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= 006521
(642 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 639 bits (1649), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 303/496 (61%), Positives = 385/496 (77%), Gaps = 3/496 (0%)
Query: 7 IVWFRRDLRIEDNPALAAAARDGSVFPVYTWCPKEEGQFYPGRVSRWWLKQSLSYLGQSL 66
IVWFRRDLR+EDNPALAAA R G V ++ W P+EEG ++PGRVSRWWLK SL+ L SL
Sbjct: 15 IVWFRRDLRVEDNPALAAAVRAGPVIALFVWAPEEEGHYHPGRVSRWWLKNSLAQLDSSL 74
Query: 67 KSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLVELGISVQ 126
+SLG L+ ++ ++A+LL+ + + A+++ FNHLYDP+SLVRDH K+ L GI+V+
Sbjct: 75 RSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVLTAQGIAVR 134
Query: 127 SYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQMEPAS-ILPPWRLVQAAGTIDGCSI 185
S+N DLLYEPWE+ DE G F+ F A+W++CL M +P S +LPP +++ +G + C
Sbjct: 135 SFNADLLYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPPKKII--SGDVSKCVA 192
Query: 186 EDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLLRYYKNRQKLGGNSTSLLSP 245
+ L ED+SEK SNALL R WSPGWSN DK LT F+ LL Y KNR+K +TS LSP
Sbjct: 193 DPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYSKNRRKADSATTSFLSP 252
Query: 246 YLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLCFNFPFTHE 305
+LHFGE+SVRKVF + +KQ+ WA E N G+ESV FL+++GLREYSRY+ FN P++HE
Sbjct: 253 HLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYISFNHPYSHE 312
Query: 306 RPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRVIVSSFAVKV 365
RPLL +LK+FPW D FKAWRQGRTGYPLVDAGMRELWATGW+H+RIRV+VSSF VKV
Sbjct: 313 RPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKV 372
Query: 366 LLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQGSKFDPEGEY 425
L LPWRWGMKYFWDTLLDADLE D LGWQYI+G+LPD E +R+D+P+ +G KFDP GEY
Sbjct: 373 LQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGYKFDPNGEY 432
Query: 426 VRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIIDLDLGRERLTQAIFKMW 485
VR+WLPEL+R+PT+WIHHPW+AP +VL+AAG+ELG NYP PI+ LD + RL +A+ +MW
Sbjct: 433 VRRWLPELSRLPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMW 492
Query: 486 EMEAADNAMDSNGTNE 501
++EAA A NG+ E
Sbjct: 493 QLEAASRAAIENGSEE 508
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 202 bits (513), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 149/478 (31%), Positives = 236/478 (49%), Gaps = 34/478 (7%)
Query: 7 IVWFRRDLRIEDNPALAAAARDGS--VFPVYTWCPKEEGQFYPGRVSRWWLKQSLSYLGQ 64
+VWFR+DLR+ DN ALAAA R+ S V +Y P++ + L+ L
Sbjct: 4 LVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQI 63
Query: 65 SLKSLGAELVLFKTESTLAALLECISAIKA----TKVVFNHLYDPVSLVRDHSIKEKLVE 120
+L G L LF+ A +E + + A T + +N+ Y+ RD ++ L
Sbjct: 64 ALAEKGIPL-LFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERAL-- 120
Query: 121 LGISVQSYNGDLLYEPWEIY---DERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAA 177
+ + ++ ++ P + E FT F W K L+ M P + P V+++
Sbjct: 121 RNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGM-PECVAAP--KVRSS 177
Query: 178 GTIDGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLLRYYKNRQKLGG 237
G+I+ L +S +++ + A L +F + Y + R
Sbjct: 178 GSIEPSPSITLNYPRQSFDTAHFPVEE------KAAIAQLRQFCQNGAGEYEQQRDFPAV 231
Query: 238 NSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLC 297
TS LS L G LS R QCL ++L + + +G + +L + RE+ R+L
Sbjct: 232 EGTSRLSASLATGGLSPR---QCL--HRLLAEQPQALDGGAG-SVWLNELIWREFYRHLI 285
Query: 298 FNFP-FTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRV 356
P RP ++ W ++ + +AW++G+TGYP+VDA MR+L +TGW+HNR+R+
Sbjct: 286 TYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRM 345
Query: 357 IVSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQG 416
I +SF VK LL+ WR G +YF L+D DL + GWQ+ + + D R+ +P QG
Sbjct: 346 ITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQG 405
Query: 417 SKFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIIDLDLGR 474
KFD EGE++RQWLPEL +P + +H PW + AGV L+YP+PI++ R
Sbjct: 406 EKFDHEGEFIRQWLPELRDVPGKVVHEPW----KWAQKAGVT--LDYPQPIVEHKEAR 457
>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 = 196 bits (499), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 163/544 (29%), Positives = 259/544 (47%), Gaps = 62/544 (11%)
Query: 3 GNRTIVWFRRDLRIEDNPALAAAARDGS-VFPVYTWCP----KEEGQFYPGR----VSRW 53
G+ +++WFR+ LR+ DNPAL A++ ++PV+ P + F PG V+R
Sbjct: 4 GSGSLIWFRKGLRVHDNPALEYASKGSEFMYPVFVIDPHYMESDPSAFSPGSSRAGVNRI 63
Query: 54 -WLKQSLSYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDH 112
+L +SL L SLK LG+ L++FK E L+ C+ K ++ F + DP D
Sbjct: 64 RFLLESLKDLDSSLKKLGSRLLVFKGEPG-EVLVRCLQEWKVKRLCFEYDTDPYYQALDV 122
Query: 113 SIKEKLVELGISVQSYNGDLLYEPWEIYDERGH----AFTTFDAYWDKCLQMQMEPA--- 165
+K+ G+ V S L+ P I ++ G ++ +F L++ EP+
Sbjct: 123 KVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSF-------LKVAGEPSCAK 175
Query: 166 -------SILPPWRLVQAAGTIDGCSIEDLGLEDESEKSSNALLGRGWSP---GWSNADK 215
S LPP + G + S+E+LG +D+ + W+P G S A K
Sbjct: 176 SELVMSYSSLPPIGDIGNLGISEVPSLEELGYKDDEQAD--------WTPFRGGESEALK 227
Query: 216 VLTEFVEQHLLRYYKNRQKLGGN-------STSLLSPYLHFGELSVRKVFQCLWMKQILW 268
LT+ + + N +K G+ +T+++SPYL FG LS R +QCL Q ++
Sbjct: 228 RLTKSISDKA--WVANFEKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCL---QNIY 282
Query: 269 AKEENFEGKESVTFFLRAMGLREYSRYLCFNFPFTHERPLLSNLKYFPWHADLGNFKAWR 328
K+ V+ L + RE+ F P + K PW+ D AWR
Sbjct: 283 -KDVKKHTSPPVSL-LGQLLWREFFYTTAFGTPNFDKMKGNRICKQIPWNEDHAMLAAWR 340
Query: 329 QGRTGYPLVDAGMRELWATGWIHNRIRVIVSSFAVKV-LLLPWRWGMKYFWDTLLDADLE 387
G+TGYP +DA M +L GW+H+ R V+ F + L + W G F L+D+D
Sbjct: 341 DGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSDWA 400
Query: 388 CDILGWQYISGSLPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWDA 447
+ W ++S S ++ R+ SP G K+DP+G+Y+R +LP L MP ++I+ PW A
Sbjct: 401 INNGNWMWLSCS-SFFYQFNRIYSPISFGKKYDPDGKYIRHFLPVLKDMPKQYIYEPWTA 459
Query: 448 PPNVLKAAGVELGLNYPKPIIDLDLGRERLTQAIFKMWEMEAADNAMDSNGTNEVVFDNS 507
P +V A +G +YPKP++ D + + KM E A + MD E + D
Sbjct: 460 PLSVQTKANCIVGKDYPKPMVLHDSASKECKR---KMGEAYALNKKMDGKVDEENLRDLR 516
Query: 508 DRIQ 511
++Q
Sbjct: 517 RKLQ 520
>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 = 194 bits (492), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 148/494 (29%), Positives = 235/494 (47%), Gaps = 31/494 (6%)
Query: 7 IVWFRRDLRIEDNPALAAA-ARDGSVFPVYTWCPK--EEGQFYPGRVSRWWLKQSLSYLG 63
+ W RRDLR+ DN LAAA A+ + ++ P+ + P RV+ +L+ L L
Sbjct: 6 LFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVA--YLQGCLQELQ 63
Query: 64 QSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLVELGI 123
Q + G+ L+L + + + + ++A V +N +P RD + L GI
Sbjct: 64 QRYQQAGSRLLLLQGDPQ-HLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGI 122
Query: 124 SVQSYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAAGTIDGC 183
LL+ P +I G+ ++ + +W K Q Q +P + P LV +
Sbjct: 123 RAVQLWDQLLHSPDQILSGSGNPYSVYGPFW-KNWQAQPKPTPVATPTELVDLSPE-QLT 180
Query: 184 SIEDLGLEDESEKSSNALLGRGWS------PGWSNADKVLTEFVEQHLLRYYKNRQKLGG 237
+I L L SE + LG W PG + A L EF ++ + Y R
Sbjct: 181 AIAPLLL---SELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAE 237
Query: 238 NSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLC 297
TS LSP L FG + +R+ +Q L + E + S+ + + + RE+ ++
Sbjct: 238 AGTSGLSPALKFGAIGIRQAWQAASAAHAL---SRSDEARNSIRVWQQELAWREFYQHAL 294
Query: 298 FNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRVI 357
++FP + P S + FPW F AW Q +TGYP+VDA MR+L TGW+HNR R+I
Sbjct: 295 YHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMI 354
Query: 358 VSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQGS 417
V+SF K L++ WR G ++F L+D DL + GWQ+ + S D L R+ +P Q
Sbjct: 355 VASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPL-RIFNPASQAK 413
Query: 418 KFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIIDLDLGRERL 477
KFD Y+++WLPEL + HP D + YP PI++ +L R++
Sbjct: 414 KFDATATYIKRWLPELRHV------HPKDLISGEITPIERR---GYPAPIVNHNL-RQKQ 463
Query: 478 TQAIFKMWEMEAAD 491
+A++ + A+
Sbjct: 464 FKALYNQLKAAIAE 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 = 193 bits (490), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 147/485 (30%), Positives = 232/485 (47%), Gaps = 31/485 (6%)
Query: 7 IVWFRRDLRIEDNPALAAA-ARDGSVFPVYTWCPK--EEGQFYPGRVSRWWLKQSLSYLG 63
+ W RRDLR+ DN LAAA A+ + ++ P+ + P RV+ +L+ L L
Sbjct: 5 LFWHRRDLRLSDNIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVA--YLQGCLQELQ 62
Query: 64 QSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLVELGI 123
Q + G+ L+L + + + + ++A V +N +P RD + L GI
Sbjct: 63 QRYQQAGSRLLLLQGDPQ-HLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGI 121
Query: 124 SVQSYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAAGTIDGC 183
LL+ P +I G+ ++ + +W K Q Q +P + P LV +
Sbjct: 122 RAVQLWDQLLHSPDQILSGSGNPYSVYGPFW-KNWQAQPKPTPVATPTELVDLSPE-QLT 179
Query: 184 SIEDLGLEDESEKSSNALLGRGWS------PGWSNADKVLTEFVEQHLLRYYKNRQKLGG 237
+I L L SE + LG W PG + A L EF ++ + Y R
Sbjct: 180 AIAPLLL---SELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAE 236
Query: 238 NSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLC 297
TS LSP L FG + +R+ +Q L + E + S+ + + + RE+ ++
Sbjct: 237 AGTSGLSPALKFGAIGIRQAWQAASAAHAL---SRSDEARNSIRVWQQELAWREFYQHAL 293
Query: 298 FNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRVI 357
++FP + P S + FPW F AW Q +TGYP+VDA MR+L TGW+HNR R+I
Sbjct: 294 YHFPSLADGPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMI 353
Query: 358 VSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQGS 417
V+SF K L++ WR G ++F L+D DL + GWQ+ + S D L R+ +P Q
Sbjct: 354 VASFLTKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKPL-RIFNPASQAK 412
Query: 418 KFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIIDLDLGRERL 477
KFD Y+++WLPEL + HP D + YP PI++ +L R++
Sbjct: 413 KFDATATYIKRWLPELRHV------HPKDLISGEITPIERR---GYPAPIVNHNL-RQKQ 462
Query: 478 TQAIF 482
+A++
Sbjct: 463 FKALY 467
>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 = 174 bits (441), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 139/480 (28%), Positives = 232/480 (48%), Gaps = 30/480 (6%)
Query: 6 TIVWFRRDLRIEDNPALAAAARDG-SVFPVYTWCPKEEGQFYPG--RVSRW---WLKQSL 59
+VWFR DLR+ D+ L A + G ++ VY + P++ Q + G + W +L+QS+
Sbjct: 8 VLVWFRNDLRLHDHEPLHRALKSGLAITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSV 67
Query: 60 SYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLV 119
L +SL+ +G +L L T + + I A + ++ L + ++ ++L
Sbjct: 68 QNLAESLQKVGNKL-LVTTGLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNLVKQLT 126
Query: 120 ELGISVQSYNGDLLYEPWEI---YDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQA 176
LGI + Y G L P ++ + FT F +K ++ + P P L
Sbjct: 127 ILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEK-KKISIRPCFFAPSQLLPSP 185
Query: 177 AGTIDGCSI--EDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLLRYYKNRQK 234
++ + E + +S A G G + G + ++ F L+ YK +
Sbjct: 186 NIKLELTAPPPEFFPQINFDHRSVLAFQG-GETAGLA---RLQDYFWHGDRLKDYKETRN 241
Query: 235 --LGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREY 292
+G + +S SP+L G LS R ++Q + E+ +S + + + R++
Sbjct: 242 GMVGADYSSKFSPWLALGCLSPRFIYQ------EVKRYEQERVSNDSTHWLIFELLWRDF 295
Query: 293 SRYLC--FNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWI 350
R++ + + LL+ K FPW D F+ WR G+TGYPLVDA MREL TG++
Sbjct: 296 FRFVAQKYGNKLFNRGGLLN--KNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFM 353
Query: 351 HNRIRVIVSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLD 410
NR R V+SF K L + WRWG ++F L+D D+ + W Y +G D + +
Sbjct: 354 SNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFN 413
Query: 411 SPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIIDL 470
P+ Q ++DP+G Y+R WLPEL +P + IH PW K GV+LG++YP+P ++
Sbjct: 414 IPK-QSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNF 472
>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 = 165 bits (417), Expect = 9e-41, Method: Compositional matrix adjust.
Identities = 131/468 (27%), Positives = 220/468 (47%), Gaps = 63/468 (13%)
Query: 7 IVWFRRDLRIEDNPALAAAARD-GSVFPVYTWCPKEE-GQFYPGRVSRWWLKQSLSYLGQ 64
I FRRDLR+EDN L A + V PV+ P++ Y + ++ SL L
Sbjct: 4 IFIFRRDLRLEDNTGLNYALSECDRVIPVFIADPRQLINNPYKSEFAVSFMINSLLELDD 63
Query: 65 SLKSLGAELVLF--KTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLVELG 122
L+ G+ L +F + E ++ + AI N Y P S+ RD I++ E G
Sbjct: 64 ELRKKGSRLNVFFGEAEKVVSRFFNKVDAIYV-----NEDYTPFSISRDEKIRKVCEENG 118
Query: 123 ISVQSYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQM-EPASILPPWRLVQAAGTID 181
I ++Y D L P ++ R F +++++ ++++ EP ++ + + ++ +D
Sbjct: 119 IEFKAYE-DYLLTPKSLFHHRN-----FTSFYNEVSKVKVREPETMEGSFDVTDSSMNVD 172
Query: 182 GCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLLRYYKNRQKLGGNSTS 241
+ K + L RG G +L V+ ++ R N+
Sbjct: 173 FLL---------TFKKIESPLFRG---GRREGLYLLHRNVD------FRRRDYPAENNNY 214
Query: 242 LLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLCFNFP 301
LSP+L FG +S+R+ + +GKE F+R + R++ L + P
Sbjct: 215 RLSPHLKFGTISMREAYYTQ-------------KGKEE---FVRELYWRDFFTLLAYYNP 258
Query: 302 FTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRVIVSSF 361
W + F+AW++GRTGYP++DAGMR L +TG+I+ R+R++V+ F
Sbjct: 259 HVFGHCYRREYDNISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFF 318
Query: 362 AVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQGSKFDP 421
VKVL + WRWG +YF L+D D + WQ+I+ + D + R+ +P Q KFDP
Sbjct: 319 LVKVLFVDWRWGERYFATKLVDYDPAINNGNWQWIASTGVD--YMFRVFNPWKQQEKFDP 376
Query: 422 EGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVELGLNYPKPIID 469
E +++++W+ EL +P IH + K G YP PI++
Sbjct: 377 EAKFIKEWVEELKDVPPSIIHSIYKT-----KVPG------YPSPIVN 413
>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 = 157 bits (398), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 129/427 (30%), Positives = 186/427 (43%), Gaps = 42/427 (9%)
Query: 7 IVWFRRDLRIEDNPALAAAARDGSVFPVYTWCPKEEGQFYPGRVSRWWLKQSLSYLGQSL 66
+VW R DLR+ D+PAL A G V + P + P R R W +++ L ++
Sbjct: 5 LVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNL-KTTPRR--RAWFLENVRALREAY 61
Query: 67 KSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKLVELGISVQ 126
++ G L + + + E +KA V + P RD ++E L V
Sbjct: 62 RARGGALWVLEG-LPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREAL-----PVP 115
Query: 127 SYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAAGTIDG-CSI 185
+ + +T F + G +G
Sbjct: 116 LHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLPP--------PEALPKGPEEGEIPR 167
Query: 186 EDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLLRYYKNRQKLGGNSTSLLSP 245
ED GL AL G L F+E L RY + R +L G S LSP
Sbjct: 168 EDPGLPLPEPGEEAALAG-------------LRAFLEAKLPRYAEERDRLDGEGGSRLSP 214
Query: 246 YLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTFFLRAMGLREYSRYLCFNFPFTHE 305
Y G LS R L A E G E ++ + R++S +L ++FP+ E
Sbjct: 215 YFALGVLSPR-----------LAAWEAERRGGEGARKWVAELLWRDFSYHLLYHFPWMAE 263
Query: 306 RPLLSNLKYFPWHADLGNFKAWRQGRTGYPLVDAGMRELWATGWIHNRIRVIVSSFAVKV 365
RPL + FPW D F+AW +G+TG PLVDA MREL ATG++ NR R+ + FAVK
Sbjct: 264 RPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKH 323
Query: 366 LLLPWRWGMKYFWDTLLDADLECDILGWQYISGSLPDGHELERLDSPEIQGSKFDPEGEY 425
LLLPW+ + F LLD D ++ GWQ+ G D R+ +P +QG + DPEG +
Sbjct: 324 LLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRW 383
Query: 426 VRQWLPE 432
+++W PE
Sbjct: 384 LKRWAPE 390
>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 = 147 bits (372), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 138/493 (27%), Positives = 221/493 (44%), Gaps = 43/493 (8%)
Query: 7 IVWFRRDLRIEDNPAL-----AAAARDGSVF--PVYTWCPKEEGQFYPGRVSRW-WLKQS 58
+ WFR+ LR+ DNPAL AA A G F P++ P G +RW +L+Q+
Sbjct: 32 VHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVG-ANRWRFLQQT 90
Query: 59 LSYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKL 118
L L L+ L + L + + + + + + F +P S+ RD ++++
Sbjct: 91 LEDLDNQLRKLNSRLFVVRGKPA-EVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLA 149
Query: 119 VELGISVQSYNGDLLYEP-WEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLV--- 174
G+ V+++ +Y P I G A T+ + Q+++ P + P +L
Sbjct: 150 KAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKV-PKVLGVPEKLKNMP 208
Query: 175 --------QAAGTIDGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLL 226
Q C ++ E N G G + A + + E ++ +
Sbjct: 209 TPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPG-----GETEALRRMEESLKDEIW 263
Query: 227 RYYKNRQKLGGNS----TSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTF 282
+ NS T++LSPYL FG LS R Q L K+I+ K + + V+
Sbjct: 264 VARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKL--KEII--KRQPKHSQPPVSL 319
Query: 283 FLRAMGLREYSRYLCFNFPFTHERPLLSNL--KYFPWHADLGNFKAWRQGRTGYPLVDAG 340
+ M RE+ + P +R +L N+ PW + +AW GRTGYP +DA
Sbjct: 320 IGQLM-WREFYYTVAAAEP-NFDR-MLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 341 MRELWATGWIHNRIRVIVSSFAVKV-LLLPWRWGMKYFWDTLLDADLECDILGWQYISGS 399
MR+L GWIHN R V+ F + L + W G + F LLD D + W ++S S
Sbjct: 377 MRQLRQEGWIHNLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 400 LPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVEL 459
H+ R+ SP G K DP+G Y+R+++PEL++ P I+ PW A +A G L
Sbjct: 437 A-FFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVL 495
Query: 460 GLNYPKPIIDLDL 472
G +YP I+ ++
Sbjct: 496 GTDYPHRIVKHEV 508
>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 = 147 bits (370), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 137/493 (27%), Positives = 222/493 (45%), Gaps = 43/493 (8%)
Query: 7 IVWFRRDLRIEDNPAL-----AAAARDGSVF--PVYTWCPKEEGQFYPGRVSRW-WLKQS 58
+ WFR+ LR+ DNPAL AA A G F P++ P G +RW +L+Q+
Sbjct: 32 VHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVG-ANRWRFLQQT 90
Query: 59 LSYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKL 118
L L L+ L + L + + + + + + F +P S+ RD ++++
Sbjct: 91 LEDLDNQLRKLNSRLFVVRGKPA-EVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLA 149
Query: 119 VELGISVQSYNGDLLYEP-WEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLV--- 174
G+ V+++ +Y P I G A T+ + Q+++ P + P +L
Sbjct: 150 KAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKV-PKVLGVPEKLKNMP 208
Query: 175 --------QAAGTIDGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLL 226
Q C ++ E N G G + A + + E ++ +
Sbjct: 209 TPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPG-----GETEALRRMEESLKDEIW 263
Query: 227 RYYKNRQKLGGNS----TSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTF 282
+ NS T++LSPYL FG LS R Q L K+I+ K + + V+
Sbjct: 264 VARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKL--KEII--KRQPKHSQPPVSL 319
Query: 283 FLRAMGLREYSRYLCFNFPFTHERPLLSNL--KYFPWHADLGNFKAWRQGRTGYPLVDAG 340
+ M RE+ + P +R +L N+ PW + +AW GRTGYP +DA
Sbjct: 320 IGQLM-WREFYYTVAAAEP-NFDR-MLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 341 MRELWATGWIHNRIRVIVSSFAVKV-LLLPWRWGMKYFWDTLLDADLECDILGWQYISGS 399
MR+L GWIH+ R+ V+ F + L + W G + F LLD D + W ++S S
Sbjct: 377 MRQLRQEGWIHHLARMAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 400 LPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVEL 459
H+ R+ SP G K DP+G Y+R+++PEL++ P I+ PW A +A G L
Sbjct: 437 A-FFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVL 495
Query: 460 GLNYPKPIIDLDL 472
G +YP I+ ++
Sbjct: 496 GTDYPHRIVKHEV 508
>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 = 145 bits (366), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 137/493 (27%), Positives = 221/493 (44%), Gaps = 43/493 (8%)
Query: 7 IVWFRRDLRIEDNPAL-----AAAARDGSVF--PVYTWCPKEEGQFYPGRVSRW-WLKQS 58
+ WFR+ LR+ DNPAL AA A G F P++ P G +RW +L+Q+
Sbjct: 32 VHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVG-ANRWRFLQQT 90
Query: 59 LSYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKL 118
L L L+ L + L + + + + + + F +P S+ RD ++++
Sbjct: 91 LEDLDNQLRKLNSRLFVVRGKPA-EVFPRIFKSWRVEMLTFETDIEPYSVTRDAAVQKLA 149
Query: 119 VELGISVQSYNGDLLYEP-WEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLV--- 174
G+ V+++ +Y P I G A T+ + Q+++ P + P +L
Sbjct: 150 KAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKV-PKVLGVPEKLKNMP 208
Query: 175 --------QAAGTIDGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFVEQHLL 226
Q C ++ E N G G + A + + E ++ +
Sbjct: 209 TPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPG-----GETEALRRMEESLKDEIW 263
Query: 227 RYYKNRQKLGGNS----TSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTF 282
+ NS T++LSPYL FG LS R Q L K+I+ K + + V+
Sbjct: 264 VARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKL--KEII--KRQPKHSQPPVSL 319
Query: 283 FLRAMGLREYSRYLCFNFPFTHERPLLSNL--KYFPWHADLGNFKAWRQGRTGYPLVDAG 340
+ M RE+ + P +R +L N+ PW + +AW GRTGYP +DA
Sbjct: 320 IGQLM-WREFYYTVAAAEP-NFDR-MLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDAI 376
Query: 341 MRELWATGWIHNRIRVIVSSFAVKV-LLLPWRWGMKYFWDTLLDADLECDILGWQYISGS 399
MR+L GWIH+ R V+ F + L + W G + F LLD D + W ++S S
Sbjct: 377 MRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSAS 436
Query: 400 LPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWDAPPNVLKAAGVEL 459
H+ R+ SP G K DP+G Y+R+++PEL++ P I+ PW A +A G L
Sbjct: 437 A-FFHQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCVL 495
Query: 460 GLNYPKPIIDLDL 472
G +YP I+ ++
Sbjct: 496 GTDYPHRIVKHEV 508
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 138 bits (348), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 142/468 (30%), Positives = 212/468 (45%), Gaps = 49/468 (10%)
Query: 2 GGNRTIVWFRRDLRIEDNPALAAA-ARDGSVFPVYTWCPK--EEGQFY----PGRVSRWW 54
G TI+WFR DLR+ DN AL A + ++ PVY P+ F+ G + +
Sbjct: 39 GKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGF 98
Query: 55 LKQSLSYLGQSLKSLGAELVL--FKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDH 112
L + L L ++L G L++ K E L +L + A + VF H +
Sbjct: 99 LMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGA----RTVFAH----KETCSEE 150
Query: 113 SIKEKLVELGISVQSYNGDLLYEPW--EIYDERGHAFTTFDA--YWDKCLQMQMEPASIL 168
E+LV G+ + N L W +Y + F FD + + + SI
Sbjct: 151 VDVERLVNQGLK-RVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIR 209
Query: 169 PPWRLVQAAGTI-------DGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFV 221
R+ + G D ++E LG+E + +G G S G +V F
Sbjct: 210 SSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVG-GESAG---VGRVFEYFW 265
Query: 222 EQHLLRYYKNRQK--LGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKES 279
++ LL+ YK + LG + ++ SP+L FG +S R +++ + E+ S
Sbjct: 266 KKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYE------EVQRYEKERVANNS 319
Query: 280 VTFFLRAMGLREYSRYL---CFNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPL 336
+ L + R+Y R+L C N F P N K W D F++WR +TGYPL
Sbjct: 320 TYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVNGK---WSQDQKLFESWRDAKTGYPL 376
Query: 337 VDAGMRELWATGWIHNRIRVIVSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYI 396
+DA M+EL TG++ NR R IV SF V+ + L WR G ++F LLD D + W Y
Sbjct: 377 IDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 436
Query: 397 SGSLPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHP 444
+G + D E P+ Q +DPEGEYV WL +L R+P E H P
Sbjct: 437 AG-VNDPREDRYFSIPK-QAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 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 = 138 bits (347), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 140/472 (29%), Positives = 214/472 (45%), Gaps = 56/472 (11%)
Query: 2 GGNRTIVWFRRDLRIEDNPALAAA-ARDGSVFPVYTWCPK--EEGQFY----PGRVSRWW 54
G TI+WFR DLR+ DN AL A + ++ PVY P+ F+ G + +
Sbjct: 39 GKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGF 98
Query: 55 LKQSLSYLGQSLKSLGAELVL--FKTESTLAALLECISAIKATKVVFNH---LYDPVSLV 109
L + L L ++L G L++ K E L +L + A + VF H + V +
Sbjct: 99 LMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGA----RTVFAHKETCSEEVDVE 154
Query: 110 RDHSIKEKLVELGISVQSYNGDLLYE----PWEIYDERGHAFTTFDAYWD-KC------- 157
R + K V ++ G +Y P++++D +T F + KC
Sbjct: 155 RLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFD-LPDVYTQFRKSVEAKCSIRSSTR 213
Query: 158 LQMQMEPASILPPWRLVQAAGTIDGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVL 217
+ + + P + W D ++E LG+E + +G G S G +V
Sbjct: 214 IPLSLGPTPSVDDWG--------DVPTLEKLGVEPQEVTRGMRFVG-GESAG---VGRVF 261
Query: 218 TEFVEQHLLRYYKNRQK--LGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFE 275
F ++ LL+ YK + LG + ++ SP+L FG +S R +++ + E+
Sbjct: 262 EYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYE------EVQRYEKERV 315
Query: 276 GKESVTFFLRAMGLREYSRYL---CFNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRT 332
S + L + R+Y R+L C N F P K W D F++WR +T
Sbjct: 316 ANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGK---WSQDQKLFESWRDAKT 372
Query: 333 GYPLVDAGMRELWATGWIHNRIRVIVSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILG 392
GYPL+DA M+EL TG++ NR R IV SF V+ + L WR G ++F LLD D +
Sbjct: 373 GYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGN 432
Query: 393 WQYISGSLPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHP 444
W Y +G D E P+ Q +DPEGEYV WL +L R+P E H P
Sbjct: 433 WTYGAGVGNDPREDRYFSIPK-QAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 483
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 138 bits (347), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 141/468 (30%), Positives = 210/468 (44%), Gaps = 48/468 (10%)
Query: 2 GGNRTIVWFRRDLRIEDNPALAAA-ARDGSVFPVYTWCPK--EEGQFY----PGRVSRWW 54
G TI+WFR DLR+ DN AL A + ++ PVY P+ F+ G + +
Sbjct: 38 GKGVTILWFRNDLRVLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGF 97
Query: 55 LKQSLSYLGQSLKSLGAELVL--FKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDH 112
L + L L ++L G L++ K E L +L + A + VF H +
Sbjct: 98 LMECLVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGA----RTVFAH----KETCSEE 149
Query: 113 SIKEKLVELGISVQSYNGDLLYEPW--EIYDERGHAFTTFDA--YWDKCLQMQMEPASIL 168
E+LV G+ + N L W +Y + F FD + + + SI
Sbjct: 150 VDVERLVNQGLK-RVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIR 208
Query: 169 PPWRLVQAAGTI-------DGCSIEDLGLEDESEKSSNALLGRGWSPGWSNADKVLTEFV 221
R+ + G D ++E LG+E + +G G S G +V F
Sbjct: 209 SSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVG-GESAG---VGRVFEYFW 264
Query: 222 EQHLLRYYKNRQK--LGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKES 279
++ LL+ YK + LG + ++ SP+L FG +S R +++ + E+ S
Sbjct: 265 KKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRFIYE------EVQRYEKERVANNS 318
Query: 280 VTFFLRAMGLREYSRYL---CFNFPFTHERPLLSNLKYFPWHADLGNFKAWRQGRTGYPL 336
+ L + R+Y R+L C N F P K W D F++WR +TGYPL
Sbjct: 319 TYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGK---WSQDQKLFESWRDAKTGYPL 375
Query: 337 VDAGMRELWATGWIHNRIRVIVSSFAVKVLLLPWRWGMKYFWDTLLDADLECDILGWQYI 396
+DA M+EL TG++ NR R IV SF V+ + L WR G ++F LLD D + W Y
Sbjct: 376 IDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 435
Query: 397 SGSLPDGHELERLDSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHP 444
+G D E P+ Q +DPEGEYV WL +L R+P E H P
Sbjct: 436 AGVGNDPREDRYFSIPK-QAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 482
>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 = 131 bits (330), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 136/528 (25%), Positives = 219/528 (41%), Gaps = 57/528 (10%)
Query: 6 TIVWFRRDLRIEDNPALAAAARDG----SVFPVYTWCPKEEGQFYPGRVSRWWLKQSLSY 61
++WFR LR+ DNPAL AA D ++ PV+ + + G G +L SL
Sbjct: 7 NVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAGTKNVGYNRMRFLLDSLQD 66
Query: 62 LGQSLKSLG---AELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHSIKEKL 118
+ L++ L++F+ E ++ ++ +P+ RD SI+
Sbjct: 67 IDDQLQAATDGRGRLLVFEGEPAYI-FRRLHEQVRLHRICIEQDCEPIWNERDESIRSLC 125
Query: 119 VELGISVQSYNGDLLYEPWEIYDERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAAG 178
EL I L++P + + G + +Q+ P RL A
Sbjct: 126 RELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQIIGLPPRPTADARLEDATF 185
Query: 179 T-IDGCSIEDLGLEDESEKSSNA---------LLGRGWSPGWSNADKVLTEF--VEQHLL 226
+D L L ++ + L W G + A +L E VEQH
Sbjct: 186 VELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAKINWRGGETQALLLLDERLKVEQHAF 245
Query: 227 R--YYKNRQKLGG--NSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKESVTF 282
+Y Q L +S +S +L FG LSVR+ + W L+ +N + + V
Sbjct: 246 ERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRFY---WSVHDLF---KNVQLRACVRG 299
Query: 283 FLRAMGL--------REYSRYLCFNFPFTHERPLLSNLKYFPWHADLGNF-KAWRQGRTG 333
G REY + N P PW N ++WR G+TG
Sbjct: 300 VQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTG 359
Query: 334 YPLVDAGMRELWATGWIHNRIRVIVSSFAVK-VLLLPWRWGMKYFWDTLLDADLECDILG 392
+PL+D MR+L A GW+H+ +R V++F + L W G+++F LLDAD
Sbjct: 360 FPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGLQHFLKYLLDADWSVCAGN 419
Query: 393 WQYISGSLPDGHELERL------DSPEIQGSKFDPEGEYVRQWLPELARMPTEWIHHPWD 446
W ++S S ERL P + DP+G Y++Q++PEL +P E++H PW
Sbjct: 420 WMWVSSS-----AFERLLDSSLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVHEPWR 474
Query: 447 APPNVLKAAGVELGLNYPKPIIDLDLGRERLTQAIFKMWEMEAADNAM 494
+ +G++YP+ IIDL + +R M M++ N++
Sbjct: 475 MSAEQQEQYECLIGVHYPERIIDLSMAVKR------NMLAMKSLRNSL 516
>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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 94/388 (24%), Positives = 151/388 (38%), Gaps = 58/388 (14%)
Query: 2 GGNRTIVWFRRDLRIEDNPALA---AAARDGSVFPVYTWCPKEEGQFYPGRVSRWWLKQS 58
G + W RD R EDN AL A A++ +V V +C +E +L+
Sbjct: 35 GDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVVVVFCLTDE-----------FLEAG 83
Query: 59 LSYLGQSLKSLGAELVLFKTESTLAALLECISAIKATKVVFNHLYDPVSLVRDHS---IK 115
+ LK L V + + L K ++ V + Y+ +LV D S IK
Sbjct: 84 IRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISRFVKD--YNAGTLVTDFSPLRIK 141
Query: 116 EKLVEL---GISVQSYNGDL--LYEPWEIYDERGHAFTTF------DAYWDKCLQMQMEP 164
+ +E GIS+ + D + WE + +A TF ++EP
Sbjct: 142 NQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEP 201
Query: 165 ASILPPWRLVQAAGTIDGCS------IEDLGLEDESEKSSNALLGR-GWSPGWSNADKVL 217
S+ P L AG ++ S ++ L E K+ + L + PG A KV+
Sbjct: 202 NSVTP--ELSAGAGMVETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVM 259
Query: 218 TEFVEQHLLRYYKNRQKLGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGK 277
F+ L Y R N S LSPYLHFG++S ++V +L ++
Sbjct: 260 ESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRV--------VLEVEKAESNPG 311
Query: 278 ESVTFFLRAMGLREYSRYLCF---------NFPFTHERPLLSNLKYFPWHADLGNFKAWR 328
F + +E S C+ +FP + L ++ H + + +
Sbjct: 312 SKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSH--IYTLEEFE 369
Query: 329 QGRTGYPLVDAGMRELWATGWIHNRIRV 356
G+T PL +A EL +TG +H R+
Sbjct: 370 AGKTHDPLWNASQMELLSTGKMHGYTRM 397
>pdb|3CBQ|A Chain A, Crystal Structure Of The Human Rem2 Gtpase With Bound Gdp
Length = 195
Score = 35.8 bits (81), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 26/112 (23%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 474 RERLTQAIFKMWEMEAA-----DNAMDSNGTNEVVFDNSDRIQTPAIPQVVLREKSTCPT 528
+E +T ++ +WE A D+ + + +VF +DR +P+ +LR ++ P
Sbjct: 69 KEEVTLVVYDIWEQGDAGGWLRDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRP- 127
Query: 529 ISSNDQKVPSFQNGKNNLPSRKRPKNVEEERQYPDELYSCKNEAGNSGAHDD 580
+P G + +R R ++EE R L SCK+ ++ H +
Sbjct: 128 ----HHDLPVILVGNKSDLARSREVSLEEGRHLAGTL-SCKHIETSAALHHN 174
>pdb|4AII|A Chain A, Crystal Structure Of The Rat Rem2 Gtpase - G Domain Bound
To Gdp
pdb|4AII|B Chain B, Crystal Structure Of The Rat Rem2 Gtpase - G Domain Bound
To Gdp
Length = 180
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 26/112 (23%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 474 RERLTQAIFKMWEMEAA-----DNAMDSNGTNEVVFDNSDRIQTPAIPQVVLREKSTCPT 528
+E +T ++ +WE A D+ + + +VF +DR +P+ +LR ++ P
Sbjct: 58 KEEVTLIVYDIWEQGDAGGWLQDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRP- 116
Query: 529 ISSNDQKVPSFQNGKNNLPSRKRPKNVEEERQYPDELYSCKNEAGNSGAHDD 580
+P G + +R R ++EE R L SCK+ ++ H +
Sbjct: 117 ----HHDLPVILVGNKSDLARSREVSLEEGRHLAGTL-SCKHIETSAALHHN 163
>pdb|3Q85|A Chain A, Crystal Structure Of Rem2 G-Domain -Gtp Analog Complex
pdb|3Q85|B Chain B, Crystal Structure Of Rem2 G-Domain -Gtp Analog Complex
Length = 169
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 26/112 (23%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 474 RERLTQAIFKMWEMEAA-----DNAMDSNGTNEVVFDNSDRIQTPAIPQVVLREKSTCPT 528
+E +T ++ +WE A D+ + + +VF +DR +P+ +LR ++ P
Sbjct: 48 KEEVTLIVYDIWEQGDAGGWLQDHCLQTGDAFLIVFSVTDRRSFSKVPETLLRLRAGRP- 106
Query: 529 ISSNDQKVPSFQNGKNNLPSRKRPKNVEEERQYPDELYSCKNEAGNSGAHDD 580
+P G + +R R ++EE R L SCK+ ++ H +
Sbjct: 107 ----HHDLPVILVGNKSDLARSREVSLEEGRHLAGTL-SCKHIETSAALHHN 153
>pdb|4E1Z|A Chain A, Structure Of Mouse Tyk-2 Complexed To A 3-Aminoindazole
Inhibitor
Length = 291
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 209 GWSNADKVLTEFVEQHLLRYYKNRQKLGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILW 268
GW ++L +H+++Y + G S L+ Y+ G L C+ + Q+L
Sbjct: 57 GWQREIEILRTLYHEHIVKYKGCCEDQGEKSVQLVMEYVPLGSLRDYLPRHCVGLAQLLL 116
Query: 269 AKEENFEGK---ESVTFFLRAMGLR 290
++ EG + + RA+ R
Sbjct: 117 FAQQICEGMAYLHAQHYIHRALAAR 141
>pdb|4E20|A Chain A, Structure Of Mouse Tyk-2 Complexed To A 3-Aminoindazole
Inhibitor
Length = 290
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 209 GWSNADKVLTEFVEQHLLRYYKNRQKLGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILW 268
GW ++L +H+++Y + G S L+ Y+ G L C+ + Q+L
Sbjct: 56 GWQREIEILRTLYHEHIVKYKGCCEDQGEKSVQLVMEYVPLGSLRDYLPRHCVGLAQLLL 115
Query: 269 AKEENFEGK---ESVTFFLRAMGLR 290
++ EG + + RA+ R
Sbjct: 116 FAQQICEGMAYLHAQHYIHRALAAR 140
>pdb|3E99|A Chain A, Crystal Structure Of The Beta Subunit Of The Benzoate
1,2-dioxygenase (benb, Bmaa0186) From Burkholderia
Mallei Atcc 23344 At 1.90 A Resolution
Length = 164
Score = 30.0 bits (66), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 206 WSPGWSNADKVLTEFVEQHLLRYYKNRQKL 235
W P W +AD ++T+ + L YY NRQ L
Sbjct: 40 WXPSWDDADALVTDPQREISLIYYPNRQGL 69
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 142 ERGHAFTTFDAYWDKCLQMQMEPASILPPWRLVQAAGT 179
ERG +F D Y + + ++ S++PP+ + GT
Sbjct: 940 ERGFSFKNIDLYRSQATEFVIDGNSLIPPFNAIPGLGT 977
>pdb|3UMV|A Chain A, Eukaryotic Class Ii Cpd Photolyase Structure Reveals A
Basis For Improved Uv-Tolerance In Plants
pdb|3UMV|B Chain B, Eukaryotic Class Ii Cpd Photolyase Structure Reveals A
Basis For Improved Uv-Tolerance In Plants
Length = 506
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 10/84 (11%)
Query: 220 FVEQHLLRYYKNRQK-LGGNSTSLLSPYLHFGELSVRKVFQCLWMKQILWAKEENFEGKE 278
F+ + + Y +R + S LSPYLHFG +S ++ L AK+ +
Sbjct: 260 FLTKRIKSYETDRNDPTKPRALSGLSPYLHFGHISAQRC--------ALEAKKCRHLSPK 311
Query: 279 SVTFFLRAMGL-REYSRYLCFNFP 301
SV FL + + RE + C+ P
Sbjct: 312 SVDAFLEELVVRRELADNFCYYQP 335
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
0.318 0.135 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,931,004
Number of Sequences: 62578
Number of extensions: 927030
Number of successful extensions: 1969
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1890
Number of HSP's gapped (non-prelim): 37
length of query: 642
length of database: 14,973,337
effective HSP length: 105
effective length of query: 537
effective length of database: 8,402,647
effective search space: 4512221439
effective search space used: 4512221439
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)