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= 014577
(422 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 685 bits (1768), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 311/415 (74%), Positives = 367/415 (88%)
Query: 1 MKVKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFLKLAGQPLWAXXXXXXX 60
+KVKDYAS+ G+EVFSPVSHTLFNPA II+KNGGKPPL+YQSFLK+AG+P A
Sbjct: 122 VKVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVAGEPSCAKSELVMS 181
Query: 61 XXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWVAN 120
GD+G ISEVP++EELGYK Q + +PFRGGESEALK+L +SISDK WVAN
Sbjct: 182 YSSLPPIGDIGNLGISEVPSLEELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVAN 241
Query: 121 FEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQLLW 180
FEKPKGDPSA+LKPATTV+SPYLKFGCLSSRYFYQCL ++Y++VKKHTSPPVSL+GQLLW
Sbjct: 242 FEKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCLQNIYKDVKKHTSPPVSLLGQLLW 301
Query: 181 RDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLRKWGW 240
R+FFYT AFGTPNFD+MKGNRICKQIPW+ D +LAAWR+ +TGYPWIDAIMVQL KWGW
Sbjct: 302 REFFYTTAFGTPNFDKMKGNRICKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWGW 361
Query: 241 MHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQYNRI 300
MHHLARHCVACFLTRGD+F+HWE+GRDVF+RLLIDSDWAINNGNW+WLSCSSFFYQ+NRI
Sbjct: 362 MHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFFYQFNRI 421
Query: 301 YSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVS 360
YSP+SFGKKYDP+G YIRHFLPVLKDMPK+YIYEPWTAPL++QT+A CI+G+DYP P+V
Sbjct: 422 YSPISFGKKYDPDGKYIRHFLPVLKDMPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVL 481
Query: 361 HDSASKECKRKLGEAYALNQKLNGQVSEDGLKNLRRKFEGEENQESGRRQKQKTL 415
HDSASKECKRK+GEAYALN+K++G+V E+ L++LRRK + +E++ES R ++ L
Sbjct: 482 HDSASKECKRKMGEAYALNKKMDGKVDEENLRDLRRKLQKDEHEESKIRNQRPKL 536
>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 = 393 bits (1009), Expect = e-109, Method: Compositional matrix adjust.
Identities = 194/391 (49%), Positives = 258/391 (65%), Gaps = 19/391 (4%)
Query: 3 VKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFL---------KLAGQPLWA 53
V+ A G+ V + SHT++NP +I KN GK P+TYQ FL K+ G P
Sbjct: 145 VQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKL 204
Query: 54 XXXXXXXXXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSP--FRGGESEALKKLRES 111
Y + PT+++L + EEL P F GGE+EAL+++ ES
Sbjct: 205 KNMPTPPKDEVEQKDSAAY----DCPTMKQLVKR---PEELGPNKFPGGETEALRRMEES 257
Query: 112 ISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPP 171
+ D+ WVA FEKP P++ L+P+TTVLSPYLKFGCLS+R F Q L ++ + KH+ PP
Sbjct: 258 LKDEIWVARFEKPNTAPNS-LEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPP 316
Query: 172 VSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAI 231
VSL+GQL+WR+F+YTVA PNFDRM GN C QIPW + L AW RTGYP+IDAI
Sbjct: 317 VSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 232 MVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCS 291
M QLR+ GW+HHLARH VACFLTRGD+++ WE+G+ VF++LL+D DWA+N GNW+WLS S
Sbjct: 377 MRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 292 SFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIYEPWTAPLTIQTRAKCIIG 351
+FF+QY R+YSPV+FGKK DP G+YIR ++P L P IYEPW A L Q C++G
Sbjct: 437 AFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLG 496
Query: 352 RDYPAPVVSHDSASKECKRKLGEAYALNQKL 382
DYP +V H+ KE +++G AY +N+++
Sbjct: 497 TDYPHRIVKHEVVHKENIKRMGAAYKVNREV 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
Score = 390 bits (1001), Expect = e-108, Method: Compositional matrix adjust.
Identities = 193/391 (49%), Positives = 258/391 (65%), Gaps = 19/391 (4%)
Query: 3 VKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFL---------KLAGQPLWA 53
V+ A G+ V + SHT++NP +I KN GK P+TYQ FL K+ G P
Sbjct: 145 VQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKL 204
Query: 54 XXXXXXXXXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSP--FRGGESEALKKLRES 111
Y + PT+++L + EEL P F GGE+EAL+++ ES
Sbjct: 205 KNMPTPPKDEVEQKDSAAY----DCPTMKQLVKR---PEELGPNKFPGGETEALRRMEES 257
Query: 112 ISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPP 171
+ D+ WVA FEKP P++ L+P+TTVLSPYLKFGCLS+R F Q L ++ + KH+ PP
Sbjct: 258 LKDEIWVARFEKPNTAPNS-LEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPP 316
Query: 172 VSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAI 231
VSL+GQL+WR+F+YTVA PNFDRM GN C QIPW + L AW RTGYP+IDAI
Sbjct: 317 VSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 232 MVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCS 291
M QLR+ GW+H+LARH VACFLTRGD+++ WE+G+ VF++LL+D DWA+N GNW+WLS S
Sbjct: 377 MRQLRQEGWIHNLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 292 SFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIYEPWTAPLTIQTRAKCIIG 351
+FF+QY R+YSPV+FGKK DP G+YIR ++P L P IYEPW A L Q C++G
Sbjct: 437 AFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLG 496
Query: 352 RDYPAPVVSHDSASKECKRKLGEAYALNQKL 382
DYP +V H+ KE +++G AY +N+++
Sbjct: 497 TDYPHRIVKHEVVHKENIKRMGAAYKVNREV 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
Score = 389 bits (999), Expect = e-108, Method: Compositional matrix adjust.
Identities = 193/391 (49%), Positives = 257/391 (65%), Gaps = 19/391 (4%)
Query: 3 VKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFL---------KLAGQPLWA 53
V+ A G+ V + SHT++NP +I KN GK P+TYQ FL K+ G P
Sbjct: 145 VQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKL 204
Query: 54 XXXXXXXXXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSP--FRGGESEALKKLRES 111
Y + PT+++L + EEL P F GGE+EAL+++ ES
Sbjct: 205 KNMPTPPKDEVEQKDSAAY----DCPTMKQLVKR---PEELGPNKFPGGETEALRRMEES 257
Query: 112 ISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPP 171
+ D+ WVA FEKP P++ L+P+TTVLSPYLKFGCLS+R F Q L ++ + KH+ PP
Sbjct: 258 LKDEIWVARFEKPNTAPNS-LEPSTTVLSPYLKFGCLSARLFNQKLKEIIKRQPKHSQPP 316
Query: 172 VSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAI 231
VSL+GQL+WR+F+YTVA PNFDRM GN C QIPW + L AW RTGYP+IDAI
Sbjct: 317 VSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 232 MVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCS 291
M QLR+ GW+HHLAR VACFLTRGD+++ WE+G+ VF++LL+D DWA+N GNW+WLS S
Sbjct: 377 MRQLRQEGWIHHLARMAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 292 SFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIYEPWTAPLTIQTRAKCIIG 351
+FF+QY R+YSPV+FGKK DP G+YIR ++P L P IYEPW A L Q C++G
Sbjct: 437 AFFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVLG 496
Query: 352 RDYPAPVVSHDSASKECKRKLGEAYALNQKL 382
DYP +V H+ KE +++G AY +N+++
Sbjct: 497 TDYPHRIVKHEVVHKENIKRMGAAYKVNREV 527
>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 = 244 bits (624), Expect = 5e-65, Method: Compositional matrix adjust.
Identities = 137/393 (34%), Positives = 211/393 (53%), Gaps = 39/393 (9%)
Query: 3 VKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFL---KLAGQPLWAXXXXXX 59
++ I+ VSHTL++P +I+ NGG PPLTYQ FL ++ G P
Sbjct: 121 IRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQIIGLP--------P 172
Query: 60 XXXXXXXXGDVGYFEI-----------SEVPTVEELGYKGYGQEELSPF--RGGESEALK 106
D + E+ ++PT E G L+ RGGE++AL
Sbjct: 173 RPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAKINWRGGETQALL 232
Query: 107 KLRE--SISDKEWVANFEKP-KGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQN 163
L E + + F P + P+ + P + +S +L+FGCLS R FY + D+++N
Sbjct: 233 LLDERLKVEQHAFERGFYLPNQALPNIHDSPKS--MSAHLRFGCLSVRRFYWSVHDLFKN 290
Query: 164 VK-------KHTSPPVSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDE-LL 215
V+ + + GQL+WR++FYT++ PN+DRM+GN IC IPW+ +E LL
Sbjct: 291 VQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSIPWAKPNENLL 350
Query: 216 AAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLID 275
+WR +TG+P ID M QL GW+HH R+ VA FLTRG ++ WE G F + L+D
Sbjct: 351 QSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGLQHFLKYLLD 410
Query: 276 SDWAINNGNWLWLSCSSF--FYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIY 333
+DW++ GNW+W+S S+F + + PV+ K+ DP+G YI+ ++P L ++PKE+++
Sbjct: 411 ADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVH 470
Query: 334 EPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASK 366
EPW Q + +C+IG YP ++ A K
Sbjct: 471 EPWRMSAEQQEQYECLIGVHYPERIIDLSMAVK 503
>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 = 155 bits (392), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 119/393 (30%), Positives = 184/393 (46%), Gaps = 33/393 (8%)
Query: 2 KVKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFLK---LAGQPLWAXXXXX 58
+V TAGI L +P D I G P Y F K +P
Sbjct: 112 QVAAALKTAGIRAVQLWDQLLHSP-DQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTE 170
Query: 59 XXXXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWV 118
+ +SE+PT+++LG+ G + P GE+ A+ +L+E D+ +
Sbjct: 171 LVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEP---GETAAIARLQE-FCDRA-I 225
Query: 119 ANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQ- 177
A+++ + P+ + T+ LSP LKFG + R +Q + + + + V Q
Sbjct: 226 ADYDPQRNFPA---EAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQ 282
Query: 178 -LLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLR 236
L WR+F+ + P+ + +Q PW N + L AW +A+TGYP +DA M QL
Sbjct: 283 ELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLT 342
Query: 237 KWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQ 296
+ GWMH+ R VA FLT+ D+ + W +G F + L+D D A NNG W W + S +
Sbjct: 343 ETGWMHNRCRMIVASFLTK-DLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPK 401
Query: 297 YNRIYSPVSFGKKYDPNGNYIRHFLPVLKDM-PKEYIYEPWTAPLTIQTRAKCIIGRDYP 355
RI++P S KK+D YI+ +LP L+ + PK+ I T I R YP
Sbjct: 402 PLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITP----------IERRGYP 451
Query: 356 APVVSHDSASKECKRKLGEAYALNQKLNGQVSE 388
AP+V+H+ K+ K AL +L ++E
Sbjct: 452 APIVNHNLRQKQFK-------ALYNQLKAAIAE 477
>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 = 155 bits (391), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 115/374 (30%), Positives = 177/374 (47%), Gaps = 26/374 (6%)
Query: 2 KVKDYASTAGIEVFSPVSHTLFNPADIIQKNGGKPPLTYQSFLK---LAGQPLWAXXXXX 58
+V TAGI L +P D I G P Y F K +P
Sbjct: 111 QVAAALKTAGIRAVQLWDQLLHSP-DQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTE 169
Query: 59 XXXXXXXXXGDVGYFEISEVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWV 118
+ +SE+PT+++LG+ G + P GE+ A+ +L+E D+ +
Sbjct: 170 LVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEP---GETAAIARLQE-FCDRA-I 224
Query: 119 ANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQ- 177
A+++ + P+ + T+ LSP LKFG + R +Q + + + + V Q
Sbjct: 225 ADYDPQRNFPA---EAGTSGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQ 281
Query: 178 -LLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLR 236
L WR+F+ + P+ + +Q PW N + L AW +A+TGYP +DA M QL
Sbjct: 282 ELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLT 341
Query: 237 KWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQ 296
+ GWMH+ R VA FLT+ D+ + W +G F + L+D D A NNG W W + S +
Sbjct: 342 ETGWMHNRCRMIVASFLTK-DLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPK 400
Query: 297 YNRIYSPVSFGKKYDPNGNYIRHFLPVLKDM-PKEYIYEPWTAPLTIQTRAKCIIGRDYP 355
RI++P S KK+D YI+ +LP L+ + PK+ I T I R YP
Sbjct: 401 PLRIFNPASQAKKFDATATYIKRWLPELRHVHPKDLISGEITP----------IERRGYP 450
Query: 356 APVVSHDSASKECK 369
AP+V+H+ K+ K
Sbjct: 451 APIVNHNLRQKQFK 464
>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 = 145 bits (367), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 94/284 (33%), Positives = 148/284 (52%), Gaps = 21/284 (7%)
Query: 97 FRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQC 156
F+GGE+ L +L++ + + ++++ + ++ SP+L GCLS R+
Sbjct: 212 FQGGETAGLARLQDYFWHGDRLKDYKETRNGMVG--ADYSSKFSPWLALGCLSPRF---- 265
Query: 157 LTDVYQNVKKHTSPPVS------LVGQLLWRDFFYTVA--FGTPNFDRMKGNRICKQIPW 208
+YQ VK++ VS L+ +LLWRDFF VA +G F+R G + K PW
Sbjct: 266 ---IYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNR--GGLLNKNFPW 320
Query: 209 SNDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDV 268
D WR +TGYP +DA M +L G+M + R VA FL + ++ + W G +
Sbjct: 321 QEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCK-NLGIDWRWGAEW 379
Query: 269 FDRLLIDSDWAINNGNWLWLSCSSFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMP 328
F+ LID D N GNW + + + R ++ ++YDP G Y+RH+LP LK++P
Sbjct: 380 FESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYLRHWLPELKNLP 439
Query: 329 KEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKECKRKL 372
+ I++PW T Q + +G DYP P V+ S E +RK+
Sbjct: 440 GDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQ-SVEARRKI 482
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 133 bits (335), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 89/276 (32%), Positives = 133/276 (48%), Gaps = 35/276 (12%)
Query: 101 ESEALKKLRESISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTDV 160
E A+ +LR+ + +E+ + P+ T+ LS L G LS R QCL +
Sbjct: 204 EKAAIAQLRQFCQNG--AGEYEQQRDFPAV---EGTSRLSASLATGGLSPR---QCLHRL 255
Query: 161 YQNVKKHTSPPVSLV--GQLLWRDFFYTVAFGTPNFDRMKGNRICKQIP---------WS 209
+ V +L+WR+F+ + P+ +CK P W
Sbjct: 256 LAEQPQALDGGAGSVWLNELIWREFYRHLITYHPS--------LCKHRPFIAWTDRVQWQ 307
Query: 210 NDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVF 269
++ L AW+E +TGYP +DA M QL GWMH+ R A FL + D+ + W +G F
Sbjct: 308 SNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVK-DLLIDWREGERYF 366
Query: 270 DRLLIDSDWAINNGNWLW-LSCSSFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMP 328
LID D A NNG W W S + Y RI++P + G+K+D G +IR +LP L+D+P
Sbjct: 367 MSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVP 426
Query: 329 KEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSA 364
+ ++EPW + K + DYP P+V H A
Sbjct: 427 GKVVHEPW------KWAQKAGVTLDYPQPIVEHKEA 456
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 124 bits (311), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 82/260 (31%), Positives = 134/260 (51%), Gaps = 6/260 (2%)
Query: 77 EVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPA- 135
+VPT+E+LG + F GGES + ++ E K+ + +++ + + L P
Sbjct: 228 DVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETR---NGMLGPDY 284
Query: 136 TTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFD 195
+T SP+L FGC+S R+ Y+ + Y+ + + ++ +L+WRD+F ++ N
Sbjct: 285 STKFSPWLAFGCISPRFIYEEVQR-YEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSL 343
Query: 196 RMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTR 255
G Q WS D +L +WR+A+TGYP IDA M +L G+M + R V FL R
Sbjct: 344 FHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR 403
Query: 256 GDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQYNRIYSPVSFGKKYDPNGN 315
DM + W G + F+ L+D D N GNW + + + +R +S + YDP G
Sbjct: 404 -DMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGE 462
Query: 316 YIRHFLPVLKDMPKEYIYEP 335
Y+ +L L+ +PKE + P
Sbjct: 463 YVAFWLQQLRRLPKEKRHWP 482
>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 = 124 bits (311), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 82/260 (31%), Positives = 134/260 (51%), Gaps = 6/260 (2%)
Query: 77 EVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPA- 135
+VPT+E+LG + F GGES + ++ E K+ + +++ + + L P
Sbjct: 229 DVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETR---NGMLGPDY 285
Query: 136 TTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFD 195
+T SP+L FGC+S R+ Y+ + Y+ + + ++ +L+WRD+F ++ N
Sbjct: 286 STKFSPWLAFGCISPRFIYEEVQR-YEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSL 344
Query: 196 RMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTR 255
G Q WS D +L +WR+A+TGYP IDA M +L G+M + R V FL R
Sbjct: 345 FHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR 404
Query: 256 GDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQYNRIYSPVSFGKKYDPNGN 315
DM + W G + F+ L+D D N GNW + + + +R +S + YDP G
Sbjct: 405 -DMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGE 463
Query: 316 YIRHFLPVLKDMPKEYIYEP 335
Y+ +L L+ +PKE + P
Sbjct: 464 YVAFWLQQLRRLPKEKRHWP 483
>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 = 120 bits (302), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 85/264 (32%), Positives = 126/264 (47%), Gaps = 35/264 (13%)
Query: 97 FRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQC 156
FRGG E L L ++ + + D A + LSP+LKFG +S R Y
Sbjct: 185 FRGGRREGLYLLHRNVDFR---------RRDYPA--ENNNYRLSPHLKFGTISMREAYYT 233
Query: 157 LTDVYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLA 216
Q K+ V +L WRDFF +A+ P+ R I W N++
Sbjct: 234 -----QKGKEE------FVRELYWRDFFTLLAYYNPHVFGHCYRREYDNISWENNESYFE 282
Query: 217 AWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDS 276
AW+E RTGYP IDA M L G+++ R VA FL + +FV W G F L+D
Sbjct: 283 AWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKV-LFVDWRWGERYFATKLVDY 341
Query: 277 DWAINNGNWLWLSCSSFFYQYNRIYSPVSFGKKYDPNGNYIRHFLPVLKDMPKEYIYEPW 336
D AINNGNW W++ + Y + R+++P +K+DP +I+ ++ LKD+P I+ +
Sbjct: 342 DPAINNGNWQWIASTGVDYMF-RVFNPWKQQEKFDPEAKFIKEWVEELKDVPPSIIHSIY 400
Query: 337 TAPLTIQTRAKCIIGRDYPAPVVS 360
+ YP+P+V+
Sbjct: 401 KTKVP-----------GYPSPIVN 413
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 81/260 (31%), Positives = 134/260 (51%), Gaps = 7/260 (2%)
Query: 77 EVPTVEELGYKGYGQEELSPFRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPA- 135
+VPT+E+LG + F GGES + ++ E K+ + +++ + + L P
Sbjct: 229 DVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETR---NGMLGPDY 285
Query: 136 TTVLSPYLKFGCLSSRYFYQCLTDVYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFD 195
+T SP+L FGC+S R+ Y+ + Y+ + + ++ +L+WRD+F ++ N
Sbjct: 286 STKFSPWLAFGCISPRFIYEEVQR-YEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSL 344
Query: 196 RMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTR 255
G WS D +L +WR+A+TGYP IDA M +L G+M + R V FL R
Sbjct: 345 FHLGGPRNVNGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR 404
Query: 256 GDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCSSFFYQYNRIYSPVSFGKKYDPNGN 315
DM + W G + F+ L+D D N GNW + + + + +R +S + YDP G
Sbjct: 405 -DMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVNDPRE-DRYFSIPKQAQNYDPEGE 462
Query: 316 YIRHFLPVLKDMPKEYIYEP 335
Y+ +L L+ +PKE + P
Sbjct: 463 YVAFWLQQLRRLPKEKRHWP 482
>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 = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 78/265 (29%), Positives = 128/265 (48%), Gaps = 12/265 (4%)
Query: 136 TTVLSPYLKFGCLSSRYFYQCLTDVYQNV-----KKHTSPPVSL-VGQLLWRDFFYTVAF 189
T+ LSP+L FG +S R + L + Q + V+L + + R++ ++F
Sbjct: 247 TSFLSPHLHFGEVSVRKVFH-LVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYISF 305
Query: 190 GTPNFDRMKGNRICKQIPWSNDDELLAAWREARTGYPWIDAIMVQLRKWGWMHHLARHCV 249
P K PW+ D+ AWR+ RTGYP +DA M +L GW+H R V
Sbjct: 306 NHPYSHERPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVV 365
Query: 250 ACFLTRGDMFVHWEKGRDVFDRLLIDSDWAINNGNWLWLSCS-SFFYQYNRIYSPVSFGK 308
+ F + + + W G F L+D+D + W +++ + +++RI +P G
Sbjct: 366 SSFFVKV-LQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGY 424
Query: 309 KYDPNGNYIRHFLPVLKDMPKEYIYEPWTAPLTIQTRAKCIIGRDYPAPVVSHDSASKEC 368
K+DPNG Y+R +LP L +P ++I+ PW AP ++ A +G +YP P+V D A
Sbjct: 425 KFDPNGEYVRRWLPELSRLPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARL 484
Query: 369 KRKLGEAYALNQKLNGQV---SEDG 390
L + + L + SE+G
Sbjct: 485 HEALSQMWQLEAASRAAIENGSEEG 509
>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 = 96.7 bits (239), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 64/224 (28%), Positives = 102/224 (45%), Gaps = 13/224 (5%)
Query: 100 GESEALKKLRESISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQCLTD 159
GE AL LR + K E+ + D + LSPY G LS R
Sbjct: 178 GEEAALAGLRAFLEAKLPRYAEERDRLDGEG-----GSRLSPYFALGVLSPR------LA 226
Query: 160 VYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAAWR 219
++ ++ V +LLWRDF Y + + P + + PW D+ L AW
Sbjct: 227 AWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWY 286
Query: 220 EARTGYPWIDAIMVQLRKWGWMHHLARHCVACFLTRGDMFVHWEKGRDVFDRLLIDSDWA 279
E +TG P +DA M +L G++ + AR A F + + + W++ + F LL+D D A
Sbjct: 287 EGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVK-HLLLPWKRCEEAFRHLLLDGDRA 345
Query: 280 INNGNWLWLSCSSF-FYQYNRIYSPVSFGKKYDPNGNYIRHFLP 322
+N W W Y R+++PV G+++DP G +++ + P
Sbjct: 346 VNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAP 389
>pdb|2XRY|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei
pdb|2XRZ|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
pdb|2XRZ|B Chain B, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
Length = 482
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 97 FRGGESEALKKLRESISDKEWVANFEKPKGDPSAYLKPATTVLSPYLKFGCLSSRYFYQC 156
F GE A K + I+D+ + ++ + DP+ K + LSPYL FG +SS+ +
Sbjct: 248 FEPGEKAAKKVMESFIADR--LDSYGALRNDPT---KNMLSNLSPYLHFGQISSQ---RV 299
Query: 157 LTDVYQNVKKHTSPPVSLVGQLLWRDFFYTVAFGTPNFD 195
+ +V + S L L+W++ + P +D
Sbjct: 300 VLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYD 338
>pdb|2RP5|A Chain A, Solution Structure Of The Oligomerization Domain In Cep-1
pdb|2RP5|B Chain B, Solution Structure Of The Oligomerization Domain In Cep-1
Length = 136
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 254 TRGDMFVHWEKGRDVFDRLLIDSD 277
T GDM +EK D+F+R+ IDS
Sbjct: 90 TMGDMIREFEKHNDIFERIGIDSS 113
>pdb|3IX1|A Chain A, Periplasmic
N-Formyl-4-Amino-5-Aminomethyl-2-Methylpyrimidine
Binding Protein From Bacillus Halodurans
pdb|3IX1|B Chain B, Periplasmic
N-Formyl-4-Amino-5-Aminomethyl-2-Methylpyrimidine
Binding Protein From Bacillus Halodurans
Length = 302
Score = 28.5 bits (62), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 183 FFYTVAFGTPNFDRMKGNRICKQIPWSNDDELLAA-WREARTGYPWI 228
+F V +G P +D + I + E+LAA WR A GY W+
Sbjct: 177 YFNPVDYGVPEYDELV--LISNEAYVEESGEVLAAFWRAALKGYEWM 221
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
0.320 0.137 0.445
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,365,792
Number of Sequences: 62578
Number of extensions: 642353
Number of successful extensions: 1427
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1366
Number of HSP's gapped (non-prelim): 21
length of query: 422
length of database: 14,973,337
effective HSP length: 101
effective length of query: 321
effective length of database: 8,652,959
effective search space: 2777599839
effective search space used: 2777599839
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)