RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4171
(309 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 = 382 bits (982), Expect = e-131
Identities = 153/294 (52%), Positives = 195/294 (66%), Gaps = 2/294 (0%)
Query: 18 RIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAP-VTPLLVRQATTPLRDDHDEKYGVPTL 76
+I KN GK P+TY +F IV ++ P P + + Y PT+
Sbjct: 169 LVIAKNLGKAPITYQKFLGIVEQLKVPKVLGVPEKLKNMPTPPKDEVEQKDSAAYDCPTM 228
Query: 77 EELGFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFL 136
++L E L P + GGETEA+RR+E L+ + WVA F +P P SL S T LSP+L
Sbjct: 229 KQLVKRPEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYL 288
Query: 137 RFGCLSTRLFYHDLNKLYKRIKKA-PPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPIC 195
+FGCLS RLF L ++ KR K PP+SL GQL+WREF+Y A PNFDRMLGN C
Sbjct: 289 KFGCLSARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYC 348
Query: 196 VQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWE 255
+QIPW + + L W + +TG+P+IDAIM QLR+EGWIHHLARHAVACFLTRGDLW+SWE
Sbjct: 349 MQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWE 408
Query: 256 EGMKIFDELLLDADWSVNAGMWMWLSCSSFFQQFFHCYCPVKFGRKADPNGDFI 309
EG ++F++LLLD DW++NAG WMWLS S+FF Q+F Y PV FG+K DP G +I
Sbjct: 409 EGQRVFEQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTDPQGHYI 462
>3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A
{Arabidopsis thaliana}
Length = 537
Score = 371 bits (955), Expect = e-127
Identities = 148/295 (50%), Positives = 192/295 (65%), Gaps = 7/295 (2%)
Query: 18 RIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLE 77
IIEKNGGK PL+Y F + + L + VP+LE
Sbjct: 148 HIIEKNGGKPPLSYQSFLKVAGEPSCAKSELVMSYSSL----PPIGDIGNLGISEVPSLE 203
Query: 78 ELGF-DIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQT-GLSPF 135
ELG+ D E ++GGE+EA++RL + + KAWVA+F +PK P + L T +SP+
Sbjct: 204 ELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKPATTVMSPY 263
Query: 136 LRFGCLSTRLFYHDLNKLYKRIKK-APPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPI 194
L+FGCLS+R FY L +YK +KK PP+SL GQLLWREFFY A PNFD+M GN I
Sbjct: 264 LKFGCLSSRYFYQCLQNIYKDVKKHTSPPVSLLGQLLWREFFYTTAFGTPNFDKMKGNRI 323
Query: 195 CVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSW 254
C QIPW+ + LA W + +TG+PWIDAIM QL + GW+HHLARH VACFLTRGDL++ W
Sbjct: 324 CKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFIHW 383
Query: 255 EEGMKIFDELLLDADWSVNAGMWMWLSCSSFFQQFFHCYCPVKFGRKADPNGDFI 309
E+G +F+ LL+D+DW++N G WMWLSCSSFF QF Y P+ FG+K DP+G +I
Sbjct: 384 EQGRDVFERLLIDSDWAINNGNWMWLSCSSFFYQFNRIYSPISFGKKYDPDGKYI 438
>3tvs_A Cryptochrome-1; circadian clock light entrainment, jetlag,
phosphorylation, gene regulation, signaling protein;
HET: TPO FAD; 2.30A {Drosophila melanogaster}
Length = 538
Score = 346 bits (891), Expect = e-117
Identities = 119/310 (38%), Positives = 158/310 (50%), Gaps = 18/310 (5%)
Query: 18 RIIEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVT--PLLVRQATTPLRDDHDEKYGVPT 75
+IE NGG PLTY F V + P A + +PT
Sbjct: 144 LVIETNGGIPPLTYQMFLHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPT 203
Query: 76 LEELGF---DIEGLLPPTWKGGETEAMRRLERHLERK--AWVASFGRPKMTPQSLLASQT 130
E ++ L W+GGET+A+ L+ L+ + A+ F P ++ S
Sbjct: 204 PEHFNVYGDNMGFLAKINWRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPK 263
Query: 131 GLSPFLRFGCLSTRLFYHDLNKLYKRIKKA--------PPPLSLHGQLLWREFFYCAATR 182
+S LRFGCLS R FY ++ L+K ++ + GQL+WRE+FY +
Sbjct: 264 SMSAHLRFGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVN 323
Query: 183 NPNFDRMLGNPICVQIPWD-VNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAV 241
NPN+DRM GN IC+ IPW N L W QTGFP ID M QL EGW+HH R+ V
Sbjct: 324 NPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTV 383
Query: 242 ACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSSFFQQFFH--CYCPVKFG 299
A FLTRG LW SWE G++ F + LLDADWSV AG WMW+S S+F + CPV
Sbjct: 384 ATFLTRGGLWQSWEHGLQHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALA 443
Query: 300 RKADPNGDFI 309
++ DP+G +I
Sbjct: 444 KRLDPDGTYI 453
>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 = 311 bits (798), Expect = e-103
Identities = 78/294 (26%), Positives = 129/294 (43%), Gaps = 16/294 (5%)
Query: 20 IEKNGGKTPLTYHQFQSIV-AKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEE 78
+ + P Y QF+ V AK S P + D+ VPTLE+
Sbjct: 183 LPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIP--------LSLGPTPSVDDWGDVPTLEK 234
Query: 79 LGFDIEGLLPPT-WKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQ--TGLSPF 135
LG + + + + GGE+ + R+ + +K + + K T +L T SP+
Sbjct: 235 LGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVY---KETRNGMLGPDYSTKFSPW 291
Query: 136 LRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPIC 195
L FGC+S R Y ++ + K + +L+WR++F + + N LG P
Sbjct: 292 LAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRN 351
Query: 196 VQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWE 255
VQ W + + W +A+TG+P IDA M +L G++ + R V FL R D+ + W
Sbjct: 352 VQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR-DMGLDWR 410
Query: 256 EGMKIFDELLLDADWSVNAGMWMWLSCSSFFQQFFHCYCPVKFGRKADPNGDFI 309
G + F+ LLD D N G W + + + + K + DP G+++
Sbjct: 411 MGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPREDRYFSIPKQAQNYDPEGEYV 464
>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 = 264 bits (677), Expect = 1e-85
Identities = 66/290 (22%), Positives = 116/290 (40%), Gaps = 7/290 (2%)
Query: 20 IEKNGGKTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEEL 79
+ + P + +F+ + K L+ L ++
Sbjct: 146 LPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQLLPSPNIKLELTAPP---PEFFPQI 202
Query: 80 GFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFG 139
FD +L ++GGET + RL+ + + + + S + SP+L G
Sbjct: 203 NFDHRSVLA--FQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYS-SKFSPWLALG 259
Query: 140 CLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPICVQIP 199
CLS R Y ++ + + L +LLWR+FF A + N G + P
Sbjct: 260 CLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKNFP 319
Query: 200 WDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMK 259
W + W + QTG+P +DA M +L G++ + R VA FL + +L + W G +
Sbjct: 320 WQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCK-NLGIDWRWGAE 378
Query: 260 IFDELLLDADWSVNAGMWMWLSCSSFFQQFFHCYCPVKFGRKADPNGDFI 309
F+ L+D D N G W + + + F + K ++ DP G ++
Sbjct: 379 WFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFNIPKQSQQYDPQGTYL 428
>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 = 126 bits (318), Expect = 4e-33
Identities = 76/298 (25%), Positives = 116/298 (38%), Gaps = 61/298 (20%)
Query: 40 KMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPTWKGGETEAM 99
P+P P + + +PTL++LGFD +G P + GET A+
Sbjct: 158 AQPKPTPVATPTELVDLSPEQLTAIAPLLLS-ELPTLKQLGFDWDGGFP--VEPGETAAI 214
Query: 100 RRLERHLERKAWVASFG----RPKMTPQSLLASQTG---LSPFLRFGCLSTRLFYHDLNK 152
RL+ +R +A + P ++ G LSP L+FG + R + +
Sbjct: 215 ARLQEFCDRA--IADYDPQRNFP---------AEAGTSGLSPALKFGAIGIRQAWQAASA 263
Query: 153 LYKRIKKAPPPLSLH---GQLLWREFFYC-------AATRN--PNFDRMLGNPICVQIPW 200
+ + S+ +L WREF+ A + + PW
Sbjct: 264 AHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQ---------FPW 314
Query: 201 DVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKI 260
+ W AQTG+P +DA M QL E GW+H+ R VA FLT+ DL + W G +
Sbjct: 315 ENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTK-DLIIDWRRGEQF 373
Query: 261 FDELLLDADWSVNAGMWMWLSCSSFFQQFFHCYC---------PVKFGRKADPNGDFI 309
F + L+D D + N G W W +S P +K D +I
Sbjct: 374 FMQHLVDGDLAANNGGWQW--SAS-------SGMDPKPLRIFNPASQAKKFDATATYI 422
>2e0i_A 432AA long hypothetical deoxyribodipyrimidine PHO; photolyase, FAD,
DNA repair, lyase; HET: FAD; 2.80A {Sulfolobus tokodaii}
Length = 440
Score = 122 bits (308), Expect = 6e-32
Identities = 64/250 (25%), Positives = 96/250 (38%), Gaps = 50/250 (20%)
Query: 74 PTLEELGFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGR--PKMTPQSLLASQTG 131
+ + + P ++GG E + L R+++ + R P +
Sbjct: 168 SMNVDFLLTFKKIESPLFRGGRREGLYLLHRNVDFR------RRDYPA------ENNNYR 215
Query: 132 LSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYC-------AATRN- 183
LSP L+FG +S R + Y K + +L WR+FF
Sbjct: 216 LSPHLKFGTISMR-------EAYYTQKGKEEFVR---ELYWRDFFTLLAYYNPHVFGHCY 265
Query: 184 -PNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVA 242
+D I W+ N W +TG+P IDA M L G+I+ R VA
Sbjct: 266 RREYDN---------ISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVA 316
Query: 243 CFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLS---CSSFFQQFFHCYCPVKFG 299
FL + L+V W G + F L+D D ++N G W W++ F+ F P K
Sbjct: 317 FFLVK-VLFVDWRWGERYFATKLVDYDPAINNGNWQWIASTGVDYMFRVF----NPWKQQ 371
Query: 300 RKADPNGDFI 309
K DP FI
Sbjct: 372 EKFDPEAKFI 381
>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 = 119 bits (301), Expect = 1e-30
Identities = 58/295 (19%), Positives = 94/295 (31%), Gaps = 53/295 (17%)
Query: 40 KMDSPSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPTWKGGETEAM 99
M + ++ + D ++ LL W G +
Sbjct: 167 SMPYDPESPLLPPKKIISGDVSKCVADPL-----VFEDDSEKGSNALLARAWSPGWSNGD 221
Query: 100 RRLERHLERKAWVASFGRPKMTPQSLLASQTG---LSPFLRFGCLSTRLFYHDLNKLYKR 156
+ L + + + + A LSP L FG +S R +H +
Sbjct: 222 KALTTFINGP--LLEYSK-----NRRKADSATTSFLSPHLHFGEVSVRKVFHLVRIKQVA 274
Query: 157 IKKAPPPLSLHG------QLLWREFFY-------CAATRN--PNFDRMLGNPICVQIPWD 201
+ RE+ + R + PW
Sbjct: 275 WANEGNEAGEESVNLFLKSIGLREYSRYISFNHPYSHERPLLGHLKF---------FPWA 325
Query: 202 VNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIF 261
V+ W +TG+P +DA M +L GW+H R V+ F + L + W GMK F
Sbjct: 326 VDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVK-VLQLPWRWGMKYF 384
Query: 262 DELLLDADWSVNAGMWMWLSCSS-------FFQQFFHCYCPVKFGRKADPNGDFI 309
+ LLDAD +A W + + F + P G K DPNG+++
Sbjct: 385 WDTLLDADLESDALGWQY--ITGTLPDSREFDRID----NPQFEGYKFDPNGEYV 433
>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 = 118 bits (298), Expect = 1e-30
Identities = 66/255 (25%), Positives = 97/255 (38%), Gaps = 49/255 (19%)
Query: 74 PTLEELGFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFG----RPKMTPQSLLASQ 129
P E+ + GL P + GE A+ L LE K + + R
Sbjct: 160 PEEGEIPREDPGL--PLPEPGEEAALAGLRAFLEAK--LPRYAEERDRLD------GEGG 209
Query: 130 TGLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFYC-------AATR 182
+ LSP+ G LS RL + + + +LLWR+F Y A R
Sbjct: 210 SRLSPYFALGVLSPRLAAWEAER-----RGGEGARKWVAELLWRDFSYHLLYHFPWMAER 264
Query: 183 N--PNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLARHA 240
P F PW + W +TG P +DA M +L G++ + AR
Sbjct: 265 PLDPRFQA---------FPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMN 315
Query: 241 VACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS------FFQQFFHCYC 294
A F + L + W+ + F LLLD D +VN W W + +F+ F
Sbjct: 316 AAQFAVK-HLLLPWKRCEEAFRHLLLDGDRAVNLQGWQW-AGGLGVDAAPYFRVF----N 369
Query: 295 PVKFGRKADPNGDFI 309
PV G + DP G ++
Sbjct: 370 PVLQGERHDPEGRWL 384
>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 = 118 bits (297), Expect = 3e-30
Identities = 67/257 (26%), Positives = 95/257 (36%), Gaps = 45/257 (17%)
Query: 74 PTLEELGFDIEGLLPPTWKGGETEAMRRLERHLERKAWVASFGR--PKMTPQSLLASQTG 131
L + + + E A+ +L + + A R P + G
Sbjct: 183 SPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFP---------AVEG 233
Query: 132 ---LSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPPLSLHGQLLWREFFY--------CAA 180
LS L G LS R H L + +L+WREF+
Sbjct: 234 TSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCK 293
Query: 181 TRN--PNFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQLREEGWIHHLAR 238
R DR + W N L W +TG+P +DA M QL GW+H+ R
Sbjct: 294 HRPFIAWTDR---------VQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLR 344
Query: 239 HAVACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWMWLSCSS------FFQQFFHC 292
A FL + DL + W EG + F L+D D + N G W W + S+ +F+ F
Sbjct: 345 MITASFLVK-DLLIDWREGERYFMSQLIDGDLAANNGGWQW-AASTGTDAAPYFRIF--- 399
Query: 293 YCPVKFGRKADPNGDFI 309
P G K D G+FI
Sbjct: 400 -NPTTQGEKFDHEGEFI 415
>2xry_A Deoxyribodipyrimidine photolyase; DNA damage, DNA repair; HET: FAD;
1.50A {Methanosarcina mazei} PDB: 2xrz_A*
Length = 482
Score = 115 bits (290), Expect = 3e-29
Identities = 47/280 (16%), Positives = 87/280 (31%), Gaps = 23/280 (8%)
Query: 44 PSPAEAPVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPTWKGGETEAMRRLE 103
P+ ++ T + K +P L P ++ GE A + +E
Sbjct: 201 PNSVTPELSAGAGMVETLSDVLETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVME 260
Query: 104 RHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPP 163
+ + + S+G + P + LSP+L FG +S++ ++ K
Sbjct: 261 SFIADR--LDSYGALRNDPT--KNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAF 316
Query: 164 LSLHGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWD-------VNMEALAKWANAQTG 216
L L+W+E NP +D P + + ++ L ++ +T
Sbjct: 317 LD--EILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTH 374
Query: 217 FPWIDAIMTQLREEGWIHHLARHAVACFLT--RGDLWVSWEEGMKIFDELLLDADWSVNA 274
P +A +L G +H R A + + E + + D LD
Sbjct: 375 DPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGY 434
Query: 275 GMWMWLSCSSFFQQFFHCYCPVKF--------GRKADPNG 306
W + + K RK D
Sbjct: 435 AGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKL 474
>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 = 94.8 bits (236), Expect = 5e-22
Identities = 42/247 (17%), Positives = 80/247 (32%), Gaps = 19/247 (7%)
Query: 48 EAPVTPLLVRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPT--WKGGETEAMRRLERH 105
+ + A P + E L +P + GE A+ L
Sbjct: 197 DEYLVEFPELPAVVPWDREQPEGVDWDALIARVCSEAENVPEIDWCEPGEEAAIEALLGS 256
Query: 106 LER--KAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLYKRIKKAPPP 163
+ + S+ + P + + +GLSP+L FG +S + + K K+
Sbjct: 257 KDGFLTKRIKSYETDRNDP-TKPRALSGLSPYLHFGHISAQRCALEAKKCRHLSPKSVD- 314
Query: 164 LSLHGQLL-WREFFYCAATRNPNFDRMLGNPICVQIPWDVN-------MEALAKWANAQT 215
+ +L+ RE P +D + G + + + + NA+T
Sbjct: 315 -AFLEELVVRRELADNFCYYQPQYDSLSGAWEWARKTLMDHAADKREHIYTREQLENAKT 373
Query: 216 GFPWIDAIMTQLREEGWIHHLARHAVACFL---TRGDLWVSWEEGMKIFDELLLDADWSV 272
P +A ++ G +H R A + T G + + + D+ +D
Sbjct: 374 HDPLWNASQLEMVHHGKMHGFMRMYWAKKILEWTSGPEE-ALSTAIYLNDKYEIDGRDPS 432
Query: 273 NAGMWMW 279
MW
Sbjct: 433 GYVGCMW 439
>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 = 47.2 bits (111), Expect = 5e-06
Identities = 48/352 (13%), Positives = 89/352 (25%), Gaps = 123/352 (34%)
Query: 7 KKLTLSLPSSRRI-IEKNGGKTPLTYHQFQSIVAK---MDSPS-PAEAP-VTPLLVRQAT 60
K++T L ++ I + LT + +S++ K P E P +
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
Query: 61 TPLRDDHD-----EKYGVPTLEE-LGFDIEGLLP-------------------PT----- 90
+RD + L + + L P PT
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394
Query: 91 -WKGGETEAMRRLERHLERKAWVASFGRPKMTPQSLLASQTGLSPFLRFGCLSTRLFYHD 149
W + + L + SL+ Q + +
Sbjct: 395 IWFDVIKSDVMVVVNKLHKY--------------SLVEKQP----------KESTISIPS 430
Query: 150 LNKLYKRIKKAPPPLSLHGQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAK 209
+ K K +LH ++ Y IP + + L
Sbjct: 431 IYLELK--VKLENEYALHRSIVDH---Y-------------------NIPKTFDSDDLIP 466
Query: 210 WANAQTGFPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLWVSWEEGMKIFDELLLDAD 269
P++D + H+ H E M +F + LD
Sbjct: 467 --------PYLDQY--------FYSHIGHHLKNIEHP---------ERMTLFRMVFLDFR 501
Query: 270 W---SVNAGMWMWLSCSS---------FFQQFFHCYCPVKFGRKADPNGDFI 309
+ + W + S F++ + P K+ R + DF+
Sbjct: 502 FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDP-KYERLVNAILDFL 552
Score = 39.1 bits (90), Expect = 0.002
Identities = 51/384 (13%), Positives = 92/384 (23%), Gaps = 144/384 (37%)
Query: 26 KTPLTYHQFQSIVAKMDSPSPAEAPVTPLLVRQATT-------PLRDDHD-------EKY 71
K+ L+ + I+ D+ S LL +Q LR ++ +
Sbjct: 43 KSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ 102
Query: 72 GVPTLEELGFDIEGLLPPTWKGGET---------EAMRRLERHLER---KAWVASFGRPK 119
P++ + + + + +L + L V G
Sbjct: 103 RQPSMMTRMY--IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG--- 157
Query: 120 M--TPQSLLASQTGLS-------PF----LRFG-CLSTRLFYHDLNKLYKRIKK------ 159
+ + ++ +A LS F L C S L KL +I
Sbjct: 158 VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRS 217
Query: 160 ---APPPLSLHGQ----------------LL----------WREF-FYC---AATRNPNF 186
+ L +H LL W F C TR
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQV 277
Query: 187 DRMLGNPICVQIPWDVN---------MEALAKWAN---------AQTGFPW-IDAIMTQL 227
L I D + L K+ + T P + I +
Sbjct: 278 TDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337
Query: 228 RE-----EGWIH---------------HLA-----RHAVACFLTRGDLWVS-------W- 254
R+ + W H L + + + W
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 255 ----EEGMKIFDEL----LLDADW 270
+ M + ++L L++
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQP 421
>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 = 44.3 bits (104), Expect = 4e-05
Identities = 59/384 (15%), Positives = 101/384 (26%), Gaps = 146/384 (38%)
Query: 4 SIEKKLTLSLPSSRRIIEKNGGKTPLTYH------QFQSIV-AKMDSPSPAEAPVTPL-L 55
S+E L +P T + QF I+ + + + P TP L
Sbjct: 15 SLE--HVLLVP------------TASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL 60
Query: 56 VRQATTPLRDDHDEKYGVPTLEELGFDIEGLLPPTWKGGETE----AMRRLER------- 104
V K+ LG+ + L+ P+ G + + E
Sbjct: 61 V------------GKF-------LGY-VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND 100
Query: 105 -H--------------LERKAWVASF-------GRP--KMTPQSLL-ASQTGLSP-FLRF 138
H ++ K + ++ RP K + +L A G + F
Sbjct: 101 IHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF 160
Query: 139 GCLSTRLFYHD-LNKLYKRIKKAPPPL-----SLHGQLLWR--------EFFYCAATRNP 184
G Y + L LY+ L + L E + T+
Sbjct: 161 GGQGNTDDYFEELRDLYQT----YHVLVGDLIKFSAETLSELIRTTLDAEKVF---TQGL 213
Query: 185 NFDRMLGNPICVQIPWDVNMEALAKWANAQTGFPWIDAIMTQL-------REEGWIHHLA 237
N L NP P + + L + P I + QL + G+
Sbjct: 214 NILEWLENP--SNTP---DKDYLL---SIPISCPLI--GVIQLAHYVVTAKLLGFTPGEL 263
Query: 238 RHA------------VACFLTRGDLWVSWEEGMKIFDELLLDADWSVNAGMWM-WLSCSS 284
R A + D SWE F A + ++
Sbjct: 264 RSYLKGATGHSQGLVTAVAIAETD---SWES----FFVS------VRKAITVLFFIGVRC 310
Query: 285 FFQQFF-HCYCPVKFGRKADPNGD 307
+ + + P + N +
Sbjct: 311 --YEAYPNTSLPPSILEDSLENNE 332
Score = 38.5 bits (89), Expect = 0.003
Identities = 25/139 (17%), Positives = 43/139 (30%), Gaps = 53/139 (38%)
Query: 157 IKKAPPPLSLH-----GQLLWREFFYCAATRNPNFDRMLGNPICVQIPWDVNM------- 204
+ P L++H G+ + RE Y A D G +I ++N
Sbjct: 1665 VINNPVNLTIHFGGEKGKRI-REN-YSAMIFETIVD---GKLKTEKIFKEINEHSTSYTF 1719
Query: 205 ----EALAKWANAQTGFPWIDAIMT-------QLREEGWI--------HHL----ARHAV 241
L+ Q P A+ L+ +G I H L A ++
Sbjct: 1720 RSEKGLLSATQFTQ---P---ALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASL 1773
Query: 242 ACFLTRGDLWVSWEEGMKI 260
A + S E +++
Sbjct: 1774 ADVM-------SIESLVEV 1785
Score = 33.1 bits (75), Expect = 0.14
Identities = 51/307 (16%), Positives = 86/307 (28%), Gaps = 130/307 (42%)
Query: 42 DSPSP---AEAPVT-PLL-VRQATTPLRDDHDEKYGVPTLEELGFD-------------- 82
++P P++ PL+ V Q H Y V T + LGF
Sbjct: 224 NTPDKDYLLSIPISCPLIGVIQLA------H---YVV-TAKLLGFTPGELRSYLKGATGH 273
Query: 83 IEGLL-------PPTWKGGETEAMRRLERHLERKAWVA-----SFGR----PKMTPQSLL 126
+GL+ +W+ + + + ++ ++ P + SL
Sbjct: 274 SQGLVTAVAIAETDSWE----SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLE 329
Query: 127 ASQTGLSPFLRFGCLSTRLFYHDLNK--LYKRIKKA----P------------------- 161
++ SP L S +L + + + K P
Sbjct: 330 NNEGVPSPML-----SIS----NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVS 380
Query: 162 -PPLSLHG-QLLWREFFYCAAT-----------RNPNFD-RMLGNPICV----------- 196
PP SL+G L R+ A + R F R L P+
Sbjct: 381 GPPQSLYGLNLTLRK--AKAPSGLDQSRIPFSERKLKFSNRFL--PVASPFHSHLLVPAS 436
Query: 197 -QIPWDVNMEALAKWANAQTGFP------WIDAIMTQLREEGWIHHLARHAVACFLTRGD 249
I D+ ++ + P D LR ++ V C +
Sbjct: 437 DLINKDLVKNNVS-FNAKDIQIPVYDTFDGSD-----LRVLS--GSISERIVDCIIR--- 485
Query: 250 LWVSWEE 256
L V WE
Sbjct: 486 LPVKWET 492
>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine,
iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter
sphaeroides}
Length = 522
Score = 34.7 bits (80), Expect = 0.031
Identities = 28/148 (18%), Positives = 49/148 (33%), Gaps = 17/148 (11%)
Query: 97 EAMRRLERHLERKAWVASFGRPK--MTPQSLLASQTGLSPFLRFGCLSTRLFYHDLNKLY 154
EA+R L+ + + FG + M S LS + G L +
Sbjct: 243 EALRALDHFIRES--LPRFGDEQDAMLADDPFLSHALLSSSMNLGLLGPMEVCRRAETEW 300
Query: 155 KRIKKAPPPLSLHG---QLL-WREFFYCAATRNPNFDRMLGNPICVQIPWDVNMEALAKW 210
+ + P ++ G Q+L WRE+ T + N + +
Sbjct: 301 R--EGRAPLNAVEGFIRQILGWREYVRGIWTLSGPDYIRS-NG------LGHSAALPPLY 351
Query: 211 ANAQTGFPWIDAIMTQLREEGWIHHLAR 238
T + A + Q R+ + HH+ R
Sbjct: 352 WGKPTRMACLSAAVAQTRDLAYAHHIQR 379
>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 = 31.8 bits (71), Expect = 0.13
Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 4/27 (14%)
Query: 148 HDLNKLYKRIKK-AP---PPLSLHGQL 170
L KL +K A P L++ +
Sbjct: 20 QALKKLQASLKLYADDSAPALAIKATM 46
Score = 29.9 bits (66), Expect = 0.60
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 9/33 (27%)
Query: 95 ETEAMRRLERHLERKAWVASFGRPKMTPQSLLA 127
E +A+++L+ L+ A P LA
Sbjct: 18 EKQALKKLQASLKLYA-------DDSAPA--LA 41
Score = 29.9 bits (66), Expect = 0.62
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 8/30 (26%)
Query: 35 QSIVAKMDSP----SPAEAPVTPLLVRQAT 60
Q++ K+ + + AP L +AT
Sbjct: 20 QAL-KKLQASLKLYADDSAPA---LAIKAT 45
>3d1u_A Putative fructosamine-3-kinase; YP_290396.1, structural genomics,
joint center for structural genomics, JCSG, protein
structure initiative; 1.85A {Thermobifida fusca} PDB:
3f7w_A
Length = 288
Score = 28.9 bits (64), Expect = 2.2
Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 7/81 (8%)
Query: 217 FPWIDAIMTQLREEGWIHHLARHAVACFLTRGDLW---VSW-EEGMKIFDELLLDADWSV 272
P ++ ++ + + HLA GDLW V W ++G + D
Sbjct: 164 TPGDVRLVEKVLD--ALDHLAGDPEPPARIHGDLWNGNVLWQDDGAVVIDPAAHGGHREA 221
Query: 273 NAGMWMWLSCSSFFQQFFHCY 293
+ M + + Y
Sbjct: 222 DLAMLALF-GLPYLDRVRDAY 241
>3ei3_A DNA damage-binding protein 1; UV-damage, DDB, nucleotide excision
repair, xeroderma pigmentosum, cytoplasm, DNA repair;
HET: DNA PG4; 2.30A {Homo sapiens} PDB: 3ei1_A* 3ei2_A*
3ei4_A* 4a0l_A* 3e0c_A* 3i7k_A* 3i7h_A* 3i7l_A* 3i7n_A*
3i7o_A* 3i7p_A* 3i89_A* 3i8c_A* 3i8e_A* 2b5l_A 2b5m_A
2hye_A* 4a11_A* 4a0k_C* 4a0a_A* ...
Length = 1158
Score = 29.2 bits (64), Expect = 2.3
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 9/73 (12%)
Query: 112 VASFGRPKMTPQSLLASQTGLSPFLRFGCLS---------TRLFYHDLNKLYKRIKKAPP 162
V F + Q+L + T + FG ++ + +Y+ L + R+ K
Sbjct: 1022 VNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIK 1081
Query: 163 PLSLHGQLLWREF 175
+ WR F
Sbjct: 1082 SVGKIEHSFWRSF 1094
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
0.323 0.137 0.455
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: 5,185,506
Number of extensions: 315107
Number of successful extensions: 884
Number of sequences better than 10.0: 1
Number of HSP's gapped: 841
Number of HSP's successfully gapped: 34
Length of query: 309
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 216
Effective length of database: 4,105,140
Effective search space: 886710240
Effective search space used: 886710240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.9 bits)