RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11420
(315 letters)
>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 = 346 bits (891), Expect = e-117
Identities = 172/274 (62%), Positives = 210/274 (76%), Gaps = 5/274 (1%)
Query: 3 YQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHL---VPTMKEMGLDESSIPLCKF 59
+ +V L+ +PK + ++P + + + PTMK++ + KF
Sbjct: 185 FLGIVEQLK-VPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKF 243
Query: 60 PGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELK 119
PGGETEAL+R+E+SL ++ WV +FEKPNTAPNSLEPSTTVLSPYLKFGCLS RLF +LK
Sbjct: 244 PGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLK 303
Query: 120 KILATGP-HAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAW 178
+I+ P H++PPVSL+GQ+ WREFYY V + PNFD+M GN C Q+ W + +LEAW
Sbjct: 304 EIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQEHPDHLEAW 363
Query: 179 SHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADW 238
+HG+TGYPFIDAIMRQLR EGWIHHLARHAVACFLTRGDL++SWEEGQ VFE+LLLD DW
Sbjct: 364 THGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDW 423
Query: 239 AMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDK 272
A+NAGNWMWLSASAFFHQ+FRVYSPVAFGKKTD
Sbjct: 424 ALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDP 457
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A
{Arabidopsis thaliana}
Length = 537
Score = 338 bits (868), Expect = e-113
Identities = 146/275 (53%), Positives = 185/275 (67%), Gaps = 3/275 (1%)
Query: 1 MTYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGL-DESSIPLCKF 59
++YQ + V K S I + VP+++E+G D+ F
Sbjct: 159 LSYQSFLKVAGEPSCAKSELVMSYSSLPPIGDIGNLGISEVPSLEELGYKDDEQADWTPF 218
Query: 60 PGGETEALKRLEKSLANKEWVRKFEKPNTAPNSL-EPSTTVLSPYLKFGCLSVRLFYHEL 118
GGE+EALKRL KS+++K WV FEKP P++ +P+TTV+SPYLKFGCLS R FY L
Sbjct: 219 RGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCL 278
Query: 119 KKILATGP-HAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEA 177
+ I H PPVSLLGQ+ WREF+Y TPNFDKMKGN+IC Q+ W+ + L A
Sbjct: 279 QNIYKDVKKHTSPPVSLLGQLLWREFFYTTAFGTPNFDKMKGNRICKQIPWNEDHAMLAA 338
Query: 178 WSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDAD 237
W GKTGYP+IDAIM QL GW+HHLARH VACFLTRGDL++ WE+G+ VFE LL+D+D
Sbjct: 339 WRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSD 398
Query: 238 WAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDK 272
WA+N GNWMWLS S+FF+QF R+YSP++FGKK D
Sbjct: 399 WAINNGNWMWLSCSSFFYQFNRIYSPISFGKKYDP 433
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 320 bits (822), Expect = e-106
Identities = 103/289 (35%), Positives = 149/289 (51%), Gaps = 19/289 (6%)
Query: 3 YQKLVSVLESLPKPKPA---DDAPTSLPRECQGILHPDEHLVPTMKEMGL---DESSIPL 56
+ V ++ P+P +DA +PT + + + +
Sbjct: 160 FLHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAK 219
Query: 57 CKFPGGETEALKRLEKSLANK--EWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLF 114
+ GGET+AL L++ L + + R F PN A ++ S +S +L+FGCLSVR F
Sbjct: 220 INWRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRF 279
Query: 115 YHELKKIL--------ATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQV 166
Y + + G + GQ+ WRE++Y + + PN+D+M+GN IC +
Sbjct: 280 YWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSI 339
Query: 167 DWD-TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEG 225
W NE L++W G+TG+P ID MRQL EGW+HH R+ VA FLTRG L+ SWE G
Sbjct: 340 PWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHG 399
Query: 226 QSVFEELLLDADWAMNAGNWMWLSASAFFHQ--FFRVYSPVAFGKKTDK 272
F + LLDADW++ AGNWMW+S+SAF V PVA K+ D
Sbjct: 400 LQHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDP 448
>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 = 286 bits (734), Expect = 1e-93
Identities = 70/264 (26%), Positives = 118/264 (44%), Gaps = 8/264 (3%)
Query: 11 ESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPL-CKFPGGETEALKR 69
E+ + + P SL D VPT++++G++ + +F GGE+ + R
Sbjct: 202 EAKCSIRSSTRIPLSLG---PTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGR 258
Query: 70 LEKSLANKEWVRKFEKP-NTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHA 128
+ + K+ ++ +++ N +T SP+L FGC+S R Y E+++
Sbjct: 259 VFEYFWKKDLLKVYKETRNGMLG--PDYSTKFSPWLAFGCISPRFIYEEVQRYEKERVAN 316
Query: 129 KPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFI 188
+L ++ WR+++ + N G Q W ++K E+W KTGYP I
Sbjct: 317 NSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRNVQGKWSQDQKLFESWRDAKTGYPLI 376
Query: 189 DAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWL 248
DA M++L G++ + R V FL R D+ L W G FE LLD D N GNW +
Sbjct: 377 DANMKELSTTGFMSNRGRQIVCSFLVR-DMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 435
Query: 249 SASAFFHQFFRVYSPVAFGKKTDK 272
+ + R +S + D
Sbjct: 436 AGVGNDPREDRYFSIPKQAQNYDP 459
>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 = 274 bits (703), Expect = 2e-89
Identities = 68/264 (25%), Positives = 114/264 (43%), Gaps = 4/264 (1%)
Query: 9 VLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALK 68
+ + +P AP+ L L ++ D S+ F GGET L
Sbjct: 164 IEKKKISIRPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVLA--FQGGETAGLA 221
Query: 69 RLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHA 128
RL+ + + ++ +++ ++ SP+L GCLS R Y E+K+
Sbjct: 222 RLQDYFWHGDRLKDYKETRNGMVGA-DYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSN 280
Query: 129 KPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFI 188
L+ ++ WR+F+ V N +G + W ++ E W G+TGYP +
Sbjct: 281 DSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFPWQEDQVRFELWRSGQTGYPLV 340
Query: 189 DAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWL 248
DA MR+L L G++ + R VA FL + +L + W G FE L+D D N GNW +
Sbjct: 341 DANMRELNLTGFMSNRGRQNVASFLCK-NLGIDWRWGAEWFESCLIDYDVCSNWGNWNYT 399
Query: 249 SASAFFHQFFRVYSPVAFGKKTDK 272
+ + FR ++ ++ D
Sbjct: 400 AGIGNDARDFRYFNIPKQSQQYDP 423
>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 = 155 bits (393), Expect = 9e-44
Identities = 81/290 (27%), Positives = 121/290 (41%), Gaps = 45/290 (15%)
Query: 3 YQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGG 62
++ + + P P + S P + I +PT+K++G D G
Sbjct: 153 WKNWQAQPKPTPVATPTELVDLS-PEQLTAIAPLLLSELPTLKQLGFDWDG--GFPVEPG 209
Query: 63 ETEALKRLEKSLANK----EWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHEL 118
ET A+ RL++ + R F P E T+ LSP LKFG + +R +
Sbjct: 210 ETAAIARLQEFCDRAIADYDPQRNF------PA--EAGTSGLSPALKFGAIGIRQAWQAA 261
Query: 119 KKILATGPHAKPPVSL---LGQIYWREFYY---------VVGSDTPNFDKMKGNKICCQV 166
A + S+ ++ WREFY G + +
Sbjct: 262 SAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFP-------- 313
Query: 167 DWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQ 226
W+ E AW+ +TGYP +DA MRQL GW+H+ R VA FLT+ DL + W G+
Sbjct: 314 -WENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTK-DLIIDWRRGE 371
Query: 227 SVFEELLLDADWAMNAGNWMWLSAS----AFFHQFFRVYSPVAFGKKTDK 272
F + L+D D A N G W W SAS + R+++P + KK D
Sbjct: 372 QFFMQHLVDGDLAANNGGWQW-SASSGMDP---KPLRIFNPASQAKKFDA 417
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD,
DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}
Length = 440
Score = 154 bits (391), Expect = 1e-43
Identities = 77/265 (29%), Positives = 112/265 (42%), Gaps = 50/265 (18%)
Query: 21 DAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLANKEWV 80
P +G + + + + PL F GG E L L +++ +
Sbjct: 149 KVKVREPETMEGSFDVTDSSMNVDFLLTFKKIESPL--FRGGRREGLYLLHRNVDFRR-- 204
Query: 81 RKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYW 140
R + P E + LSP+LKFG +S+R Y+ K + ++YW
Sbjct: 205 RDY------PA--ENNNYRLSPHLKFGTISMREAYYTQKGK----------EEFVRELYW 246
Query: 141 REFYY--------VVGSD-TPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAI 191
R+F+ V G +D + W+ NE Y EAW G+TGYP IDA
Sbjct: 247 RDFFTLLAYYNPHVFGHCYRREYDNIS---------WENNESYFEAWKEGRTGYPIIDAG 297
Query: 192 MRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWLSAS 251
MR L G+I+ R VA FL + L++ W G+ F L+D D A+N GNW W AS
Sbjct: 298 MRMLNSTGYINGRVRMLVAFFLVK-VLFVDWRWGERYFATKLVDYDPAINNGNWQW-IAS 355
Query: 252 ----AFFHQFFRVYSPVAFGKKTDK 272
FRV++P +K D
Sbjct: 356 TGVDY----MFRVFNPWKQQEKFDP 376
>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 = 152 bits (387), Expect = 6e-43
Identities = 81/281 (28%), Positives = 112/281 (39%), Gaps = 52/281 (18%)
Query: 11 ESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRL 70
E +P+ A +S E P + D + FP E A+ +L
Sbjct: 163 EGMPECVAAPKVRSSGSIE------PSPSITLNYPRQSFDTA-----HFPVEEKAAIAQL 211
Query: 71 EKSLANK----EWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGP 126
+ N E R F P T+ LS L G LS R H L
Sbjct: 212 RQFCQNGAGEYEQQRDF------PA--VEGTSRLSASLATGGLSPRQCLHRLLAEQPQAL 263
Query: 127 HAKPPVSLLGQIYWREFYYVV----------GSDTPNFDKMKGNKICCQVDWDTNEKYLE 176
L ++ WREFY + D+++ W +N +L+
Sbjct: 264 DGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQ---------WQSNPAHLQ 314
Query: 177 AWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDA 236
AW GKTGYP +DA MRQL GW+H+ R A FL + DL + W EG+ F L+D
Sbjct: 315 AWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVK-DLLIDWREGERYFMSQLIDG 373
Query: 237 DWAMNAGNWMWLSAS----AFFHQ-FFRVYSPVAFGKKTDK 272
D A N G W W +AS A +FR+++P G+K D
Sbjct: 374 DLAANNGGWQW-AASTGTDA---APYFRIFNPTTQGEKFDH 410
>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 = 151 bits (383), Expect = 9e-43
Identities = 72/280 (25%), Positives = 106/280 (37%), Gaps = 62/280 (22%)
Query: 11 ESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRL 70
P P +A P E E+ ++ +PL GE AL L
Sbjct: 144 RGAAPPLPPPEALPKGPEE---------------GEIPREDPGLPL--PEPGEEAALAGL 186
Query: 71 EKSLANKEWVRKFEK----PNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGP 126
L K + ++ + + + LSPY G LS RL E ++ G
Sbjct: 187 RAFLEAK--LPRYAEERDRLD------GEGGSRLSPYFALGVLSPRLAAWEAERRGGEGA 238
Query: 127 HAKPPVSLLGQIYWREFYY---------VVGSDTPNFDKMKGNKICCQVDWDTNEKYLEA 177
+ ++ WR+F Y P F W +E +A
Sbjct: 239 RK-----WVAELLWRDFSYHLLYHFPWMAERPLDPRFQAFP---------WQEDEALFQA 284
Query: 178 WSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDAD 237
W GKTG P +DA MR+L G++ + AR A F + L L W+ + F LLLD D
Sbjct: 285 WYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVK-HLLLPWKRCEEAFRHLLLDGD 343
Query: 238 WAMNAGNWMWLSAS----AFFHQ-FFRVYSPVAFGKKTDK 272
A+N W W + A +FRV++PV G++ D
Sbjct: 344 RAVNLQGWQW-AGGLGVDA---APYFRVFNPVLQGERHDP 379
>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 = 146 bits (371), Expect = 2e-40
Identities = 64/287 (22%), Positives = 98/287 (34%), Gaps = 46/287 (16%)
Query: 9 VLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALK 68
L P+ P + D + E G + + G + K
Sbjct: 165 CLSMPYDPESPLLPPKKIISGDVSKCVADPLVFEDDSEKGSNALLARA--WSPGWSNGDK 222
Query: 69 RLEKSLANK----EWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILAT 124
L + R+ + +T+ LSP+L FG +SVR +H ++
Sbjct: 223 ALTTFINGPLLEYSKNRRK------AD--SATTSFLSPHLHFGEVSVRKVFHLVRIKQVA 274
Query: 125 GPHAKPPVSL------LGQIYWREFYY---------VVGSDTPNFDKMKGNKICCQVDWD 169
+ L I RE+ + W
Sbjct: 275 WANEGNEAGEESVNLFLKSIGLREYSRYISFNHPYSHERPLLGHLKFFP---------WA 325
Query: 170 TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVF 229
+E Y +AW G+TGYP +DA MR+L GW+H R V+ F + L L W G F
Sbjct: 326 VDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVK-VLQLPWRWGMKYF 384
Query: 230 EELLLDADWAMNAGNWMWLSAS----AFFHQFFRVYSPVAFGKKTDK 272
+ LLDAD +A W + + +F R+ +P G K D
Sbjct: 385 WDTLLDADLESDALGWQY-ITGTLPDS--REFDRIDNPQFEGYKFDP 428
>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD;
1.50A {Methanosarcina mazei} PDB: 2xrz_A*
Length = 482
Score = 136 bits (345), Expect = 6e-37
Identities = 57/297 (19%), Positives = 95/297 (31%), Gaps = 39/297 (13%)
Query: 3 YQKLVSVLESLPKPKPADDAPTSLPRECQGILHPD------EHLVPTMKEMGLDESSIPL 56
Y L LE P+ +P P D + L+P + +
Sbjct: 186 YALLPEFLEEFPELEPNSVTPELSAGAGMVETLSDVLETGVKALLPERALLKNKDPLFEP 245
Query: 57 CKFPGGETEALKRLEKSLANKEWVRKFEK----PNTAPNSLEPSTTVLSPYLKFGCLSVR 112
F GE A K +E +A++ + + P + + LSPYL FG +S +
Sbjct: 246 WHFEPGEKAAKKVMESFIADR--LDSYGALRNDPT------KNMLSNLSPYLHFGQISSQ 297
Query: 113 LFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKG-------NKICCQ 165
E++K + K L + W+E P +D + + +
Sbjct: 298 RVVLEVEKAESNPGSKK--AFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHR 355
Query: 166 VDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLT--RGDLYLSWE 223
D ++ LE + GKT P +A +L G +H R A + + E
Sbjct: 356 NDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALE 415
Query: 224 EGQSVFEELLLDADWAMNAGNWMWLSAS-----AFFHQ----FFRVYSPVAFGKKTD 271
+ + LD W S A+ + R S +K D
Sbjct: 416 IAICLNDRYELDGRDPNGYAGIAW-SIGGVHDRAWGEREVTGKIRYMSYEGCKRKFD 471
>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 = 112 bits (282), Expect = 4e-28
Identities = 51/285 (17%), Positives = 89/285 (31%), Gaps = 30/285 (10%)
Query: 9 VLESLPKPKPADDAPTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALK 68
V++ P A RE + D + E+ + GE A++
Sbjct: 195 VMDEYLVEFPELPAVVPWDREQPEGVDWDA---LIARVCSEAENVPEIDWCEPGEEAAIE 251
Query: 69 RLEKSLAN--KEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGP 126
L S + ++ +E P + + LSPYL FG +S + E KK P
Sbjct: 252 ALLGSKDGFLTKRIKSYETDRNDPTKPR-ALSGLSPYLHFGHISAQRCALEAKKCRHLSP 310
Query: 127 HAKPPVSLLGQ-IYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEK-------YLEAW 178
+ + L + + RE P +D + G + + E
Sbjct: 311 KSV--DAFLEELVVRRELADNFCYYQPQYDSLSGAWEWARKTLMDHAADKREHIYTREQL 368
Query: 179 SHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFL---TRGDLYLSWEEGQSVFEELLLD 235
+ KT P +A ++ G +H R A + T G + + ++ +D
Sbjct: 369 ENAKTHDPLWNASQLEMVHHGKMHGFMRMYWAKKILEWTSGPEE-ALSTAIYLNDKYEID 427
Query: 236 ADWAMNAGNWMWLSASAFFHQFF---------RVYSPVAFGKKTD 271
MW S Q + R + +K D
Sbjct: 428 GRDPSGYVGCMW-SICGLHDQGWKERPVFGKIRYMNYAGCKRKFD 471
>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 = 46.1 bits (108), Expect = 2e-06
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 63 ETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTV 99
E +ALK+L+ SL K ++AP +L T+
Sbjct: 18 EKQALKKLQASL-------KLYADDSAP-ALAIKATM 46
Score = 27.6 bits (60), Expect = 4.2
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 4/20 (20%)
Query: 4 QKLVSVLESLPKPKPADDAP 23
+KL + SL K D AP
Sbjct: 23 KKLQA---SL-KLYADDSAP 38
>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 = 48.7 bits (115), Expect = 2e-06
Identities = 44/288 (15%), Positives = 79/288 (27%), Gaps = 86/288 (29%)
Query: 23 PTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLANKEWVR- 81
P LPRE +P ++ I R + W
Sbjct: 315 PQDLPREVLTT-NP---RRLSI---------IA----------ESIRDGLAT-WDNWKHV 350
Query: 82 KFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWR 141
+K T +E S VL P R + L + P A P LL + W
Sbjct: 351 NCDKLTTI---IESSLNVLEPAE------YRKMFDRLS-VFP--PSAHIPTILL-SLIWF 397
Query: 142 EF-YYVVGSDTPNFDKM----KGNK------------ICCQVDWDTN------EKY--LE 176
+ V K K K + +++ + + Y +
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457
Query: 177 AWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDA 236
+ P++D + H+ H L + F + LD
Sbjct: 458 TFDSDDLIPPYLDQY--------FYSHIGHH-----LKNIEHPERMTL----FRMVFLDF 500
Query: 237 DW---AMNAGNWMWLSASAFFHQF--FRVYSPVAFGKKTDKFELLLDA 279
+ + + W ++ + + + Y P K+E L++A
Sbjct: 501 RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY-ICDNDPKYERLVNA 547
>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine,
iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter
sphaeroides}
Length = 522
Score = 34.4 bits (79), Expect = 0.044
Identities = 12/69 (17%), Positives = 25/69 (36%), Gaps = 7/69 (10%)
Query: 138 IYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRL 197
+ WRE+ + + + D ++ N + + T + A + Q R
Sbjct: 318 LGWREYVRGIWTLSGP-DYIRSN------GLGHSAALPPLYWGKPTRMACLSAAVAQTRD 370
Query: 198 EGWIHHLAR 206
+ HH+ R
Sbjct: 371 LAYAHHIQR 379
>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 = 33.9 bits (77), Expect = 0.073
Identities = 30/198 (15%), Positives = 53/198 (26%), Gaps = 69/198 (34%)
Query: 49 LDESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGC 108
+ S+ L + +A K + L EW+ E P+ P+ YL
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWL---ENPSNTPDK---------DYL---- 231
Query: 109 LSVRLFYHELKKILATGPHAKPPVSL----LGQIYWREFYYVV----GSDTPNF-DKMKG 159
P+S + Q+ Y V G +KG
Sbjct: 232 -------------------LSIPISCPLIGVIQLAH---YVVTAKLLGFTPGELRSYLKG 269
Query: 160 NKICCQ-----VDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWI----HHLARHAVA 210
Q V A + + F ++ + + + +I + +
Sbjct: 270 ATGHSQGLVTAV----------AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPN--- 316
Query: 211 CFLTRGDLYLSWEEGQSV 228
L L S E + V
Sbjct: 317 TSLPPSILEDSLENNEGV 334
Score = 30.8 bits (69), Expect = 0.73
Identities = 30/163 (18%), Positives = 40/163 (24%), Gaps = 68/163 (41%)
Query: 23 PTSLPRECQGILHPDEHLVPTMKEMGLDESSIPLCKFPGGETEALKRLEKSLANKEWVRK 82
P SL L GLD+S IP + RK
Sbjct: 383 PQSLYGLNL-------TLRKAKAPSGLDQSRIPFSE----------------------RK 413
Query: 83 --FEK---PNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKK--ILATGPHAKPPVSLL 135
F P +P S L + L +L K + + PV
Sbjct: 414 LKFSNRFLPVASP--------FHSHLLV---PASDLINKDLVKNNVSFNAKDIQIPV--- 459
Query: 136 GQIY-------WREFYYVVGSDTPNFDKMKGNKICCQ-VDWDT 170
Y R + GS + I V W+T
Sbjct: 460 ---YDTFDGSDLRV---LSGSISERIVDC----IIRLPVKWET 492
Score = 28.5 bits (63), Expect = 3.5
Identities = 43/238 (18%), Positives = 74/238 (31%), Gaps = 95/238 (39%)
Query: 47 MGLD--ESSIPLCKFPGGETEALKRLEKSLANK------EWVRKFEKPNTAPNSLEPSTT 98
MG+D ++S + + R + + + V N P +L T
Sbjct: 1631 MGMDLYKTS-KAAQ------DVWNRADNHFKDTYGFSILDIVIN----N--PVNL----T 1673
Query: 99 VLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMK 158
+ FG G K +I RE Y + +T K+K
Sbjct: 1674 IH-----FG-----------------GEKGK-------RI--RENYSAMIFETIVDGKLK 1702
Query: 159 GNKICCQVDWDTNEKYLEAWSHGK-----TGY--PFI----DAIMRQLRLEGWI---HHL 204
KI +++ + Y + K T + P + A L+ +G I
Sbjct: 1703 TEKIFKEINEHST-SYT--FRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATF 1759
Query: 205 ARH------AVACFLTRGDLYLSWEE--------GQSVFEELLLD----ADWAMNAGN 244
A H A+A D +S E G ++ + D +++ M A N
Sbjct: 1760 AGHSLGEYAALASL---AD-VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAIN 1813
>2kp6_A Uncharacterized protein; unknown function, structural genomics,
PSI-2, protein struct initiative; NMR {Chromobacterium
violaceum}
Length = 82
Score = 28.1 bits (63), Expect = 0.97
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 222 WEEGQSVF--EELLLDADWAM 240
W Q+ F + L DA+W+
Sbjct: 48 WTPAQAAFLRQALECDAEWSE 68
>2csk_A Sorting nexin 12; SNX12, PX domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 146
Score = 27.5 bits (61), Expect = 4.0
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 9/63 (14%)
Query: 172 EKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVAC-------FLTRGDLYLSWEE 224
+ G FI+ R+ LE +I+ +A H +A FL + ++
Sbjct: 81 RQLPFRGDEGIFEESFIE--ERRQGLEQFINKIAGHPLAQNERCLHMFLQEEAIDRNYVP 138
Query: 225 GQS 227
G+S
Sbjct: 139 GKS 141
>2y4o_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: DLL; 1.90A {Burkholderia cenocepacia}
Length = 443
Score = 27.7 bits (62), Expect = 5.6
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 39 HLVPTMKEMGLDESSIPLCK-FPGGE--TEAL-KRLEKSL 74
+L+ M G+D + L G E T+AL +E +
Sbjct: 197 NLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRV 236
>2y27_A Phenylacetate-coenzyme A ligase; phenylacetic acid degradation
pathway; HET: MSE PG4 ATP; 1.60A {Burkholderia
cenocepacia} PDB: 2y4n_A*
Length = 437
Score = 27.6 bits (62), Expect = 5.8
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 4/40 (10%)
Query: 39 HLVPTMKEMGLDESSIPLCK-FPGGE--TEAL-KRLEKSL 74
+ ++ GLD L G E T + +E+ +
Sbjct: 195 SIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRM 234
>3evn_A Oxidoreductase, GFO/IDH/MOCA family; structural genomics; 2.00A
{Streptococcus agalactiae serogroup V}
Length = 329
Score = 27.2 bits (61), Expect = 7.3
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 188 IDAIMRQLRLEGWIHHL 204
I+ + R EG HH
Sbjct: 312 IEDLYRSWGKEGHHHHH 328
>3kjd_A Poly [ADP-ribose] polymerase 2; transferase, enzyme-inhibitor
complex, catalytic fragment, S genomics, structural
genomics consortium, SGC; HET: 78P; 1.95A {Homo
sapiens} PDB: 3kcz_A* 1gs0_A
Length = 368
Score = 27.4 bits (60), Expect = 7.7
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 7/78 (8%)
Query: 15 KPKPADDAPTSLPRECQG---ILHPDEHLVPTMKEMGLDESSIPLCKFPGGE----TEAL 67
+ S+ Q ++ + + M EM + PL K + ++L
Sbjct: 12 DLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSL 71
Query: 68 KRLEKSLANKEWVRKFEK 85
K++E + + R +
Sbjct: 72 KKIEDCIRAGQHGRALME 89
>2sas_A Sarcoplasmic calcium-binding protein; 2.40A {Branchiostoma
lanceolatum} SCOP: a.39.1.5
Length = 185
Score = 26.8 bits (59), Expect = 8.1
Identities = 6/43 (13%), Positives = 12/43 (27%), Gaps = 2/43 (4%)
Query: 205 ARHAVACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMW 247
G + + ++ LL +AGN +
Sbjct: 141 VPAVYNVITDGGKVTFDLNRYKELYYRLLTSPA--ADAGNTLM 181
>3ke3_A Putative serine-pyruvate aminotransferase; structural genomi center
for structural genomics, JCSG, protein structure INI
PSI-2; HET: LLP; 2.20A {Psychrobacter arcticus 273-4}
Length = 379
Score = 27.0 bits (60), Expect = 8.8
Identities = 7/58 (12%), Positives = 16/58 (27%), Gaps = 9/58 (15%)
Query: 167 DWDTNEKYLEAWSHGKTGYPF---IDAI------MRQLRLEGWIHHLARHAVACFLTR 215
D + A+ +G Y D++ + + + G+ R
Sbjct: 231 DLKQWLTIMRAYENGGHAYHATMPTDSLRQFRDAILEAKEIGFDILRDAQWELGNRVR 288
>1efy_A Poly (ADP-ribose) polymerase; benzimidazole, inhibitor, catalytic
fragment, transferase; HET: BZC; 2.20A {Gallus gallus}
SCOP: a.41.1.1 d.166.1.2 PDB: 1a26_A* 1pax_A* 2paw_A
2pax_A* 3pax_A* 4pax_A* 2rcw_A* 1uk1_A* 1wok_A* 1uk0_A*
2rd6_A* 3gjw_A* 3gn7_A* 3l3l_A* 3l3m_A*
Length = 350
Score = 27.0 bits (59), Expect = 9.3
Identities = 8/52 (15%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 38 EHLVPTMKEMGLDESSIPLCKFPGGE----TEALKRLEKSLANKEWVRKFEK 85
E + M E +D +PL K + L +++++++ +
Sbjct: 19 ESMKKAMVEFEIDLQKMPLGKLSKRQIQSAYSILNEVQQAVSDGGSESQILD 70
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
0.321 0.136 0.446
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,155,710
Number of extensions: 304161
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 671
Number of HSP's successfully gapped: 43
Length of query: 315
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 222
Effective length of database: 4,105,140
Effective search space: 911341080
Effective search space used: 911341080
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: 57 (25.9 bits)