RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14494
(470 letters)
>1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin
enzyme, photoreactivating enzyme; HET: FAD; 1.80A
{Synechococcus elongatus} SCOP: a.99.1.1 c.28.1.1 PDB:
1owm_A* 1own_A* 1owo_A* 1owp_A* 1qnf_A* 1tez_A*
Length = 484
Score = 539 bits (1392), Expect = 0.0
Identities = 143/466 (30%), Positives = 225/466 (48%), Gaps = 24/466 (5%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
++ +F D IL R+ ++ + EL Q S L++ I
Sbjct: 30 QLIGLFCLDPQILQSADMA----PARVAYLQGCLQELQQRYQQAGSRLLLLQGDPQHLIP 85
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+L +L +AV N D EP RD + LK G + DQ++ ++IL+ +G P
Sbjct: 86 QLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAVQLWDQLLHSPDQILSGSGNP 145
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSN 181
YS++ + K W + K + + L+ + + ++ + + +L LGF
Sbjct: 146 YSVYGPFWKNWQAQPKPT--PVATPTELVDLSP-EQLTAIAPLLLSELPTLKQLGFDWDG 202
Query: 182 LSSLGIKTGASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLV-K 239
++ G + A L F I +Y+ RN+P+ GTS LS L+FG I IR+
Sbjct: 203 --GFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQA 260
Query: 240 LIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYA 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 IHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKN 465
+ S I + YP PI+ H+L +K YN +K
Sbjct: 437 LISGEITP---------IERRGYPAPIVNHNLRQKQFKALYNQLKA 473
>1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein;
HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} SCOP:
a.99.1.1 c.28.1.1 PDB: 1u3c_A*
Length = 509
Score = 536 bits (1382), Expect = 0.0
Identities = 120/470 (25%), Positives = 216/470 (45%), Gaps = 22/470 (4%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAI-ASKEI 60
V +F++ ++ S+ +L +L++ + LI + + + +
Sbjct: 38 PVIALFVWAPEEEGHYHPGR----VSRWWLKNSLAQLDSSLRSLGTCLITKRSTDSVASL 93
Query: 61 KKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGK 120
+V + NH Y+P +++RD K L G S+ +++E E+ ++ G+
Sbjct: 94 LDVVKSTGASQIFFNHLYDPLSLVRDHRAKDVLTAQGIAVRSFNADLLYEPWEVTDELGR 153
Query: 121 PYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKS 180
P+S+F+ + ++ + P K ++ V + D S
Sbjct: 154 PFSMFAAFWERCLSMPYDP--ESPLLPPKKIISGDVSKCVAD------PLVFEDDSEKGS 205
Query: 181 N-LSSLGIKTGASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLV 238
N L + G S L FI + Y+ NR TS+LS HL FG +S+RK+
Sbjct: 206 NALLARAWSPGWSNGDKALTTFINGPLLEYSKNRRKADSATTSFLSPHLHFGEVSVRKVF 265
Query: 239 KLI----FKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWE 294
L+ + + + +L + R++ + I + +P + W
Sbjct: 266 HLVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYISFNHPYSHERPLLGHLKFFPWA 325
Query: 295 SDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGEN 354
D + F W +G TGYPL+D+ + +L ++G++H+R+R+V +SF +K + + W+WG
Sbjct: 326 VD---ENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWRWGMK 382
Query: 355 YFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSK 414
YF + L D DL S+ WQ+ + S+ F RI NP + KFD G ++R++LP+LS+
Sbjct: 383 YFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGYKFDPNGEYVRRWLPELSR 442
Query: 415 LSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIK 464
L +IH PW A L+ AGI LG NYP PI+ +K + + + +
Sbjct: 443 LPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKARLHEALSQMW 492
>1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy
transfer, carbon-carbon, lyase (carbon-carbon); HET: DNA
FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1
c.28.1.1
Length = 471
Score = 533 bits (1376), Expect = 0.0
Identities = 134/470 (28%), Positives = 236/470 (50%), Gaps = 35/470 (7%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIR----YAIAS 57
V ++I R+ E I + L I L L+ R + +
Sbjct: 29 RVLALYIATPRQWATHNMS----PRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASV 84
Query: 58 KEIKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNK 117
+ +K++ + ++ + N+ YE RD +++ L+ + D VI ++
Sbjct: 85 EIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALR--NVVCEGFDDSVILPPGAVMTG 142
Query: 118 TGKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGF 177
+ Y +F+ ++ W+++++ + ++ L +
Sbjct: 143 NHEMYKVFTPFKNAWLKRLREG--MPECVAAPKVRSSGSIEP----------SPSITLNY 190
Query: 178 CKSNLSSLGIKTGASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRK 236
+ + + A L F + Y R++P++ GTS LS L G +S R+
Sbjct: 191 PRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQ 250
Query: 237 LVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVV-NKSFKKEYDNILWES 295
+ + ++ D WL++LIWR+FY+ ++ +P++ ++ F D + W+S
Sbjct: 251 CLHRLLA--EQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQS 308
Query: 296 DNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENY 355
+ + W +G TGYP++D+A+ QLNS+G+MHNRLRM+TASFL+K++ I+W+ GE Y
Sbjct: 309 N---PAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERY 365
Query: 356 FANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKL 415
F ++L D DLA+NNG WQW+AS+G + P+FRIFNP Q +KFD++G FIR++LP+L +
Sbjct: 366 FMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDV 425
Query: 416 SNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKN 465
K +H PWK + +KAG+ L YP+PI+EH ++ L Y +
Sbjct: 426 PGKVVHEPWKWA----QKAGVTLD--YPQPIVEHKEARVQTLAAYEAARK 469
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A
{Arabidopsis thaliana}
Length = 537
Score = 517 bits (1333), Expect = 0.0
Identities = 125/473 (26%), Positives = 209/473 (44%), Gaps = 25/473 (5%)
Query: 2 EVYCVFIFDKNILDPLRSQGI-----IEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIA 56
+Y VF+ D + ++ S RI F+ +S+ +L +L+ S L++
Sbjct: 32 FMYPVFVIDPHYMESDPSAFSPGSSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEP 91
Query: 57 SKEIKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILN 116
+ + + + + + + +D +P D +K G + FS +F I+
Sbjct: 92 GEVLVRCLQEWKVKRLCFEYDTDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAHIIE 151
Query: 117 KTG-KPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDL 175
K G KP + + K E + + SY + ++ + + + SL +L
Sbjct: 152 KNGGKPPLSYQSFLKVAGEPSCAKSELVMSYSSLPPIGDIGNLGI------SEVPSLEEL 205
Query: 176 GFCKSNLSSLGI-KTGASGAKILLNNFIKK---IKNYNINRNYPSI---NGTSYLSIHLR 228
G+ + + G S A L I + N+ + PS T+ +S +L+
Sbjct: 206 GYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKPATTVMSPYLK 265
Query: 229 FGTISIRKLVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEY 288
FG +S R + + + I K K + L QL+WR+F+ + PN +
Sbjct: 266 FGCLSSRYFYQCL-QNIYKDVKKHTSPPVSLLGQLLWREFFYTTAFGTPNFDKMKGNRIC 324
Query: 289 DNILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIK-NMGI 347
I W D W G TGYP ID+ ++QL G+MH+ R A FL + ++ I
Sbjct: 325 KQIPWNED---HAMLAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFI 381
Query: 348 NWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRK 407
+W+ G + F L D D A NNGNW W + S F RI++PI KK+D G +IR
Sbjct: 382 HWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFF-YQFNRIYSPISFGKKYDPDGKYIRH 440
Query: 408 YLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRY 460
+LP L + +YI+ PW A KA I+GK+YPKP++ H + K ++
Sbjct: 441 FLPVLKDMPKQYIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKM 493
>2wq7_A RE11660P; lyase-DNA complex, DNA repair, DNA lesion, lyase; HET:
TDY Z FAD; 2.00A {Drosophila melanogaster} PDB: 2wb2_A*
2wq6_A* 3cvu_A* 3cvv_A* 3cvy_A* 3cvw_A* 3cvx_A*
Length = 543
Score = 513 bits (1324), Expect = e-180
Identities = 118/469 (25%), Positives = 203/469 (43%), Gaps = 17/469 (3%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
V +FI D ILD ++ + R F+ +++ +L L+ +S L + ++ +
Sbjct: 63 VRPIFILDPGILDWMQ----VGANRWRFLQQTLEDLDNQLRKLNSRLFVVRGKPAEVFPR 118
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKT-GKP 121
+ ++ + D EP ++ RD ++K K G + ++ I+ ++ K GK
Sbjct: 119 IFKSWRVEMLTFETDIEPYSVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKA 178
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSN 181
+ + E++K K +K+ + + ++ L
Sbjct: 179 PITYQKFLGIV-EQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEE 237
Query: 182 LSSLGIKTGASGAKILLNNFIKK---IKNYNINRNYPSI--NGTSYLSIHLRFGTISIRK 236
L G + A + +K + + P+ T+ LS +L+FG +S R
Sbjct: 238 LGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARL 297
Query: 237 LVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESD 296
+ + K I K + + QL+WR+FY + PN I W+
Sbjct: 298 FNQKL-KEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEH 356
Query: 297 NYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKN-MGINWKWGENY 355
+ W G TGYP ID+ + QL G++H+ R A FL + + I+W+ G+
Sbjct: 357 ---PDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRV 413
Query: 356 FANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKL 415
F L D D A N GNW W ++S +FR+++P+ KK D QG +IRKY+P+LSK
Sbjct: 414 FEQLLLDQDWALNAGNWMWLSASAFF-HQYFRVYSPVAFGKKTDPQGHYIRKYVPELSKY 472
Query: 416 SNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIK 464
I+ PWKAS G +LG +YP I++H + K +KR
Sbjct: 473 PAGCIYEPWKASLVDQRAYGCVLGTDYPHRIVKHEVVHKENIKRMGAAY 521
>1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A
{Synechocystis SP} SCOP: a.99.1.1 c.28.1.1
Length = 489
Score = 510 bits (1315), Expect = e-179
Identities = 111/466 (23%), Positives = 212/466 (45%), Gaps = 18/466 (3%)
Query: 2 EVYCVFIFDKNILDPLRSQGI-IEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEI 60
+ V+ +D R F+ +S+ L+ +LQ + L++ + + I
Sbjct: 33 AITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQSVQNLAESLQKVGNKLLVTTGLPEQVI 92
Query: 61 KKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGK 120
++ ++N + + + + + ++ + K+L ++G + Y + ++
Sbjct: 93 PQIAKQINAKTIYYHREVTQEELDVERNLVKQLTILGIEAKGYWGSTLCHPEDLPFSIQD 152
Query: 121 PYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKS 180
+F+ ++K +K S + + N+ + F
Sbjct: 153 LPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPE-----FFPQINF--D 205
Query: 181 NLSSLGIKTGASGAKILLNNFI---KKIKNYNINRN-YPSINGTSYLSIHLRFGTISIRK 236
+ S L + G + L ++ ++K+Y RN + +S S L G +S R
Sbjct: 206 HRSVLAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRF 265
Query: 237 LVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESD 296
+ + + ++ ++ D + +L+WRDF++ + Y N + N W+ D
Sbjct: 266 IYQEVKRYEQERVSND--STHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQED 323
Query: 297 NYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYF 356
+ F W G TGYPL+D+ + +LN +G+M NR R ASFL KN+GI+W+WG +F
Sbjct: 324 ---QVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWRWGAEWF 380
Query: 357 ANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLS 416
+ L D+D+ SN GNW ++A G ++ FR FN QS+++D QG ++R +LP+L L
Sbjct: 381 ESCLIDYDVCSNWGNWNYTAGIGNDARD-FRYFNIPKQSQQYDPQGTYLRHWLPELKNLP 439
Query: 417 NKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNF 462
IH PW S+ + ++ G+ LG +YP+P + S + K
Sbjct: 440 GDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQSVEARRKIEQM 485
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 495 bits (1277), Expect = e-173
Identities = 101/485 (20%), Positives = 196/485 (40%), Gaps = 28/485 (5%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSD---LIIRYAIASKE 59
+ VFIFD + R+ F+ S+ ++ LQ L++ +
Sbjct: 35 LIPVFIFDGESAGTKN----VGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYI 90
Query: 60 IKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNK-T 118
++L ++ + + I D EP RD+ I+ + + F +++ ++
Sbjct: 91 FRRLHEQVRLHRICIEQDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNG 150
Query: 119 GKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFC 178
G P + + + + + L + + +
Sbjct: 151 GIPPLTYQMFLHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVY 210
Query: 179 KSNLSSLGIKT---GASGAKILLNNFIK-KIKNYNINRNYPSIN------GTSYLSIHLR 228
N+ L G + A +LL+ +K + + P+ +S HLR
Sbjct: 211 GDNMGFLAKINWRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPKSMSAHLR 270
Query: 229 FGTISIRKLVKLIFKFIKK------HYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNK 282
FG +S+R+ + K G QLIWR+++ + PN
Sbjct: 271 FGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRM 330
Query: 283 SFKKEYDNILWESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLI 342
+I W N + +W G TG+PLID A+ QL + G++H+ LR A+FL
Sbjct: 331 EGNDICLSIPWAKPN--ENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLT 388
Query: 343 KN-MGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQPFF-RIFNPIIQSKKFDY 400
+ + +W+ G +F L D D + GNW W +SS + P+ +K+ D
Sbjct: 389 RGGLWQSWEHGLQHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDP 448
Query: 401 QGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRY 460
G +I++Y+P+L + +++H PW+ S+ + E+ ++G +YP+ I++ S++ K +
Sbjct: 449 DGTYIKQYVPELMNVPKEFVHEPWRMSAEQQEQYECLIGVHYPERIIDLSMAVKRNMLAM 508
Query: 461 NFIKN 465
++N
Sbjct: 509 KSLRN 513
>2j4d_A Cryptochrome 3, cryptochrome DASH; DNA-binding protein,
flavoprotein, FAD, mitochondrion, plastid, chromophore,
chloroplast; HET: FAD MHF; 1.9A {Arabidopsis thaliana}
PDB: 2vtb_A* 2ijg_X* 2vtb_B*
Length = 525
Score = 489 bits (1262), Expect = e-171
Identities = 94/473 (19%), Positives = 185/473 (39%), Gaps = 38/473 (8%)
Query: 2 EVYCVFIFDKNILDPLRSQGI--IEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKE 59
+ V+ D + R F+ + +++L NL +L+IR +
Sbjct: 67 TILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMECLVDLRKNLMKRGLNLLIRSGKPEEI 126
Query: 60 IKKLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIG--CKFFSYKDQVIFEKNEILNK 117
+ L V + + + + ++L+ + LK +G K ++ K+++
Sbjct: 127 LPSLAKDFGARTVFAHKETCSEEVDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFD 186
Query: 118 TGKPYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGF 177
+++ ++K K P+ V ++ +L LG
Sbjct: 187 VFDLPDVYTQFRKSVEAKCSIRSS--TRIPLSLGPTPSVDDWG-------DVPTLEKLGV 237
Query: 178 CKSNL-SSLGIKTGASGAKILLNNFI---KKIKNYNINRN-YPSINGTSYLSIHLRFGTI 232
+ + G S + + +K Y RN + ++ S L FG I
Sbjct: 238 EPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCI 297
Query: 233 SIRKLVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNIL 292
S R + + + ++ K+ + + L +LIWRD+++ + N +
Sbjct: 298 SPRFIYEEVQRYEKERVANN--STYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGK 355
Query: 293 WESDNYAKKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWG 352
W D +K F +W TGYPLID+ + +L+++G+M NR R + SFL+++MG++W+ G
Sbjct: 356 WSQD---QKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMG 412
Query: 353 ENYFANKLNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQL 412
+F L D+D SN GNW + A G + R F+ Q++ +D +G ++ +L QL
Sbjct: 413 AEWFETCLLDYDPCSNYGNWTYGAGVGNDPRE-DRYFSIPKQAQNYDPEGEYVAFWLQQL 471
Query: 413 SKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKN 465
+L + H P + Y ++ +
Sbjct: 472 RRLPKEKRHWPGRLM--------------YMDTVVPLKHGNGPMAGGSKSGGG 510
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD,
DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}
Length = 440
Score = 486 bits (1253), Expect = e-171
Identities = 135/469 (28%), Positives = 223/469 (47%), Gaps = 61/469 (13%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
V VFI D L + + + F+ S++EL L+ S L + + A K +
Sbjct: 28 RVIPVFIADPRQLINNPYKS---EFAVSFMINSLLELDDELRKKGSRLNVFFGEAEKVVS 84
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+ K +DA+ +N DY P +I RD+ I+K + G +F +Y+D ++ K +
Sbjct: 85 RFFNK--VDAIYVNEDYTPFSISRDEKIRKVCEENGIEFKAYEDYLLTPK------SLFH 136
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSN 181
+ F+ + + + + + ++++ L F
Sbjct: 137 HRNFTSFYNEVSKV---------------KVREPETMEGSFDVTDSSMNVDFLLTF--KK 179
Query: 182 LSSLGIKTGASGAKILLNNFIKKIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLI 241
+ S + G LL+ + R+YP+ N LS HL+FGTIS+R+
Sbjct: 180 IESPLFRGGRREGLYLLHRNV-----DFRRRDYPAENNNYRLSPHLKFGTISMREAYY-- 232
Query: 242 FKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYAKK 301
G ++ +L WRDF+ ++ Y P+V +++EYDNI WE++ +
Sbjct: 233 ----------TQKGKEEFVRELYWRDFFTLLAYYNPHVFGHCYRREYDNISWENN---ES 279
Query: 302 NFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANKLN 361
F W +G TGYP+ID+ + LNS+GY++ R+RM+ A FL+K + ++W+WGE YFA KL
Sbjct: 280 YFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDWRWGERYFATKLV 339
Query: 362 DFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIH 421
D+D A NNGNWQW AS+G FR+FNP Q +KFD + FI++++ +L + IH
Sbjct: 340 DYDPAINNGNWQWIASTGV--DYMFRVFNPWKQQEKFDPEAKFIKEWVEELKDVPPSIIH 397
Query: 422 SPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKNILNRN 470
S +K YP PI+ + Y +K +L +
Sbjct: 398 SIYKTK-----------VPGYPSPIVNWLERVNYVKSEYKNVKAVLLEH 435
>2j07_A Deoxyribodipyrimidine photo-lyase; flavoprotein,
nucleotide-binding, DNA repair; HET: FAD HDF; 1.95A
{Thermus thermophilus} SCOP: a.99.1.1 c.28.1.1 PDB:
1iqu_A* 1iqr_A* 2j08_A* 2j09_A*
Length = 420
Score = 478 bits (1233), Expect = e-168
Identities = 89/466 (19%), Positives = 178/466 (38%), Gaps = 76/466 (16%)
Query: 2 EVYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIK 61
V + + D N L RR + +++ L + L + + +++
Sbjct: 28 PVVGLVVLDPNNLKTT-------PRRRAWFLENVRALREAYRARGGALWVLEGLPWEKVP 80
Query: 62 KLVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP 121
+ +L AV + P RD +++ L ++ + + +
Sbjct: 81 EAARRLKAKAVYALTSHTPYGRYRDGRVREAL--------PVPLHLLPAPHLLPPDLPRA 132
Query: 122 YSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCKSN 181
Y +++ + + + P L + G
Sbjct: 133 YRVYTPFSRLYRGA-------APPLPPPEALP-----------------KGPEEGEIPRE 168
Query: 182 LSSLGIKT-GASGAKILLNNFIK-KIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVK 239
L + G A L F++ K+ Y R+ G S LS + G +S R
Sbjct: 169 DPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFALGVLSPRLAAW 228
Query: 240 LIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWESDNYA 299
+ + G W+++L+WRDF +LY +P + + + W+ D
Sbjct: 229 EAERRGGE-------GARKWVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFPWQED--- 278
Query: 300 KKNFLNWCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWGENYFANK 359
+ F W +G TG PL+D+A+ +L+++G++ NR RM A F +K++ + WK E F +
Sbjct: 279 EALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHL 338
Query: 360 LNDFDLASNNGNWQWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKY 419
L D D A N WQW+ G + P+FR+FNP++Q ++ D +G +++++ P+ +
Sbjct: 339 LLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYA--- 395
Query: 420 IHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKKNILKRYNFIKN 465
P+++ +++ L+ +
Sbjct: 396 ----------------------PKDPVVDLEEARRRYLRLARDLAR 419
>3umv_A Deoxyribodipyrimidine photo-lyase; CPD cyclobutane pyrimidine
dimers, UV damaged DNA, DNA repai flavoprotein; HET:
FAD; 1.71A {Oryza sativa japonica group}
Length = 506
Score = 318 bits (818), Expect = e-104
Identities = 82/477 (17%), Positives = 145/477 (30%), Gaps = 65/477 (13%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
+ F L P R++ F+ + + L+ + + EI
Sbjct: 70 LAVAFA-----LFPRPFLLSARRRQLGFLLRGLRRLAADAAARHLPFFLFTGGP-AEIPA 123
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELK--VIGCKFFSYKDQVIFEKNEILNKTGK 120
LV +L ++ + + +L+ G + K
Sbjct: 124 LVQRLGASTLVADFSPLRPVREALDAVVGDLRREAPGVAVHQVDAHNVVPVWTASAKMEY 183
Query: 121 PYSIFS-FYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLNDLGFCK 179
F K E + P V L + + ++ ++ +C+
Sbjct: 184 SAKTFRGKVSKVMDEYLVEFPELPAVVPWDREQPEGVDWDALIARVCSEAENVPEIDWCE 243
Query: 180 SNLSSLGIKTGASGAKILLNNFI-KKIKNYNINRNYPSI-NGTSYLSIHLRFGTISIRKL 237
G + + F+ K+IK+Y +RN P+ S LS +L FG IS ++
Sbjct: 244 P-----GEEAAIEALLGSKDGFLTKRIKSYETDRNDPTKPRALSGLSPYLHFGHISAQRC 298
Query: 238 VKLIFKFIKKHYKTDCIGYFTWLSQLI-WRDFYQMILYCYPNVVNKSFKKEYDNILWESD 296
K K +L +L+ R+ Y P + S E+
Sbjct: 299 ALEAKKCRHLSPK----SVDAFLEELVVRRELADNFCYYQPQYDSLSGAWEWARKTLMDH 354
Query: 297 NYAKKNFLN----WCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKWG 352
K+ + T PL +++ +++ G MH +RM A +++ W G
Sbjct: 355 AADKREHIYTREQLENAKTHDPLWNASQLEMVHHGKMHGFMRMYWAKKILE-----WTSG 409
Query: 353 ENYF---ANKLN-----DFDLASNNGNWQWSA----SSGCSSQPFF---RIFNPIIQSKK 397
A LN D S WS G +P F R N +K
Sbjct: 410 PEEALSTAIYLNDKYEIDGRDPSGYVGCMWSICGLHDQGWKERPVFGKIRYMNYAGCKRK 469
Query: 398 FDYQGIFIRKYLPQLSKLSNKYIHSPWKASSYKLEKAGIILGKNYPKPILEHSLSKK 454
FD Y+ +L+ S K P P+++ S S+
Sbjct: 470 FDVDA--YISYVKRLAGQSKKRNAEE------------------SPNPVVKLSKSQH 506
>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD;
1.50A {Methanosarcina mazei} PDB: 2xrz_A*
Length = 482
Score = 308 bits (791), Expect = e-100
Identities = 79/432 (18%), Positives = 141/432 (32%), Gaps = 47/432 (10%)
Query: 3 VYCVFIFDKNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
V VF L+ R+ EF+ K + EL ++L ++I +
Sbjct: 69 VVVVFCLTDEFLEA-------GIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKISR 121
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPY 122
V N ++ + I+++ I+K + I FF + E K
Sbjct: 122 FVKDYNAGTLVTDFSPLR---IKNQWIEKVISGISIPFFEVDAHNVVPCWEASQKHEYAA 178
Query: 123 SIFS-FYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISL----NDLGF 177
F E ++ + L ++ + +L L
Sbjct: 179 HTFRPKLYALLPEFLEEFPELEPNSVTPELSAGAGMVETLSDVLETGVKALLPERALLKN 238
Query: 178 CKSNLSSLGIKTGASGAKILLNNFI-KKIKNYNINRNYPSINGTSYLSIHLRFGTISIRK 236
+ G AK ++ +FI ++ +Y RN P+ N S LS +L FG IS ++
Sbjct: 239 KDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQR 298
Query: 237 LVKLIFKFIKKHYKTDCIGYFTWLSQ-LIWRDFYQMILYCYPNVVNKSFKKEYDNILWES 295
+V + K +L + LIW++ Y P + +
Sbjct: 299 VVLEVEKAESNP-----GSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNA 353
Query: 296 DNYAKKNFLN----WCKGYTGYPLIDSAIIQLNSSGYMHNRLRMVTASFLIKNMGINWKW 351
++ + + G T PL +++ ++L S+G MH RM A +++ W
Sbjct: 354 HRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILE-----WSE 408
Query: 352 GENYF---ANKLN-----DFDLASNNGNWQWSASSGC-------SSQPFFRIFNPIIQSK 396
A LN D + WS R + +
Sbjct: 409 SPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKR 468
Query: 397 KFDYQGIFIRKY 408
KFD + +I KY
Sbjct: 469 KFDVKL-YIEKY 479
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 57.6 bits (138), Expect = 7e-09
Identities = 75/525 (14%), Positives = 160/525 (30%), Gaps = 161/525 (30%)
Query: 7 FIFD---KNILDPLRSQGIIEDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKKL 63
F+ + K++ D +S I+ I+ I S +S + + + + SK+ +++
Sbjct: 29 FVDNFDCKDVQDMPKS--ILSKEEIDHIIMSKDAVS------GTLRLF-WTLLSKQ-EEM 78
Query: 64 VIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKPYS 123
V K + + IN+ + + IK E + Y +Q + L + ++
Sbjct: 79 VQKFVEEVLRINYKF-----LMSP-IKTEQRQPSMMTRMYIEQR-----DRLYNDNQVFA 127
Query: 124 IFSFYQKKWIEKVKSNKCYLQSYPV----------KSYL-NNLVHSSKLHKIINNNIISL 172
++ + + K++ L+ K+++ ++ S K+ ++ I L
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWL 187
Query: 173 NDLGFCKSNLSSLGIKTGASGAKILLNNFIKKI-KNYNINRNYPSINGTSYLSIHLRFGT 231
N L C S + L +L + +I N+ ++ S +++
Sbjct: 188 N-LKNCNSPETVL----------EMLQKLLYQIDPNWTSRSDHSS---------NIKLRI 227
Query: 232 ISIRKLVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNI 291
SI+ ++ + K K Y+ +C L+ +L N+
Sbjct: 228 HSIQAELRRLLK--SKPYE-NC---------LL-------VL---------------LNV 253
Query: 292 LWESDNYAKKNFLNWCKGYTGYPLI---DSAII-QLNSSGYMHNRLRMVTASFLIKNMGI 347
+ A F CK L+ + L+++ H L + +
Sbjct: 254 -Q--NAKAWNAFNLSCK-----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE--- 302
Query: 348 NWKWGENYFANKLN--DFDLAS-------------------NNGNWQWSASSGCSS---- 382
++ L+ DL W C
Sbjct: 303 ----VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 383 -QPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKYIHSPWKASSY--------KLEK 433
+ + P K FD +F P + + + W KL K
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVF-----PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Query: 434 AGIILGKNYPKPILEHSLSK-------------KNILKRYNFIKN 465
++ + I S+ ++I+ YN K
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458
Score = 54.9 bits (131), Expect = 4e-08
Identities = 45/262 (17%), Positives = 89/262 (33%), Gaps = 76/262 (29%)
Query: 32 FKSIIELSINLQNYDSDLIIRYAIASKEIKKLVIKLNI--DAVMINHDYEPQAIIR---D 86
+IIE S+N+ E +K+ +L++ + I P ++
Sbjct: 355 LTTIIESSLNVLE------------PAEYRKMFDRLSVFPPSAHI-----PTILLSLIWF 397
Query: 87 KLIKKELKVIGCKFFSYKDQVIFEKNEILNKTGKP--YSIFSFYQ-------------KK 131
+IK ++ V+ K Y ++ K K SI S Y +
Sbjct: 398 DVIKSDVMVVVNKLHKYS---------LVEKQPKESTISIPSIYLELKVKLENEYALHRS 448
Query: 132 WIEKVKSNKCYLQSYPVKSYLNN---------LVHSSKLHKIINNNIISLNDLGFCKSNL 182
++ K + + YL+ L + ++ ++ L D F + +
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL-DFRFLEQKI 507
Query: 183 SSLGIKTGASGAKILLNNFIKKIKNYNINRNYPSINGTSYLSIHLRFGTISIRKLVKLIF 242
ASG+ + N ++++K Y + Y N Y +LV I
Sbjct: 508 RHDSTAWNASGS---ILNTLQQLKFY---KPYICDNDPKY------------ERLVNAIL 549
Query: 243 KFIKKHYKTDCIGY-FTWLSQL 263
F+ K + + I +T L ++
Sbjct: 550 DFLPKI-EENLICSKYTDLLRI 570
Score = 35.6 bits (81), Expect = 0.044
Identities = 26/174 (14%), Positives = 54/174 (31%), Gaps = 20/174 (11%)
Query: 7 FIFDKNILDPLRSQGII----EDRRIEFIFKSIIELSINLQNYDSDLIIRYAIASKEIKK 62
+F + P +I + + + + S+ + I +I + K
Sbjct: 379 SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVK 438
Query: 63 LVIKLNIDAVMINHDYEPQAIIRDKLIKKELKVIGCKFFSY--KDQVIFEKNEILNKTGK 120
L + + +++H P+ D LI L + K+ E+ +
Sbjct: 439 LENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV-- 496
Query: 121 PYSIFSFYQKKWIEKVKSNKCYLQSYPVKSYLNNLVHSSKLHKIINNNIISLND 174
+ F F ++K I + + N + K +K I ND
Sbjct: 497 -FLDFRFLEQK-IRHDSTAWN------ASGSILNTLQQLKFYK----PYICDND 538
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 43.9 bits (103), Expect = 1e-04
Identities = 47/285 (16%), Positives = 71/285 (24%), Gaps = 114/285 (40%)
Query: 175 LGFCKSNLSSLGIKTGASGAKILLNNFIKKIKNYNINRNYPSINGTSYLSIH---LRFGT 231
LG+ S + + + L F Y + G IH +
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEF---------ENCY--LEGN---DIHALAAKLLQ 110
Query: 232 ISIRKLVKLIFKFIKKHYKTDCIG-----------------------Y--F-------TW 259
+ LVK + IK + + F +
Sbjct: 111 ENDTTLVK-TKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY 169
Query: 260 LSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILWE---SDNYAKK------NFLNWCKG- 309
+L RD YQ Y +V K L E + A+K N L W +
Sbjct: 170 FEEL--RDLYQT----YHVLV-GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENP 222
Query: 310 -------YTGY-----PLIDSAIIQL-------NSSGYMHNRLR------------MVTA 338
Y PLI +IQL G+ LR +VTA
Sbjct: 223 SNTPDKDYLLSIPISCPLI--GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA 280
Query: 339 SFLIKNMGINWKWGENYFANKLNDFDLASNNGNWQWSASSGCSSQ 383
+ +W E++F + G
Sbjct: 281 VAI--AETDSW---ESFFVSVRKAI---------TVLFFIGVRCY 311
Score = 37.0 bits (85), Expect = 0.016
Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 25/115 (21%)
Query: 91 KELKVIGCKFFSYKDQVIFEKNEILNKTGK-PYSIFSFYQK-----KWIEKVKS--NKCY 142
+EL+ + + +I E L++ + + + +W+E + +K Y
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY 230
Query: 143 LQSYPVKSY----LNNLVHSSKLHKIINNNIISLNDLGFCKSNLSSLGIKTGASG 193
L S P+ S + L H +++ LGF L S GA+G
Sbjct: 231 LLSIPI-SCPLIGVIQLAHY----------VVTAKLLGFTPGELRS--YLKGATG 272
Score = 34.6 bits (79), Expect = 0.093
Identities = 43/227 (18%), Positives = 68/227 (29%), Gaps = 71/227 (31%)
Query: 217 INGTSYLSIHLRFGTISIRKLVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCY 276
++ S + L G++ LV T +F SQL ++ + IL
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVP-----------TAS--FFI-ASQL--QEQFNKIL--- 41
Query: 277 PNVVNKSFKKEYDNILWESDN-------YAKKNFLNWCKGYTGYPLIDSAIIQLNS---- 325
P D K FL GY + S + Q +
Sbjct: 42 PEPTEG---------FAADDEPTTPAELVGK--FL----GYVSSLVEPSKVGQFDQVLNL 86
Query: 326 ------SGYMH-NRLRMVTASFLIKNMGINWK---WGENYF-ANKLND--FDLASNNGNW 372
+ Y+ N + + A L +N K +NY A + FD SN+ +
Sbjct: 87 CLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146
Query: 373 QWSASSGCSSQPFFRIFNPIIQSKKFDYQGIFIRKYLPQLSKLSNKY 419
+ + G + IF QG Y +L L Y
Sbjct: 147 R-AVGEGNAQ--LVAIFGG---------QGN-TDDYFEELRDLYQTY 180
>1ybz_A Chorismate mutase; conserved hypothetical protein,
hyperthermophIle, structural genomics, PSI, protein
structu initiative; 1.82A {Pyrococcus furiosus} SCOP:
a.130.1.1
Length = 91
Score = 29.6 bits (67), Expect = 0.51
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 10 DKNILDPLRSQGIIEDRR-IEFIFKSIIELSINLQ 43
+ I D R + ++ IF+ I+E+S ++Q
Sbjct: 55 NLPIEDRKREEEVLRRAGEFREIFEKILEVSKDVQ 89
>2gtv_X CM, chorismate mutase; four-helix bundle, isomerase; HET: TSA;
NMR {Methanocaldococcus jannaschii} SCOP: a.130.1.3
Length = 104
Score = 29.7 bits (67), Expect = 0.56
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 12/47 (25%)
Query: 10 DKNILDPLRSQGIIEDRR------------IEFIFKSIIELSINLQN 44
I DP R + I + R IF+ +IE + LQ
Sbjct: 49 GIPINDPEREKYIYDRIRKLCKEHNVDENIGIKIFQRLIEHNKALQK 95
>1ecm_A Endo-oxabicyclic transition state analogue; P-protein, chorismate
mutase domain, chorismate mutase; HET: TSA; 2.20A
{Escherichia coli} SCOP: a.130.1.1
Length = 109
Score = 29.2 bits (66), Expect = 0.95
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 12/44 (27%)
Query: 13 ILDPLRSQGIIEDRR------------IEFIFKSIIELSINLQN 44
+ D R + ++E I +F+ IIE S+ Q
Sbjct: 46 VRDIDRERDLLERLITLGKAHHLDAHYITRLFQLIIEDSVLTQQ 89
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 1.2
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 17/33 (51%)
Query: 58 KEIKKL--VIKLNIDAVMINHDYEPQ-----AI 83
+ +KKL +KL Y AI
Sbjct: 20 QALKKLQASLKL----------YADDSAPALAI 42
Score = 29.1 bits (64), Expect = 2.0
Identities = 7/27 (25%), Positives = 17/27 (62%), Gaps = 5/27 (18%)
Query: 129 QKKWIEKVKSN-KCYL-QSYP---VKS 150
+K+ ++K++++ K Y S P +K+
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKA 44
>3rmi_A Chorismate mutase protein; emerald biostructures, structural
genomics, seattle structur genomics center for
infectious disease, ssgcid; 2.40A {Bartonella henselae}
Length = 114
Score = 28.6 bits (64), Expect = 1.9
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 12/44 (27%)
Query: 13 ILDPLRSQGIIEDRR------------IEFIFKSIIELSINLQN 44
+DPLR Q I+ R E K II+ ++
Sbjct: 53 AVDPLREQYQIKRLRKLAIDTHFDPDFAEKFLKFIIKEVVHQHE 96
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 29.5 bits (67), Expect = 1.9
Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 21/88 (23%)
Query: 3 VYCVFIFDKNILDPLRSQGII------EDRRIEFIFKSIIELSINLQNYDSDLIIRYAIA 56
V V + D+ ++ LR G+ +R E +F +I++ +
Sbjct: 19 VIGVAVIDEKNIERLRDIGVKDSKQLTPGQR-EKLFSKLIDIL---------DDYYVLLV 68
Query: 57 S-KEIKKLVIKLNIDAVMINHDYEPQAI 83
+ KEI + +N + + A+
Sbjct: 69 TPKEIDERHHSMNE----LEAEKFVVAL 92
>1vq8_X 50S ribosomal protein L31E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: d.29.1.1 PDB: 1vq4_X*
1vq5_X* 1vq6_X* 1vq7_X* 1s72_X* 1vq9_X* 1vqk_X* 1vql_X*
1vqm_X* 1vqn_X* 1vqo_X* 1vqp_X* 1yhq_X* 1yi2_X* 1yij_X*
1yit_X* 1yj9_X* 1yjn_X* 1yjw_X* 2otj_X* ...
Length = 92
Score = 27.8 bits (62), Expect = 2.1
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 18/51 (35%)
Query: 231 TISIRKL------------VKLIFKFIKKHYKTD----CIGYFTWLSQLIW 265
TI +R + LI + + KH+ D + +++ W
Sbjct: 12 TIPLRDARAEPNHKRADKAMILIREHLAKHFSVDEDAVRLD--PSINEAAW 60
>3ret_A Salicylate biosynthesis protein PCHB; intertwined dimer, lyase,
mutase; HET: SAL; 1.79A {Pseudomonas aeruginosa} PDB:
2h9d_A 3rem_A* 3hgx_A* 3hgw_C 2h9c_A
Length = 101
Score = 27.7 bits (62), Expect = 2.6
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 12/43 (27%)
Query: 13 ILDPLRSQGIIEDRR------------IEFIFKSIIELSINLQ 43
I P R ++ +R +E +F II I Q
Sbjct: 48 IPAPERVAAMLPERARWAEENGLDAPFVEGLFAQIIHWYIAEQ 90
>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain,
TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma
parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*
Length = 223
Score = 28.8 bits (65), Expect = 3.7
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 49 LIIRYAIASKEIKKLV--IKLNIDAVMINHDYEPQAIIRDKLIKKELKVIG---CKFFSY 103
L+ + I ++ I+ + ++ +V + E I E KVIG +FF
Sbjct: 44 LVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGIDEVQFFD- 102
Query: 104 KDQVIFEKNEILNKTGKP 121
D++ N + G
Sbjct: 103 -DRICEVANILAEN-GFV 118
>2d8d_A Aroag, phospho-2-dehydro-3-deoxyheptonate aldolase/chori mutase;
chorismate, dimer, structural genomics, NPPSFA; 1.15A
{Thermus thermophilus} SCOP: a.130.1.1 PDB: 2d8e_A
Length = 90
Score = 27.2 bits (61), Expect = 3.9
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 11/46 (23%)
Query: 10 DKNILDPLR-----------SQGIIEDRRIEFIFKSIIELSINLQN 44
DP R + G D I +FK I + S++L+
Sbjct: 41 GLPHYDPKREEEMLAYLTAENPGPFPDETIRKLFKEIFKASLDLEE 86
>3jxy_A Alkylpurine DNA glycosylase ALKD; heat repeat, DNA binding, DNA
glycosylase, DNA alkylation, L complex, hydrolase-DNA
complex; HET: DNA; 1.50A {Bacillus cereus} PDB: 3jx7_A*
3bvs_A 3jy1_A* 3jxz_A*
Length = 232
Score = 27.8 bits (61), Expect = 7.2
Identities = 10/73 (13%), Positives = 21/73 (28%), Gaps = 5/73 (6%)
Query: 234 IRKLVKLIFKFIKKHYKTDCIGYFTWLSQLIWRDFYQMILYCYPNVVNKSFKKEYDNILW 293
R+L+K I + + D L W + +++ K K + +
Sbjct: 43 RRQLLKDIIQIHTLPDQKDFQIIIREL----WDLPEREFQAAALDIMQKYKKHINETHIP 98
Query: 294 ESDNYAKKNFLNW 306
+ W
Sbjct: 99 FLEELIVT-KSWW 110
>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET:
ATP; NMR {Saccharomyces cerevisiae}
Length = 608
Score = 27.7 bits (62), Expect = 9.2
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 53 YAIASKEIKKLVIKLNIDAVMINHDYEPQAIIRDKLI 89
I SK I++ ++ A ++ HD+ + DK+I
Sbjct: 503 RIICSKVIRRFILHNKKTAFIVEHDFIMATYLADKVI 539
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.139 0.423
Gapped
Lambda K H
0.267 0.0628 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,260,373
Number of extensions: 433887
Number of successful extensions: 1095
Number of sequences better than 10.0: 1
Number of HSP's gapped: 998
Number of HSP's successfully gapped: 50
Length of query: 470
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 373
Effective length of database: 3,993,456
Effective search space: 1489559088
Effective search space used: 1489559088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.7 bits)