BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 013801
(436 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NP7|A Chain A, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
pdb|1NP7|B Chain B, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
Length = 489
Score = 212 bits (539), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 115/313 (36%), Positives = 176/313 (56%), Gaps = 27/313 (8%)
Query: 127 IVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRASFLIESVS 186
+VWFRNDLR+HD+E L+ A +++ VYC+DPR + ++ GF KTGP+R++FL +SV
Sbjct: 9 LVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQ 68
Query: 187 DLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAMKDE 246
+L ++LQ G+ L+V G PE V+ ++AK I A +Y HREV+ +E+ E + +
Sbjct: 69 NLAESLQKVGNKLLVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLTIL 128
Query: 247 GIEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKV--KGVEIRKTIEALDQLKGLPSRG 304
GIE K +WGSTL H +DLPF + ++P + FR+ + K + IR A QL P+
Sbjct: 129 GIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIK 188
Query: 305 DVEPGDIPSLL-DLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEYQAQPPKGNK 363
P + + + + +GGET L RL+ + + K K
Sbjct: 189 LELTAPPPEFFPQINFDHRSVL---------AFQGGETAGLARLQDYF--WHGDRLKDYK 237
Query: 364 DGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGESGSSGAGSN 423
+ + + GA++S K SPWLA+GCLSPR ++ E+K+ + S ++
Sbjct: 238 E-TRNGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYE------------QERVSNDSTH 284
Query: 424 WLMFELLWRDFFR 436
WL+FELLWRDFFR
Sbjct: 285 WLIFELLWRDFFR 297
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 204 bits (519), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 119/316 (37%), Positives = 180/316 (56%), Gaps = 27/316 (8%)
Query: 125 ASIVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSS-GFDKTGPYRASFLIE 183
+I+WFRNDLRV DN++L A + S ++LPVYC DPR + + F KTG R FL+E
Sbjct: 42 VTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLME 101
Query: 184 SVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAM 243
+ DLRKNL RG +L++R GKPE +L LAK GA V+AH+E +EV E + +
Sbjct: 102 CLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGL 161
Query: 244 KDEG--IEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKG-VEIRKTIEALDQLKGL 300
K G +++ WGST+YH DDLPF + ++P Y FR+ V+ IR + L
Sbjct: 162 KRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPT 221
Query: 301 PSRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEYQAQPPK 360
PS D GD+P+L LG+ + +++G + GGE+ + R+ F ++ K
Sbjct: 222 PSVDDW--GDVPTLEKLGV-EPQEVTRGMR-----FVGGESAGVGRV--FEYFWKKDLLK 271
Query: 361 GNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGESGSSGA 420
K+ + + G ++S K SPWLA GC+SPR +++E+++ A +
Sbjct: 272 VYKE-TRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNS----------- 319
Query: 421 GSNWLMFELLWRDFFR 436
+ W++FEL+WRD+FR
Sbjct: 320 -TYWVLFELIWRDYFR 334
>pdb|2IJG|X Chain X, Crystal Structure Of Cryptochrome 3 From Arabidopsis
Thaliana
pdb|2VTB|A Chain A, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|C Chain C, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|D Chain D, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|E Chain E, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|F Chain F, Structure Of Cryptochrome 3 - Dna Complex
Length = 526
Score = 204 bits (519), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 119/316 (37%), Positives = 180/316 (56%), Gaps = 27/316 (8%)
Query: 125 ASIVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSS-GFDKTGPYRASFLIE 183
+I+WFRNDLRV DN++L A + S ++LPVYC DPR + + F KTG R FL+E
Sbjct: 42 VTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLME 101
Query: 184 SVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAM 243
+ DLRKNL RG +L++R GKPE +L LAK GA V+AH+E +EV E + +
Sbjct: 102 CLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGL 161
Query: 244 KDEG--IEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKG-VEIRKTIEALDQLKGL 300
K G +++ WGST+YH DDLPF + ++P Y FR+ V+ IR + L
Sbjct: 162 KRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPT 221
Query: 301 PSRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEYQAQPPK 360
PS D GD+P+L LG+ + +++G + GGE+ + R+ F ++ K
Sbjct: 222 PSVDDW--GDVPTLEKLGV-EPQEVTRGMR-----FVGGESAGVGRV--FEYFWKKDLLK 271
Query: 361 GNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGESGSSGA 420
K+ + + G ++S K SPWLA GC+SPR +++E+++ A +
Sbjct: 272 VYKE-TRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNS----------- 319
Query: 421 GSNWLMFELLWRDFFR 436
+ W++FEL+WRD+FR
Sbjct: 320 -TYWVLFELIWRDYFR 334
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 204 bits (519), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 119/316 (37%), Positives = 180/316 (56%), Gaps = 27/316 (8%)
Query: 125 ASIVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSS-GFDKTGPYRASFLIE 183
+I+WFRNDLRV DN++L A + S ++LPVYC DPR + + F KTG R FL+E
Sbjct: 41 VTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLME 100
Query: 184 SVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAM 243
+ DLRKNL RG +L++R GKPE +L LAK GA V+AH+E +EV E + +
Sbjct: 101 CLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVDVERLVNQGL 160
Query: 244 KDEG--IEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKG-VEIRKTIEALDQLKGL 300
K G +++ WGST+YH DDLPF + ++P Y FR+ V+ IR + L
Sbjct: 161 KRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPT 220
Query: 301 PSRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEYQAQPPK 360
PS D GD+P+L LG+ + +++G + GGE+ + R+ F ++ K
Sbjct: 221 PSVDDW--GDVPTLEKLGV-EPQEVTRGMR-----FVGGESAGVGRV--FEYFWKKDLLK 270
Query: 361 GNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGESGSSGA 420
K+ + + G ++S K SPWLA GC+SPR +++E+++ A +
Sbjct: 271 VYKE-TRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVANNS----------- 318
Query: 421 GSNWLMFELLWRDFFR 436
+ W++FEL+WRD+FR
Sbjct: 319 -TYWVLFELIWRDYFR 333
>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure
pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure
pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure
Length = 537
Score = 94.7 bits (234), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 93/319 (29%), Positives = 141/319 (44%), Gaps = 27/319 (8%)
Query: 125 ASIVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPR----DYGKSSSGFDKTGPYRASF 180
S++WFR LRVHDN +L A+ S + PV+ DP D S G + G R F
Sbjct: 6 GSLIWFRKGLRVHDNPALEYASKGSEFMYPVFVIDPHYMESDPSAFSPGSSRAGVNRIRF 65
Query: 181 LIESVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIE 240
L+ES+ DL +L+ GS L+V G+P VLV + + + + K++
Sbjct: 66 LLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKVKRLCFEYDTDPYYQALDVKVK 125
Query: 241 AAMKDEGIEVKYFWGSTLYHLDDLPFK-LGEMPTNYGGFREKVKGVEIRKTIEALDQLKG 299
G+EV TL++ + K G+ P +Y F KV G E +
Sbjct: 126 DYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFL-KVAGEPSCAKSELVMSYSS 184
Query: 300 LPSRGDV---EPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEYQA 356
LP GD+ ++PSL +LG +GGE+EAL+RL K ++ +A
Sbjct: 185 LPPIGDIGNLGISEVPSLEELGYKDDEQADW------TPFRGGESEALKRLTKSISD-KA 237
Query: 357 QPPKGNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGESG 416
K S + + +SP+L GCLS R + L+ + D +
Sbjct: 238 WVANFEKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCLQNI---------YKDVKKH 288
Query: 417 SSGAGSNWLMFELLWRDFF 435
+S S L+ +LLWR+FF
Sbjct: 289 TSPPVS--LLGQLLWREFF 305
>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion
pdb|3CVY|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Repaired
Ds Dna
pdb|2WB2|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Double
Stranded Dna Containing A T(6-4)c Photolesion
pdb|3CVV|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion And F0 Cofactor
pdb|2WQ6|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(Dewar)c Lesion
pdb|2WQ7|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(6-4)c Lesion
Length = 543
Score = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 86/336 (25%), Positives = 147/336 (43%), Gaps = 56/336 (16%)
Query: 123 RRASIV-WFRNDLRVHDNESLN---TANNES---VSVLPVYCFDPRDYGKSSSGFDKTGP 175
+R+++V WFR LR+HDN +L+ TA N + V P++ DP + + G
Sbjct: 27 QRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDP-----GILDWMQVGA 81
Query: 176 YRASFLIESVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKS 235
R FL +++ DL L+ S L V GKP V + K+ + + ++ V
Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTR 141
Query: 236 EEKIEAAMKDEGIEVKYFWGSTLYHLDDLPFK-LGEMPTNYGGFREKVKGVEIRKTIEAL 294
+ ++ K EG+ V+ T+Y+ + + K LG+ P Y F V+ +++ K +
Sbjct: 142 DAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVP 201
Query: 295 DQLKGLPS--RGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAA 352
++LK +P+ + +VE D + + Q + P N GGETEAL+R+
Sbjct: 202 EKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGP--NKFPGGETEALRRM----- 254
Query: 353 EYQAQPPKGNKDGNHDSIYGANF-------------SCKISPWLAMGCLSPRSMFDELKK 399
++ D I+ A F + +SP+L GCLS R +LK+
Sbjct: 255 ----------EESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE 304
Query: 400 TATSISAASKWNDGESGSSGAGSNWLMFELLWRDFF 435
I K + G +L+WR+F+
Sbjct: 305 I---IKRQPKHSQPPVSLIG--------QLMWREFY 329
>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
Score = 85.5 bits (210), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 86/336 (25%), Positives = 147/336 (43%), Gaps = 56/336 (16%)
Query: 123 RRASIV-WFRNDLRVHDNESLN---TANNES---VSVLPVYCFDPRDYGKSSSGFDKTGP 175
+R+++V WFR LR+HDN +L+ TA N + V P++ DP + + G
Sbjct: 27 QRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDP-----GILDWMQVGA 81
Query: 176 YRASFLIESVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKS 235
R FL +++ DL L+ S L V GKP V + K+ + + ++ V
Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTR 141
Query: 236 EEKIEAAMKDEGIEVKYFWGSTLYHLDDLPFK-LGEMPTNYGGFREKVKGVEIRKTIEAL 294
+ ++ K EG+ V+ T+Y+ + + K LG+ P Y F V+ +++ K +
Sbjct: 142 DAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVP 201
Query: 295 DQLKGLPS--RGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAA 352
++LK +P+ + +VE D + + Q + P N GGETEAL+R+
Sbjct: 202 EKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGP--NKFPGGETEALRRM----- 254
Query: 353 EYQAQPPKGNKDGNHDSIYGANF-------------SCKISPWLAMGCLSPRSMFDELKK 399
++ D I+ A F + +SP+L GCLS R +LK+
Sbjct: 255 ----------EESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE 304
Query: 400 TATSISAASKWNDGESGSSGAGSNWLMFELLWRDFF 435
I K + G +L+WR+F+
Sbjct: 305 I---IKRQPKHSQPPVSLIG--------QLMWREFY 329
>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
Score = 85.1 bits (209), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 86/336 (25%), Positives = 147/336 (43%), Gaps = 56/336 (16%)
Query: 123 RRASIV-WFRNDLRVHDNESLN---TANNES---VSVLPVYCFDPRDYGKSSSGFDKTGP 175
+R+++V WFR LR+HDN +L+ TA N + V P++ DP + + G
Sbjct: 27 QRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDP-----GILDWMQVGA 81
Query: 176 YRASFLIESVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKS 235
R FL +++ DL L+ S L V GKP V + K+ + + ++ V
Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPRIFKSWRVEMLTFETDIEPYSVTR 141
Query: 236 EEKIEAAMKDEGIEVKYFWGSTLYHLDDLPFK-LGEMPTNYGGFREKVKGVEIRKTIEAL 294
+ ++ K EG+ V+ T+Y+ + + K LG+ P Y F V+ +++ K +
Sbjct: 142 DAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVP 201
Query: 295 DQLKGLPS--RGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAA 352
++LK +P+ + +VE D + + Q + P N GGETEAL+R+
Sbjct: 202 EKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGP--NKFPGGETEALRRM----- 254
Query: 353 EYQAQPPKGNKDGNHDSIYGANF-------------SCKISPWLAMGCLSPRSMFDELKK 399
++ D I+ A F + +SP+L GCLS R +LK+
Sbjct: 255 ----------EESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE 304
Query: 400 TATSISAASKWNDGESGSSGAGSNWLMFELLWRDFF 435
I K + G +L+WR+F+
Sbjct: 305 I---IKRQPKHSQPPVSLIG--------QLMWREFY 329
>pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans
pdb|1OWM|A Chain A, Data1:dna Photolyase RECEIVED X-Rays Dose 1.2 Exp15
PhotonsMM2
pdb|1OWN|A Chain A, Data3:dna Photolyase RECEIVED X-Rays Dose 4.8 Exp15
PhotonsMM2
pdb|1OWO|A Chain A, Data4:photoreduced Dna Photolyase RECEIVED X-Rays Dose
1.2 Exp15 PhotonsMM2
pdb|1OWP|A Chain A, Data6:photoreduced Dna Pholyase RECEIVED X-Rays Dose 4.8
Exp15 PhotonsMM2
pdb|1QNF|A Chain A, Structure Of Photolyase
Length = 484
Score = 81.6 bits (200), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 58/231 (25%), Positives = 108/231 (46%), Gaps = 21/231 (9%)
Query: 127 IVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRASFLIESVS 186
+ W R DLR+ DN L A +S ++ ++C DP+ + P R ++L +
Sbjct: 6 LFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSAD-----MAPARVAYLQGCLQ 60
Query: 187 DLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAMKDE 246
+L++ Q GS L++ G P+ ++ +LA+ + A+AVY ++++ + ++ AA+K
Sbjct: 61 ELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTA 120
Query: 247 GIEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKGVEIRKTIEALDQLKGLPSRGDV 306
GI W L+ D + G + YG F + + + +L D+
Sbjct: 121 GIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELV------DL 174
Query: 307 EPGDIPSLLDLGLSQSAAMSQ------GGKPAANSMKGGETEALQRLKKFA 351
P + ++ L LS+ + Q GG P ++ GET A+ RL++F
Sbjct: 175 SPEQLTAIAPLLLSELPTLKQLGFDWDGGFP----VEPGETAAIARLQEFC 221
>pdb|1TEZ|A Chain A, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|B Chain B, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|C Chain C, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|D Chain D, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
Length = 474
Score = 81.3 bits (199), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 58/231 (25%), Positives = 108/231 (46%), Gaps = 21/231 (9%)
Query: 127 IVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRASFLIESVS 186
+ W R DLR+ DN L A +S ++ ++C DP+ + P R ++L +
Sbjct: 5 LFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSAD-----MAPARVAYLQGCLQ 59
Query: 187 DLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEAAMKDE 246
+L++ Q GS L++ G P+ ++ +LA+ + A+AVY ++++ + ++ AA+K
Sbjct: 60 ELQQRYQQAGSRLLLLQGDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTA 119
Query: 247 GIEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKGVEIRKTIEALDQLKGLPSRGDV 306
GI W L+ D + G + YG F + + + +L D+
Sbjct: 120 GIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELV------DL 173
Query: 307 EPGDIPSLLDLGLSQSAAMSQ------GGKPAANSMKGGETEALQRLKKFA 351
P + ++ L LS+ + Q GG P ++ GET A+ RL++F
Sbjct: 174 SPEQLTAIAPLLLSELPTLKQLGFDWDGGFP----VEPGETAAIARLQEFC 220
>pdb|2E0I|A Chain A, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|B Chain B, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|C Chain C, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|D Chain D, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
Length = 440
Score = 68.2 bits (165), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 80/321 (24%), Positives = 124/321 (38%), Gaps = 84/321 (26%)
Query: 126 SIVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRA----SFL 181
I FR DLR+ DN LN A +E V+PV+ DPR PY++ SF+
Sbjct: 3 CIFIFRRDLRLEDNTGLNYALSECDRVIPVFIADPRQL--------INNPYKSEFAVSFM 54
Query: 182 IESVSDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEVKSEEKIEA 241
I S+ +L L+ +GS L V G+ E V+ + DA+Y + + + + +EKI
Sbjct: 55 INSLLELDDELRKKGSRLNVFFGEAEKVVSRFFNKV--DAIYVNEDYTPFSISRDEKIRK 112
Query: 242 AMKDEGIEVKYFWG-----STLYHLDDLPFKLGEMPTNYGGFREKVKGVEIR--KTIEAL 294
++ GIE K + +L+H N+ F +V V++R +T+E
Sbjct: 113 VCEENGIEFKAYEDYLLTPKSLFH-----------HRNFTSFYNEVSKVKVREPETME-- 159
Query: 295 DQLKGLPSRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKFAAEY 354
G + D +D L+ K + +GG E L L +
Sbjct: 160 ---------GSFDVTDSSMNVDFLLTFK-------KIESPLFRGGRREGLYLLHR----- 198
Query: 355 QAQPPKGNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGE 414
N D N + ++SP L G +S R E
Sbjct: 199 -------NVDFRRRDYPAENNNYRLSPHLKFGTISMR----------------------E 229
Query: 415 SGSSGAGSNWLMFELLWRDFF 435
+ + G + EL WRDFF
Sbjct: 230 AYYTQKGKEEFVRELYWRDFF 250
>pdb|4GU5|A Chain A, Structure Of Full-Length Drosophila Cryptochrome
pdb|4GU5|B Chain B, Structure Of Full-Length Drosophila Cryptochrome
Length = 539
Score = 65.9 bits (159), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 84/346 (24%), Positives = 141/346 (40%), Gaps = 60/346 (17%)
Query: 121 AIRRASIVWFRNDLRVHDNESLNTA---NNESVSVLPVYCFDPRDYGKSSSGFDKTGPYR 177
A R A+++WFR+ LR+HDN +L A ++ ++++PV+ FD G + G++ R
Sbjct: 2 ATRGANVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAGTKNVGYN-----R 56
Query: 178 ASFLIESVSDLRKNLQA----RGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSHDEV 233
FL++S+ D+ LQA RG LV G+P + L + + + ++
Sbjct: 57 MRFLLDSLQDIDDQLQAATDGRGRLLVFE-GEPAYIFRRLHEQVRLHRICIEQDCEPIWN 115
Query: 234 KSEEKIEAAMKDEGIEVKYFWGSTLYHLDDLPFKLGEM-PTNYGGFREKVKGVEIRKTIE 292
+ +E I + ++ I+ TL+ + G + P Y F V
Sbjct: 116 ERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTV---------- 165
Query: 293 ALDQLKGLPSR--GDVEPGDIPSL-LDLGLSQSAAMSQG--------------GKPAANS 335
Q+ GLP R D D + LD +S + + G A +
Sbjct: 166 ---QIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAKIN 222
Query: 336 MKGGETEAL----QRLK--KFAAEYQAQPPKGNKDGNHDSIYGANFSCKISPWLAMGCLS 389
+GGET+AL +RLK + A E P HDS +S L GCLS
Sbjct: 223 WRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDS------PKSMSAHLRFGCLS 276
Query: 390 PRSMFDELKKTATSISAASKWNDGESGSSGAGSNWLMFELLWRDFF 435
R + + ++ + G G + +L+WR++F
Sbjct: 277 VRRFYWSVHDLFKNVQLRA----CVRGVQMTGGAHITGQLIWREYF 318
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 82/322 (25%), Positives = 135/322 (41%), Gaps = 55/322 (17%)
Query: 127 IVWFRNDLRVHDNESLNTA-NNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRASFLIESV 185
+VWFR DLR+HDN +L A N S VL +Y PR + + P +A + +
Sbjct: 4 LVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHN-----MSPRQAELINAQL 58
Query: 186 SDLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYAHREVSH----DEVKSEEKIEA 241
+ L+ L +G L+ R VE+ K + A+ H ++ +E + ++E
Sbjct: 59 NGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVER 118
Query: 242 AMKDEGIEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKVKGVEIRKTIEALDQLKGLP 301
A+++ + + F S + + EM + F K +++ E + + P
Sbjct: 119 ALRN--VVCEGFDDSVILPPGAVMTGNHEMYKVFTPF----KNAWLKRLREGMPECVAAP 172
Query: 302 ---SRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETEALQRLKKF----AAEY 354
S G +EP PS+ QS + E A+ +L++F A EY
Sbjct: 173 KVRSSGSIEPS--PSITLNYPRQSFDTAH--------FPVEEKAAIAQLRQFCQNGAGEY 222
Query: 355 QAQPPKGNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELKKTATSISAASKWNDGE 414
+ Q +G + ++S LA G LSPR L ++ + DG
Sbjct: 223 EQQRDFPAVEG----------TSRLSASLATGGLSPRQCLHRL------LAEQPQALDG- 265
Query: 415 SGSSGAGSNWLMFELLWRDFFR 436
GAGS WL EL+WR+F+R
Sbjct: 266 ----GAGSVWLN-ELIWREFYR 282
>pdb|1IQR|A Chain A, Crystal Structure Of Dna Photolyase From Thermus
Thermophilus
pdb|1IQU|A Chain A, Crystal Structure Of Photolyase-Thymine Complex
pdb|2J07|A Chain A, Thermus Dna Photolyase With 8-Hdf Antenna Chromophore
pdb|2J08|A Chain A, Thermus Dna Photolyase With 8-Iod-Riboflavin Antenna
Chromophore
pdb|2J09|A Chain A, Thermus Dna Photolyase With Fmn Antenna Chromophore
Length = 420
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 35/98 (35%), Positives = 51/98 (52%), Gaps = 9/98 (9%)
Query: 127 IVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRASFLIESVS 186
+VW R DLR+HD+ +L A V+ + DP + KT P R ++ +E+V
Sbjct: 5 LVWHRGDLRLHDHPALLEALARG-PVVGLVVLDPNNL--------KTTPRRRAWFLENVR 55
Query: 187 DLRKNLQARGSDLVVRVGKPETVLVELAKAIGADAVYA 224
LR+ +ARG L V G P + E A+ + A AVYA
Sbjct: 56 ALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYA 93
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 44/96 (45%), Gaps = 23/96 (23%)
Query: 339 GETEALQRLKKFAAEYQAQPPKGNKDGNHDSIYGANFSCKISPWLAMGCLSPRSMFDELK 398
GE AL L+ F +A+ P+ ++ D + G S ++SP+ A+G LSPR
Sbjct: 178 GEEAALAGLRAF---LEAKLPRYAEE--RDRLDGEGGS-RLSPYFALGVLSPR------- 224
Query: 399 KTATSISAASKWNDGESGSSGAGSNWLMFELLWRDF 434
+ W G GA W+ ELLWRDF
Sbjct: 225 --------LAAWEAERRGGEGA-RKWVA-ELLWRDF 250
>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana
pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana With Amppnp Bound
Length = 509
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 39/159 (24%), Positives = 74/159 (46%), Gaps = 11/159 (6%)
Query: 127 IVWFRNDLRVHDNESLNTANNESVSVLPVYCFDPRDYGKSSSGFDKTGPYRAS--FLIES 184
IVWFR DLRV DN +L A V+ ++ + P + G G R S +L S
Sbjct: 15 IVWFRRDLRVEDNPALAAAVRAG-PVIALFVWAPEEEGHYHPG-------RVSRWWLKNS 66
Query: 185 VSDLRKNLQARGSDLVVRVGKPETV-LVELAKAIGADAVYAHREVSHDEVKSEEKIEAAM 243
++ L +L++ G+ L+ + L+++ K+ GA ++ + + + + + +
Sbjct: 67 LAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVL 126
Query: 244 KDEGIEVKYFWGSTLYHLDDLPFKLGEMPTNYGGFREKV 282
+GI V+ F LY ++ +LG + + F E+
Sbjct: 127 TAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERC 165
>pdb|2LTA|A Chain A, Solution Nmr Structure Of De Novo Designed Protein,
Rossmann 3x1 Fold, Northeast Structural Genomics
Consortium Target Or157
Length = 110
Score = 29.6 bits (65), Expect = 3.8, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 196 GSDLVVRVGKPETVLVELAKAIGADAVYAHREVS-HDEVKSEEKIEAAMKDEGIEVK 251
GS ++V + +T L ELA+ I + + + + DE + EEKI+ +K +G EV+
Sbjct: 2 GSKIIVIISSDDTTLEELARKIKDEGLEVYILLKDKDEKRLEEKIQ-KLKSQGFEVR 57
>pdb|1BI8|B Chain B, Mechanism Of G1 Cyclin Dependent Kinase Inhibition From
The Structures Cdk6-P19ink4d Inhibitor Complex
pdb|1BI8|D Chain D, Mechanism Of G1 Cyclin Dependent Kinase Inhibition From
The Structures Cdk6-P19ink4d Inhibitor Complex
Length = 166
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 3/63 (4%)
Query: 291 IEALDQLKGLPSRGDVEPGDIPSLLDLGLSQSAAMSQGGKPAANSMKGGETE-ALQRLKK 349
+ A D+L G +RGDV+ ++ LL L A+++ GK A M G T AL+ LK+
Sbjct: 6 VRAGDRLSGAAARGDVQ--EVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQ 63
Query: 350 FAA 352
A+
Sbjct: 64 GAS 66
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.313 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,018,383
Number of Sequences: 62578
Number of extensions: 524391
Number of successful extensions: 934
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 877
Number of HSP's gapped (non-prelim): 35
length of query: 436
length of database: 14,973,337
effective HSP length: 102
effective length of query: 334
effective length of database: 8,590,381
effective search space: 2869187254
effective search space used: 2869187254
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)