             CCHHhcCChhhcch------hhCcCCCCccccCCHHHHHHHH----HHHHHHh
Confidence            68999999997653      3556889999999999999955    5556554

>d1owla1 a.99.1.1 (A:205-475) C-terminal domain of DNA photolyase {Synechococcus elongatus [TaxId: 32046]}

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: Synechococcus elongatus [TaxId: 32046]

Probab=98.39  E-value=4.2e-08  Score=69.93  Aligned_cols=42  Identities=24%  Similarity=0.402  Sum_probs=32.2

Q ss_pred             CCccccccCCCCCHhHHHHhhhhcCCCCCCCCCChHHHHHHHHHHHHHHHHHhhh
Q 036667            1 MPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKLGEAYALNQK   55 (96)
Q Consensus         1 vP~~~IH~Pw~~~~~~~~~~~~~lg~~YP~PIVDh~~ar~~a~~r~~~a~~~~~~   55 (96)
                      ||+++||+||..+.         .+.+||.|||||+.+++++    +++|+..+.
T Consensus       228 ~~~~~i~~~~~~~~---------~~~~Yp~pivd~~~~~~~~----~~~~~~~k~  269 (271)
T d1owla1         228 VHPKDLISGEITPI---------ERRGYPAPIVNHNLRQKQF----KALYNQLKA  269 (271)
T ss_dssp             SCHHHHHHTCCCHH---------HHTTSCCCSSCHHHHHHHH----HHHHHHHHH
T ss_pred             CChHHhcCcccCcc---------ccCCCCccccCHHHHHHHH----HHHHHHHhh
Confidence            57899999997652         3568999999999999954    566655543