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= psy14494
(470 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 237 bits (605), Expect = 1e-62, Method: Compositional matrix adjust.
Identities = 138/448 (30%), Positives = 226/448 (50%), Gaps = 31/448 (6%)
Query: 23 IEDRRIEFIFKSIIELSINLQNYDSDLIIRYA---IASKEIKKLVIKLN-IDAVMINHDY 78
+ R+ E I + L I L L+ R +AS EI K V N + + N+ Y
Sbjct: 46 MSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQY 105
Query: 79 EPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPYSIFSFYQKKWIEKVKS 138
E RD +++ L+ + C+ F D VI ++ + Y +F+ ++ W+++++
Sbjct: 106 EVNERARDVEVERALRNVVCEGFD--DSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLRE 163
Query: 139 NKCYLQSYPVKSYLNNLVHSSKLHKXXXXXXXSLNDLGFCKSNLSSLGIKTGASGAXXXX 198
+ V + K+ L + + + + A
Sbjct: 164 G------------MPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQL 211
Query: 199 XXXXXXXXXXXXXXXX-PSINGTSYLSIHLRFGTISIRXXXXXXXXXXXXHYKTDCIGYF 257
P++ GTS LS L G +S R D
Sbjct: 212 RQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQ--ALDGGAGS 269
Query: 258 TWLSQLIWRDFYQMILYCYPNVV-NKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLI 316
WL++LIWR+FY+ ++ +P++ ++ F D + W+S+ + W +G TGYP++
Sbjct: 270 VWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSN---PAHLQAWQEGKTGYPIV 326
Query: 317 DSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSA 376
D+A+ QLNS+G+MHNRLRM+TASFL+K++ I+W+ GE YF ++L D DLA+NNG WQW+A
Sbjct: 327 DAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAA 386
Query: 377 SSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGI 436
S+G + P+FRIFNP Q +KFD++G FIR++LP+L + K +H PWK + +KAG+
Sbjct: 387 STGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWA----QKAGV 442
Query: 437 ILGKNYPKPILEHSLSKKNILKRYNFIK 464
L +YP+PI+EH ++ L Y +
Sbjct: 443 TL--DYPQPIVEHKEARVQTLAAYEAAR 468
>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 = 223 bits (569), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 140/468 (29%), Positives = 215/468 (45%), Gaps = 24/468 (5%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
++ +F D IL + R+ ++ + EL Q S L++ I
Sbjct: 29 QLIGLFCLDPQIL----QSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIP 84
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+L +L +AV N D EP RD + LK G + DQ++ ++IL+ +G P
Sbjct: 85 QLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNP 144
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKXXXXXXXSLNDLGFCKSN 181
YS++ + K W + K + V L + L +L LGF
Sbjct: 145 YSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPL---LLSELPTLKQLGFDWDG 201
Query: 182 LSSLGIKTGASGAXXXXXXX-XXXXXXXXXXXXXPSINGTSYLSIHLRFGTISIRXXXXX 240
++ G + A P+ GTS LS L+FG I IR
Sbjct: 202 --GFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQA 259
Query: 241 XXXXXXXHYKTDCIGYF-TWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYA 299
+ W +L WR+FYQ LY +P++ + ++ + WE+
Sbjct: 260 ASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENR--- 316
Query: 300 KKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANK 359
+ F W + TGYP++D+A+ QL +G+MHNR RM+ ASFL K++ I+W+ GE +F
Sbjct: 317 EALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQH 376
Query: 360 LNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKY 419
L D DLA+NNG WQWSASSG +P RIFNP Q+KKFD +I+++LP+L + K
Sbjct: 377 LVDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAKKFDATATYIKRWLPELRHVHPKD 435
Query: 420 IHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKNIL 467
+ S +E+ G YP PI+ H+L +K YN +K +
Sbjct: 436 LIS---GEITPIERRG------YPAPIVNHNLRQKQFKALYNQLKAAI 474
>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 = 223 bits (568), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 140/468 (29%), Positives = 215/468 (45%), Gaps = 24/468 (5%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
++ +F D IL + R+ ++ + EL Q S L++ I
Sbjct: 30 QLIGLFCLDPQIL----QSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIP 85
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+L +L +AV N D EP RD + LK G + DQ++ ++IL+ +G P
Sbjct: 86 QLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNP 145
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKXXXXXXXSLNDLGFCKSN 181
YS++ + K W + K + V L + L +L LGF
Sbjct: 146 YSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLTAIAPL---LLSELPTLKQLGFDWDG 202
Query: 182 LSSLGIKTGASGAXXXXXXX-XXXXXXXXXXXXXPSINGTSYLSIHLRFGTISIRXXXXX 240
++ G + A P+ GTS LS L+FG I IR
Sbjct: 203 --GFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQA 260
Query: 241 XXXXXXXHYKTDCIGYF-TWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYA 299
+ W +L WR+FYQ LY +P++ + ++ + WE+
Sbjct: 261 ASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENR--- 317
Query: 300 KKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANK 359
+ F W + TGYP++D+A+ QL +G+MHNR RM+ ASFL K++ I+W+ GE +F
Sbjct: 318 EALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRRGEQFFMQH 377
Query: 360 LNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKY 419
L D DLA+NNG WQWSASSG +P RIFNP Q+KKFD +I+++LP+L + K
Sbjct: 378 LVDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAKKFDATATYIKRWLPELRHVHPKD 436
Query: 420 IHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKNIL 467
+ S +E+ G YP PI+ H+L +K YN +K +
Sbjct: 437 LIS---GEITPIERRG------YPAPIVNHNLRQKQFKALYNQLKAAI 475
>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 = 196 bits (499), Expect = 2e-50, Method: Compositional matrix adjust.
Identities = 145/465 (31%), Positives = 227/465 (48%), Gaps = 72/465 (15%)
Query: 3 VYCVFIFDKNIL--DPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEI 60
V VFI D L +P +S+ + F+ S++EL L+ S L + + A K +
Sbjct: 29 VIPVFIADPRQLINNPYKSEFAVS-----FMINSLLELDDELRKKGSRLNVFFGEAEKVV 83
Query: 61 KKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGK 120
+ K +DA+ +N DY P +I RD+ I+K + G +F +Y+D ++ K+ ++
Sbjct: 84 SRFFNK--VDAIYVNEDYTPFSISRDEKIRKVCEENGIEFKAYEDYLLTPKSLFHHR--- 138
Query: 121 PYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKXXXXXXXSLNDLGFCKS 180
+ SFY + KV+ + S+ V N+ K +S
Sbjct: 139 --NFTSFYNEVSKVKVREPETMEGSFDVTDSSMNVDFLLTFKK--------------IES 182
Query: 181 NLSSLGIKTGASGAXXXXXXXXXXXXXXXXXXXXPSINGTSYLSIHLRFGTISIRXXXXX 240
L G + G P+ N LS HL+FGTIS+R
Sbjct: 183 PLFRGGRREG---------LYLLHRNVDFRRRDYPAENNNYRLSPHLKFGTISMREAYYT 233
Query: 241 XXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAK 300
G ++ +L WRDF+ ++ Y P+V +++EYDNI WE++ +
Sbjct: 234 QK------------GKEEFVRELYWRDFFTLLAYYNPHVFGHCYRREYDNISWENN---E 278
Query: 301 KNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKL 360
F W +G TGYP+ID+ + LNS+GY++ R+RM+ A FL+K + ++W+WGE YFA KL
Sbjct: 279 SYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDWRWGERYFATKL 338
Query: 361 NDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYI 420
D+D A NNGNWQW AS+G FR+FNP Q +KFD + FI++++ +L + I
Sbjct: 339 VDYDPAINNGNWQWIASTGVDYM--FRVFNPWKQQEKFDPEAKFIKEWVEELKDVPPSII 396
Query: 421 HSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKN 465
H S YK + G YP PI+ N L+R N++K+
Sbjct: 397 H-----SIYKTKVPG------YPSPIV-------NWLERVNYVKS 423
>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 = 153 bits (387), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 115/425 (27%), Positives = 194/425 (45%), Gaps = 26/425 (6%)
Query: 34 SIIELSINLQNYDSDLIIRYAIAS-KEIKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKE 92
S+ +L +L++ + LI + + S + +V + NH Y+P +++RD K
Sbjct: 66 SLAQLDSSLRSLGTCLITKRSTDSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKDV 125
Query: 93 LKVIGCKFFSYKDQVIFEKNEILNKTGKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYL 152
L G S+ +++E E+ ++ G+P+S+F+ + ++ C Y +S L
Sbjct: 126 LTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWER---------CLSMPYDPESPL 176
Query: 153 --NNLVHSSKLHKXXXXXXXSLNDLGFCKSNLSSLGIKTGAS-GAXXXXXXXXXXXXXXX 209
+ S + K +D + L + G S G
Sbjct: 177 LPPKKIISGDVSKCVADPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYS 236
Query: 210 XXXXXPSINGTSYLSIHLRFGTISIRXX------XXXXXXXXXXHYKTDCIGYFTWLSQL 263
TS+LS HL FG +S+R + + F L +
Sbjct: 237 KNRRKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVNLF--LKSI 294
Query: 264 IWRDFYQMILYCYPNVVNKSFKKEYDNILWESD-NYAKKNFLNWCKGYTGYPLIDSAIIQ 322
R++ + I + +P + W D NY F W +G TGYPL+D+ + +
Sbjct: 295 GLREYSRYISFNHPYSHERPLLGHLKFFPWAVDENY----FKAWRQGRTGYPLVDAGMRE 350
Query: 323 LNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSS 382
L ++G++H+R+R+V +SF +K + + W+WG YF + L D DL S+ WQ+ + S
Sbjct: 351 LWATGWLHDRIRVVVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDS 410
Query: 383 QPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNY 442
+ F RI NP + KFD G ++R++LP+LS+L +IH PW A L+ AGI LG NY
Sbjct: 411 REFDRIDNPQFEGYKFDPNGEYVRRWLPELSRLPTDWIHHPWNAPESVLQAAGIELGSNY 470
Query: 443 PKPIL 447
P PI+
Sbjct: 471 PLPIV 475
>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 = 149 bits (376), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 122/470 (25%), Positives = 197/470 (41%), Gaps = 29/470 (6%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
V +FI D ILD ++ + R F+ +++ +L L+ +S L + ++ +
Sbjct: 63 VRPIFILDPGILDWMQ----VGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPR 118
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIG------CKFFSYKDQVIFEKNEILN 116
+ ++ + D EP ++ RD ++K K G C Y +++ KN L
Sbjct: 119 IFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKN--LG 176
Query: 117 KTGKPYSIF-SFYQKKWIEKVKSNKCYLQSYPVK-----SYLNNLVHSSKLHKXXXXXXX 170
K Y F ++ + KV L++ P ++ + K
Sbjct: 177 KAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPE 236
Query: 171 SLNDLGFCKSNLSSLGIKTGASGAXXXXXXXXXXXXXXXXXXXXPSINGTSYLSIHLRFG 230
L F +L + PS T+ LS +L+FG
Sbjct: 237 ELGPNKFPGGETEAL--RRMEESLKDEIWVARFEKPNTAPNSLEPS---TTVLSPYLKFG 291
Query: 231 TISIRXXXXXXXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDN 290
+S R K + + QL+WR+FY + PN
Sbjct: 292 CLSARLFNQKLKEIIKRQPKHSQPP-VSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQ 350
Query: 291 ILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIK-NMGINW 349
I W+ + W G TGYP ID+ + QL G++H+ RM A FL + ++ I+W
Sbjct: 351 IPWQEH---PDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARMAVACFLTRGDLWISW 407
Query: 350 KWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYL 409
+ G+ F L D D A N GNW W ++S Q +FR+++P+ KK D QG +IRKY+
Sbjct: 408 EEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQ-YFRVYSPVAFGKKTDPQGHYIRKYV 466
Query: 410 PQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKR 459
P+LSK I+ PWKAS G +LG +YP I++H + K +KR
Sbjct: 467 PELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKR 516
>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 = 148 bits (374), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 124/474 (26%), Positives = 199/474 (41%), Gaps = 31/474 (6%)
Query: 3 VYCVFIFDKNILD-------PLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAI 55
+Y VF+ D + ++ P S+ + RI F+ +S+ +L +L+ S L++
Sbjct: 33 MYPVFVIDPHYMESDPSAFSPGSSRAGVN--RIRFLLESLKDLDSSLKKLGSRLLVFKGE 90
Query: 56 ASKEIKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEIL 115
+ + + + + + + +D +P D +K G + FS +F I+
Sbjct: 91 PGEVLVRCLQEWKVKRLCFEYDTDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAHII 150
Query: 116 NKTG--KPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKXXXXXXXSLN 173
K G P S SF KV +S V SY ++L + SL
Sbjct: 151 EKNGGKPPLSYQSFL------KVAGEPSCAKSELVMSY-SSLPPIGDIGNLGISEVPSLE 203
Query: 174 DLGFCKSNLSSLGIKTGASGAXXXXXXXXXXXXXXXXXXXXPSIN-------GTSYLSIH 226
+LG+ + G P + T+ +S +
Sbjct: 204 ELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKPATTVMSPY 263
Query: 227 LRFGTISIRXXXXXXXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKK 286
L+FG +S R K + L QL+WR+F+ + PN +
Sbjct: 264 LKFGCLSSRYFYQCLQNIYK-DVKKHTSPPVSLLGQLLWREFFYTTAFGTPNFDKMKGNR 322
Query: 287 EYDNILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIK-NM 345
I W D+ W G TGYP ID+ ++QL G+MH+ R A FL + ++
Sbjct: 323 ICKQIPWNEDHAM---LAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDL 379
Query: 346 GINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFI 405
I+W+ G + F L D D A NNGNW W + S Q F RI++PI KK+D G +I
Sbjct: 380 FIHWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFFYQ-FNRIYSPISFGKKYDPDGKYI 438
Query: 406 RKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKR 459
R +LP L + +YI+ PW A KA I+GK+YPKP++ H + K ++
Sbjct: 439 RHFLPVLKDMPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRK 492
>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 = 148 bits (374), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 122/470 (25%), Positives = 196/470 (41%), Gaps = 29/470 (6%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
V +FI D ILD ++ + R F+ +++ +L L+ +S L + ++ +
Sbjct: 63 VRPIFILDPGILDWMQ----VGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPR 118
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIG------CKFFSYKDQVIFEKNEILN 116
+ ++ + D EP ++ RD ++K K G C Y +++ KN L
Sbjct: 119 IFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKN--LG 176
Query: 117 KTGKPYSIF-SFYQKKWIEKVKSNKCYLQSYPVK-----SYLNNLVHSSKLHKXXXXXXX 170
K Y F ++ + KV L++ P ++ + K
Sbjct: 177 KAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPE 236
Query: 171 SLNDLGFCKSNLSSLGIKTGASGAXXXXXXXXXXXXXXXXXXXXPSINGTSYLSIHLRFG 230
L F +L + PS T+ LS +L+FG
Sbjct: 237 ELGPNKFPGGETEAL--RRMEESLKDEIWVARFEKPNTAPNSLEPS---TTVLSPYLKFG 291
Query: 231 TISIRXXXXXXXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDN 290
+S R K + + QL+WR+FY + PN
Sbjct: 292 CLSARLFNQKLKEIIKRQPKHSQPP-VSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQ 350
Query: 291 ILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIK-NMGINW 349
I W+ + W G TGYP ID+ + QL G++HN R A FL + ++ I+W
Sbjct: 351 IPWQEH---PDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHNLARHAVACFLTRGDLWISW 407
Query: 350 KWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYL 409
+ G+ F L D D A N GNW W ++S Q +FR+++P+ KK D QG +IRKY+
Sbjct: 408 EEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQ-YFRVYSPVAFGKKTDPQGHYIRKYV 466
Query: 410 PQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKR 459
P+LSK I+ PWKAS G +LG +YP I++H + K +KR
Sbjct: 467 PELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKR 516
>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 = 146 bits (369), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 121/470 (25%), Positives = 196/470 (41%), Gaps = 29/470 (6%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
V +FI D ILD ++ + R F+ +++ +L L+ +S L + ++ +
Sbjct: 63 VRPIFILDPGILDWMQ----VGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPR 118
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIG------CKFFSYKDQVIFEKNEILN 116
+ ++ + D EP ++ RD ++K K G C Y +++ KN L
Sbjct: 119 IFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKN--LG 176
Query: 117 KTGKPYSIF-SFYQKKWIEKVKSNKCYLQSYPVK-----SYLNNLVHSSKLHKXXXXXXX 170
K Y F ++ + KV L++ P ++ + K
Sbjct: 177 KAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPE 236
Query: 171 SLNDLGFCKSNLSSLGIKTGASGAXXXXXXXXXXXXXXXXXXXXPSINGTSYLSIHLRFG 230
L F +L + PS T+ LS +L+FG
Sbjct: 237 ELGPNKFPGGETEAL--RRMEESLKDEIWVARFEKPNTAPNSLEPS---TTVLSPYLKFG 291
Query: 231 TISIRXXXXXXXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDN 290
+S R K + + QL+WR+FY + PN
Sbjct: 292 CLSARLFNQKLKEIIKRQPK-HSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQ 350
Query: 291 ILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIK-NMGINW 349
I W+ + W G TGYP ID+ + QL G++H+ R A FL + ++ I+W
Sbjct: 351 IPWQEH---PDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISW 407
Query: 350 KWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYL 409
+ G+ F L D D A N GNW W ++S Q +FR+++P+ KK D QG +IRKY+
Sbjct: 408 EEGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQ-YFRVYSPVAFGKKTDPQGHYIRKYV 466
Query: 410 PQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKR 459
P+LSK I+ PWKAS G +LG +YP I++H + K +KR
Sbjct: 467 PELSKYPAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKR 516
>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 = 146 bits (368), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 73/186 (39%), Positives = 112/186 (60%), Gaps = 4/186 (2%)
Query: 262 QLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDSAII 321
+L+WRDF++ + Y N + N W+ D F W G TGYPL+D+ +
Sbjct: 289 ELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQV---RFELWRSGQTGYPLVDANMR 345
Query: 322 QLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCS 381
+LN +G+M NR R ASFL KN+GI+W+WG +F + L D+D+ SN GNW ++A G
Sbjct: 346 ELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGND 405
Query: 382 SQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKN 441
++ FR FN QS+++D QG ++R +LP+L L IH PW S+ + ++ G+ LG +
Sbjct: 406 ARD-FRYFNIPKQSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVD 464
Query: 442 YPKPIL 447
YP+P +
Sbjct: 465 YPRPCV 470
>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 = 131 bits (329), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 61/201 (30%), Positives = 106/201 (52%), Gaps = 10/201 (4%)
Query: 218 NGTSYLSIHLRFGTISIRXXXXXXXXXXXXHYKTDCIGYFTWLSQLIWRDFYQMILYCYP 277
G S LS + G +S R + G W+++L+WRDF +LY +P
Sbjct: 207 EGGSRLSPYFALGVLSPRLAAWEAE-------RRGGEGARKWVAELLWRDFSYHLLYHFP 259
Query: 278 NVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVT 337
+ + + W+ D + F W +G TG PL+D+A+ +L+++G++ NR RM
Sbjct: 260 WMAERPLDPRFQAFPWQED---EALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNA 316
Query: 338 ASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKK 397
A F +K++ + WK E F + L D D A N WQW+ G + P+FR+FNP++Q ++
Sbjct: 317 AQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGER 376
Query: 398 FDYQGIFIRKYLPQLSKLSNK 418
D +G +++++ P+ + K
Sbjct: 377 HDPEGRWLKRWAPEYPSYAPK 397
>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 = 120 bits (300), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 78/253 (30%), Positives = 132/253 (52%), Gaps = 29/253 (11%)
Query: 223 LSIHLRFGTISIRXXXXXXXXXXXXHYKTDCI------GYFTWLSQLIWRD-FYQMILYC 275
+S HLRFG +S+R C+ G QLIWR+ FY M
Sbjct: 266 MSAHLRFGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTM---- 321
Query: 276 YPNVVNKSFKKEYDNILWESDNYAKKN---FLNWCKGYTGYPLIDSAIIQLNSSGYMHNR 332
+V N ++ + N + S +AK N +W G TG+PLID A+ QL + G++H+
Sbjct: 322 --SVNNPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHT 379
Query: 333 LRMVTASFLIKN-MGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFN- 390
LR A+FL + + +W+ G +F L D D + GNW W +SS F R+ +
Sbjct: 380 LRNTVATFLTRGGLWQSWEHGLQHFLKYLLDADWSVCAGNWMWVSSSA-----FERLLDS 434
Query: 391 -----PIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKP 445
P+ +K+ D G +I++Y+P+L + +++H PW+ S+ + E+ ++G +YP+
Sbjct: 435 SLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVHEPWRMSAEQQEQYECLIGVHYPER 494
Query: 446 ILEHSLS-KKNIL 457
I++ S++ K+N+L
Sbjct: 495 IIDLSMAVKRNML 507
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 99.0 bits (245), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 55/164 (33%), Positives = 91/164 (55%), Gaps = 5/164 (3%)
Query: 260 LSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDSA 319
L +LIWRD+++ + N + N W D +K F +W TGYPLID+
Sbjct: 324 LFELIWRDYFRFLSIKCGNSLFHLGGPRNVNGKWSQD---QKLFESWRDAKTGYPLIDAN 380
Query: 320 IIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSG 379
+ +L+++G+M NR R + SFL+++MG++W+ G +F L D+D SN GNW + A G
Sbjct: 381 MKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGA--G 438
Query: 380 CSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSP 423
+ R F+ Q++ +D +G ++ +L QL +L + H P
Sbjct: 439 VNDPREDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 482
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 98.6 bits (244), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 54/165 (32%), Positives = 94/165 (56%), Gaps = 6/165 (3%)
Query: 260 LSQLIWRDFYQMI-LYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDS 318
L +LIWRD+++ + + C ++ + + W D +K F +W TGYPLID+
Sbjct: 323 LFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGK-WSQD---QKLFESWRDAKTGYPLIDA 378
Query: 319 AIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASS 378
+ +L+++G+M NR R + SFL+++MG++W+ G +F L D+D SN GNW + A
Sbjct: 379 NMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGV 438
Query: 379 GCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSP 423
G + R F+ Q++ +D +G ++ +L QL +L + H P
Sbjct: 439 GNDPRE-DRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 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 = 98.6 bits (244), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 54/165 (32%), Positives = 94/165 (56%), Gaps = 6/165 (3%)
Query: 260 LSQLIWRDFYQMI-LYCYPNVVNKSFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDS 318
L +LIWRD+++ + + C ++ + + W D +K F +W TGYPLID+
Sbjct: 324 LFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGK-WSQD---QKLFESWRDAKTGYPLIDA 379
Query: 319 AIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASS 378
+ +L+++G+M NR R + SFL+++MG++W+ G +F L D+D SN GNW + A
Sbjct: 380 NMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGV 439
Query: 379 GCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSP 423
G + R F+ Q++ +D +G ++ +L QL +L + H P
Sbjct: 440 GNDPRE-DRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWP 483
>pdb|3ZF7|J Chain J, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 214
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 20 QGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYA 54
Q +++DR+ E FK I+L +NL+NYD R++
Sbjct: 14 QNVLKDRK-ERKFKESIDLQVNLKNYDPQKDKRFS 47
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
0.322 0.138 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,083,828
Number of Sequences: 62578
Number of extensions: 523603
Number of successful extensions: 1182
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1123
Number of HSP's gapped (non-prelim): 28
length of query: 470
length of database: 14,973,337
effective HSP length: 102
effective length of query: 368
effective length of database: 8,590,381
effective search space: 3161260208
effective search space used: 3161260208
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)