RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine photolyase [Candidatus Liberibacter asiaticus str. psy62] (483 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 = 386 bits (993), Expect = e-108 Identities = 131/510 (25%), Positives = 206/510 (40%), Gaps = 38/510 (7%) Query: 1 MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAK-----VIAVFIATPEQWRQHGISA 55 M + + VH W R LR+ DN AL ++A V +FI P + A Sbjct: 24 MDSQRSTLVH--WFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGA 81 Query: 56 RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115 + F+ +L + L + + E RV L + E Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRG----KPAEVFPRIFKSWRVEMLTFETDIEPY 137 Query: 116 EVRRDKLLEKRL-QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADL 174 V RD ++K V ++ + P ++ L + +++ L + Sbjct: 138 SVTRDAAVQKLAKAEGVRVETHCSHTIYNPELVIAKNLGKAPITYQKFLGIVEQLKVPKV 197 Query: 175 RSLPVPAIRLTGP------------VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKF 222 +P + P + + P + FP GE AL + + Sbjct: 198 LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKRPEELGPNKFPGGETEALRRMEES 257 Query: 223 CKEKVYYYVEQRDIPAI----QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGA 278 K++++ ++ A T+ LSPYL G LS R +LKE + K Sbjct: 258 LKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLSARLFNQKLKE-IIKRQPKHSQPP 316 Query: 279 FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDA 338 S + +L+WREFY + A P+ + +I W + L+AW G TG+P IDA Sbjct: 317 VSLIGQLMWREFYYTVAAAEPN-FDRMLGNVYCMQIPWQEHPDHLEAWTHGRTGYPFIDA 375 Query: 339 AMRQLNTIGWMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAAS 397 MRQL GW+H+ R A FL + DL + W G+ F LLD D A N G W W ++ Sbjct: 376 IMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVFEQLLLDQDWALNAGNWMWLSA 435 Query: 398 TGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------D 451 + YFR+++P GK+ DPQG +IR ++PEL+ P I+ P + Sbjct: 436 SAFFH-QYFRVYSPVAFGKKTDPQGHYIRKYVPELSKYPAGCIYEPWKASLVDQRAYGCV 494 Query: 452 LSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481 L +YP IV H+ + + AA K + Sbjct: 495 LGTDYPHRIVKHEVVHKENIKRMGAAYKVN 524 >1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} 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 = 354 bits (910), Expect = 2e-98 Identities = 156/479 (32%), Positives = 222/479 (46%), Gaps = 19/479 (3%) Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70 L W R DLR++DN L AA S ++I +F P+ + ++ + ++ L ++Q+ Sbjct: 6 LFWHRRDLRLSDNIGLAAARAQSA-QLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQ 64 Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHR 130 Q G Q D + Q + +++N+ E RD + L+ Sbjct: 65 RYQQAGSRLLLLQG----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTA 120 Query: 131 -VICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVT 189 + D +L P IL+ + Y VY PF K + + +T Sbjct: 121 GIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVATPTELVDLSPEQLT 180 Query: 190 PSNIPRFFDYPFQAIDPM-------FPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGT 242 + P GE A+ L++FC + Y QR+ PA GT Sbjct: 181 AIAPLLLSELPTLKQLGFDWDGGFPVEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGT 240 Query: 243 SQLSPYLSIGVLSPRQCWNRLKEEF-VDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSV 301 S LSP L G + RQ W + + ++ W EL WREFY+H + +PS+ Sbjct: 241 SGLSPALKFGAIGIRQAWQAASAAHALSRSDEARNSIRVWQQELAWREFYQHALYHFPSL 300 Query: 302 CMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFL 361 P+ ++ W L AW Q TG+PI+DAAMRQL GWMHNR RMI ASFL Sbjct: 301 AD-GPYRSLWQQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFL 359 Query: 362 VKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQ 421 KDL++DWR GE++FM L+DGDLA+NNGGWQW+AS+G D P RIFNP Q K+FD Sbjct: 360 TKDLIIDWRRGEQFFMQHLVDGDLAANNGGWQWSASSGMDPKP-LRIFNPASQAKKFDAT 418 Query: 422 GTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQ 480 T+I+ WLPEL +V + + + YP PIV+H Y K Sbjct: 419 ATYIKRWLPELRHVHPKDLISGEIT---PIERRGYPAPIVNHNLRQKQFKALYNQLKAA 474 >1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} SCOP: a.99.1.1 c.28.1.1 Length = 471 Score = 342 bits (877), Expect = 1e-94 Identities = 243/472 (51%), Positives = 324/472 (68%), Gaps = 3/472 (0%) Query: 8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQ 67 + HLVW R DLR+ DN AL AAC NS A+V+A++IATP QW H +S RQ+ I A L Sbjct: 1 TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNG 60 Query: 68 VQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL 127 +Q +L++KGI + + +F S+E + C + VT LFYN QYE+NE RD +E+ L Sbjct: 61 LQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERAL 120 Query: 128 QHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGP 187 ++ +C+ FDDSV+LPPG+++ +MYKV+TPF+ A ++ L + + P +R +G Sbjct: 121 RNV-VCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGS 179 Query: 188 VTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSP 247 + PS FP+ E+ A+ LR+FC+ Y +QRD PA++GTS+LS Sbjct: 180 IEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSA 239 Query: 248 YLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPF 307 L+ G LSPRQC +RL E WLNELIWREFYRHL+ ++PS+C +PF Sbjct: 240 SLATGGLSPRQCLHRLLAEQPQ--ALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPF 297 Query: 308 IPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLV 367 I WT++++W + LQAW++G TG+PI+DAAMRQLN+ GWMHNRLRMITASFLVKDLL+ Sbjct: 298 IAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLI 357 Query: 368 DWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRH 427 DWR GE YFMSQL+DGDLA+NNGGWQWAASTG D+ PYFRIFNPT QG++FD +G FIR Sbjct: 358 DWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQ 417 Query: 428 WLPELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479 WLPEL +VP + +H P W K ++L+YP PIV+HK+A TL Y AA+K Sbjct: 418 WLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARK 469 >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 = 336 bits (861), Expect = 8e-93 Identities = 136/479 (28%), Positives = 225/479 (46%), Gaps = 31/479 (6%) Query: 9 VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH-----GISARQSHFIYA 63 LVW RNDLR+ D++ L+ A + + AV+ P Q+ Q +S+F+ Sbjct: 7 TVLVWFRNDLRLHDHEPLHRALKSGL-AITAVYCYDPRQFAQTHQGFAKTGPWRSNFLQQ 65 Query: 64 SLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLL 123 S+ + +SL + G + + Q ++Y+R+ E+ ++ L Sbjct: 66 SVQNLAESLQKVGNKLLVTT----GLPEQVIPQIAKQINAKTIYYHREVTQEELDVERNL 121 Query: 124 EKRLQ-HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQ------ADLRS 176 K+L + K + S L P + + ++T FRK + + + A + Sbjct: 122 VKQLTILGIEAKGYWGSTLCHPEDLPFSIQDLPDLFTKFRKDIEKKKISIRPCFFAPSQL 181 Query: 177 LPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKV---YYYVEQ 233 LP P I+L P ++ +++ F GE L L+ + Y + Sbjct: 182 LPSPNIKLELTAPPPEFFPQINFDHRSVLA-FQGGETAGLARLQDYFWHGDRLKDYKETR 240 Query: 234 RDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRH 293 + +S+ SP+L++G LSPR + +K + + + + EL+WR+F+R Sbjct: 241 NGMVGADYSSKFSPWLALGCLSPRFIYQEVKRYEQERVSNDSTHWLIF--ELLWRDFFRF 298 Query: 294 LMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRL 353 + Y + + + W +D + W+ G TG+P++DA MR+LN G+M NR Sbjct: 299 VAQKYGNKLFNRGG-LLNKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRG 357 Query: 354 RMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTI 413 R ASFL K+L +DWR G E+F S L+D D+ SN G W + A GND+ FR FN Sbjct: 358 RQNVASFLCKNLGIDWRWGAEWFESCLIDYDVCSNWGNWNYTAGIGNDARD-FRYFNIPK 416 Query: 414 QGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------DLSLNYPLPIVDHKKA 466 Q +++DPQGT++RHWLPEL N+P IH P L ++YP P V+ ++ Sbjct: 417 QSQQYDPQGTYLRHWLPELKNLPGDKIHQPWLLSATEQKQWGVQLGVDYPRPCVNFHQS 475 >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 = 274 bits (702), Expect = 2e-74 Identities = 118/491 (24%), Positives = 217/491 (44%), Gaps = 27/491 (5%) Query: 8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG------ISARQSHFI 61 V ++W RNDLR+ DN ALY A +SD ++ V+ P + A + F+ Sbjct: 40 GVTILWFRNDLRVLDNDALYKAWSSSD-TILPVYCLDPRLFHTTHFFNFPKTGALRGGFL 98 Query: 62 YASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDK 121 L+ ++K+L ++G+ E L S +F +++ EV ++ Sbjct: 99 MECLVDLRKNLMKRGLNLLIRSG----KPEEILPSLAKDFGARTVFAHKETCSEEVDVER 154 Query: 122 LLEKRLQ---HRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLP 178 L+ + L+ + + S + + + VYT FRK++ +P Sbjct: 155 LVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIP 214 Query: 179 VPAIRLTGPVTPSNIPRFFDYPFQAIDP----MFPIGEQNALHILRKFCKEK---VYYYV 231 + ++P + + F GE + + ++ +K Y Sbjct: 215 LSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKE 274 Query: 232 EQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFY 291 + + +++ SP+L+ G +SPR + ++ + + + L ELIWR+++ Sbjct: 275 TRNGMLGPDYSTKFSPWLAFGCISPRFIYEEVQRYEKE--RVANNSTYWVLFELIWRDYF 332 Query: 292 RHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHN 351 R L + P + +W++D L ++W+ TG+P+IDA M++L+T G+M N Sbjct: 333 RFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSN 391 Query: 352 RLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNP 411 R R I SFLV+D+ +DWR+G E+F + LLD D SN G W + A GND R F+ Sbjct: 392 RGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVGNDPRED-RYFSI 450 Query: 412 TIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPH--SWLDKNDLSLNYPLPIVDHKKACHH 469 Q + +DP+G ++ WL +L +P + H P ++D + P+ K+ Sbjct: 451 PKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKHGNGPMAGGSKSGGG 510 Query: 470 TLNQYYAAKKQ 480 + + + Sbjct: 511 FRGSHSGRRSR 521 >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 = 256 bits (653), Expect = 1e-68 Identities = 136/490 (27%), Positives = 222/490 (45%), Gaps = 22/490 (4%) Query: 6 AMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASL 65 + +VW R DLR+ DN AL AA VIA+F+ PE+ + ++ SL Sbjct: 10 SGGCSIVWFRRDLRVEDNPALAAAVRAG--PVIALFVWAPEEEGHYHPGRVSRWWLKNSL 67 Query: 66 LQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEK 125 Q+ SL G + + DS+ L +++F+N Y+ + RD + Sbjct: 68 AQLDSSLRSLGTCLITKRST---DSVASLLDVVKSTGASQIFFNHLYDPLSLVRDHRAKD 124 Query: 126 RLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRL 184 L + I +SF+ +L P + + + + ++ F + + + LP I Sbjct: 125 VLTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPPKKIIS 184 Query: 185 TGPVTPSNIPRFFDYPFQ-----AIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAI 239 P F+ + + + G N L F + Y + R Sbjct: 185 GDVSKCVADPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYSKNRRKADS 244 Query: 240 QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLN----ELIWREFYRHLM 295 TS LSP+L G +S R+ ++ ++ + V + +N + RE+ R++ Sbjct: 245 ATTSFLSPHLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYIS 304 Query: 296 AFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRM 355 F +P + + W D + +AW+QG TG+P++DA MR+L GW+H+R+R+ Sbjct: 305 -FNHPYSHERPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRV 363 Query: 356 ITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQG 415 + +SF VK L + WR G +YF LLD DL S+ GWQ+ T DS + RI NP +G Sbjct: 364 VVSSFFVKVLQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEG 423 Query: 416 KRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKN------DLSLNYPLPIVDHKKACHH 469 +FDP G ++R WLPEL+ +PT +IH P + + +L NYPLPIV +A Sbjct: 424 YKFDPNGEYVRRWLPELSRLPTDWIHHPWNAPESVLQAAGIELGSNYPLPIVGLDEAKAR 483 Query: 470 TLNQYYAAKK 479 + Sbjct: 484 LHEALSQMWQ 493 >2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} Length = 440 Score = 255 bits (651), Expect = 2e-68 Identities = 140/473 (29%), Positives = 221/473 (46%), Gaps = 44/473 (9%) Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGI-SARQSHFIYASLLQVQ 69 + R DLR+ DN L A D +VI VFIA P Q + S F+ SLL++ Sbjct: 4 IFIFRRDLRLEDNTGLNYALSECD-RVIPVFIADPRQLINNPYKSEFAVSFMINSLLELD 62 Query: 70 KSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQH 129 L +KG F ++ + + + + + R +K+ + ++ Sbjct: 63 DELRKKGSRLNVF----FGEAEKVVSRFF-NKVDAIYVNEDYTPFSISRDEKIRKVCEEN 117 Query: 130 RVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVT 189 + K+++D +L P +L ++ +T F + + V+ P Sbjct: 118 GIEFKAYEDYLLTP------KSLFHHRNFTSFYNEVSKVKVRE-----PETMEGSFDVTD 166 Query: 190 PSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYL 249 S F + P+F G + L++L + + +RD PA +LSP+L Sbjct: 167 SSMNVDFLLTFKKIESPLFRGGRREGLYLLHRNVDFR------RRDYPAENNNYRLSPHL 220 Query: 250 SIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIP 309 G +S R+ + + G ++ EL WR+F+ L + P V + Sbjct: 221 KFGTISMREAYYT------------QKGKEEFVRELYWRDFFTLLAYYNPHVFG-HCYRR 267 Query: 310 WTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDW 369 + I W + +AWK+G TG+PIIDA MR LN+ G+++ R+RM+ A FLVK L VDW Sbjct: 268 EYDNISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDW 327 Query: 370 RIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWL 429 R GE YF ++L+D D A NNG WQW ASTG D FR+FNP Q ++FDP+ FI+ W+ Sbjct: 328 RWGERYFATKLVDYDPAINNGNWQWIASTGVD--YMFRVFNPWKQQEKFDPEAKFIKEWV 385 Query: 430 PELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKKQSL 482 EL +VP IH+ + YP PIV+ + ++ ++Y K L Sbjct: 386 EELKDVPPSIIHSIYKTKVP-----GYPSPIVNWLERVNYVKSEYKNVKAVLL 433 >3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} Length = 537 Score = 245 bits (626), Expect = 1e-65 Identities = 131/504 (25%), Positives = 202/504 (40%), Gaps = 41/504 (8%) Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG---------ISARQSHFI 61 L+W R LR+ DN AL A S+ + VF+ P + F+ Sbjct: 8 LIWFRKGLRVHDNPALEYASKGSE-FMYPVFVIDPHYMESDPSAFSPGSSRAGVNRIRFL 66 Query: 62 YASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDK 121 SL + SL + G + + E L + +V +L + + D Sbjct: 67 LESLKDLDSSLKKLGSRLLVFKG----EPGEVLVRCLQEWKVKRLCFEYDTDPYYQALDV 122 Query: 122 LLEKRLQHRVICKSFDDSVLLPPGS--ILNHALQMYKVYTPFRKALIQNLVQADLRSLPV 179 ++ + S L + I + + Y F K + + Sbjct: 123 KVKDYASSTGVEVFSPVSHTLFNPAHIIEKNGGKPPLSYQSFLKVAGEPSCAKSELVMSY 182 Query: 180 PAIRLTGPVTPSNIPR-------FFDYPFQAIDPMFPIGEQNALHILRKFCK--EKVYYY 230 ++ G + I + QA F GE AL L K V + Sbjct: 183 SSLPPIGDIGNLGISEVPSLEELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANF 242 Query: 231 VEQRDIPAI---QGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIW 287 + + P+ T+ +SPYL G LS R + L+ + D+ S L +L+W Sbjct: 243 EKPKGDPSAFLKPATTVMSPYLKFGCLSSRYFYQCLQNIYKDVKKHTSP-PVSLLGQLLW 301 Query: 288 REFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIG 347 REF+ P ++I WN+D +L AW+ G TG+P IDA M QL G Sbjct: 302 REFFYTTAFGTP-NFDKMKGNRICKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWG 360 Query: 348 WMHNRLRMITASFLVK-DLLVDWRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYF 406 WMH+ R A FL + DL + W G + F L+D D A NNG W W + + + Sbjct: 361 WMHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFFY-QFN 419 Query: 407 RIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLD------KNDLSLNYPLPI 460 RI++P GK++DP G +IRH+LP L ++P QYI+ P + + +YP P+ Sbjct: 420 RIYSPISFGKKYDPDGKYIRHFLPVLKDMPKQYIYEPWTAPLSVQTKANCIVGKDYPKPM 479 Query: 461 VDHKKA---CHHTLNQYYAAKKQS 481 V H A C + + YA K+ Sbjct: 480 VLHDSASKECKRKMGEAYALNKKM 503 >2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; 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 = 229 bits (585), Expect = 8e-61 Identities = 128/469 (27%), Positives = 198/469 (42%), Gaps = 54/469 (11%) Query: 11 LVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQK 70 LVW R DLR+ D+ AL A V+ + + P + + R+ + ++ +++ Sbjct: 5 LVWHRGDLRLHDHPALLEALAR--GPVVGLVVLDPNNLKT---TPRRRAWFLENVRALRE 59 Query: 71 SLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRLQHR 130 + +G + ++ + + V L + Y R + H Sbjct: 60 AYRARGGALWVLEGLPWEK-VPEAARRLKAKAVYALTSHTPYGRYRDGRVREALPVPLHL 118 Query: 131 VICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTP 190 + + + Y+VYTPF + Sbjct: 119 LPAPHL----------LPPDLPRAYRVYTPFSRLYRGAAPPLPPPEALPKGPEE------ 162 Query: 191 SNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLS 250 P+ GE+ AL LR F + K+ Y E+RD +G S+LSPY + Sbjct: 163 -----GEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEERDRLDGEGGSRLSPYFA 217 Query: 251 IGVLSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPW 310 +GVLSPR + + GA W+ EL+WR+F H + ++ +P P Sbjct: 218 LGVLSPRLAAWEAERRGGE-------GARKWVAELLWRDFSYH-LLYHFPWMAERPLDPR 269 Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370 + W +D L QAW +G TG P++DAAMR+L+ G++ NR RM A F VK LL+ W+ Sbjct: 270 FQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWK 329 Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430 EE F LLDGD A N GWQWA G D+ PYFR+FNP +QG+R DP+G +++ W P Sbjct: 330 RCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAP 389 Query: 431 ELNNVPTQYIHAPHSWLDKNDLSLNYPLPIVDHKKACHHTLNQYYAAKK 479 E + P+VD ++A L + Sbjct: 390 EYPSYA-------------------PKDPVVDLEEARRRYLRLARDLAR 419 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 56.1 bits (135), Expect = 2e-08 Identities = 92/560 (16%), Positives = 145/560 (25%), Gaps = 253/560 (45%) Query: 50 QHGISARQSHFIYASLLQVQ--KSLSQK--GIVFQYHQCSNFDDSIE-WLD--SYCLQQ- 101 +H + + F AS LQ Q K L + G + E Y Sbjct: 17 EHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTT----PAELVGKFLGYVSSLV 72 Query: 102 ---------RVTKLFYN---RQY----EINEV------RRDKLLEKRLQHRVI------C 133 +V L Y +I+ + D L K +I Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKT--KELIKNYITAR 130 Query: 134 KSFDDSVLLPPGSIL------NHA------------------LQ-MYKVYTPFRKALIQN 168 S L +A L+ +Y+ Y LI+ Sbjct: 131 IMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIK- 189 Query: 169 LVQADLRSL---PVPAIR-----------LTGP-VTPSNIPRFFDYPFQAIDPM-FP-IG 211 L L + A + L P TP DY P+ P IG Sbjct: 190 FSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK-----DYLLSI--PISCPLIG 242 Query: 212 EQNALHILRKFCKEKVYYYV----------EQRDIPAIQGT---SQLSPYLSIGV----- 253 + + +Y V E R ++G SQ G+ Sbjct: 243 -------VIQLA----HYVVTAKLLGFTPGELRS--YLKGATGHSQ-------GLVTAVA 282 Query: 254 LSPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFY---RHLMAFYPSVCMGKPFIPW 310 ++ W E F + K A + L F+ R A YP+ +P Sbjct: 283 IAETDSW----ESFFVSVRK----AITVL-------FFIGVRCYEA-YPNT-----SLP- 320 Query: 311 TEKIEWNKDSHLLQAWKQGYTGFP-----IIDAAMRQLNT-IGWMHNRL---RMITASFL 361 S L + + G P I + Q+ + ++ L + + S Sbjct: 321 --------PSILEDSLENN-EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS-- 369 Query: 362 VKDLLVDWRIGEEYFM-----SQL--LDGDLASNNGGWQWAASTGNDS--VPY----FRI 408 LV+ G + + L L+ L A +G D +P+ + Sbjct: 370 ----LVN---GAKNLVVSGPPQSLYGLNLTLRKAK------APSGLDQSRIPFSERKLKF 416 Query: 409 FNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAP-HS-WLD------KNDL-------- 452 N RF LP + +P HS L DL Sbjct: 417 SN------RF----------LP---------VASPFHSHLLVPASDLINKDLVKNNVSFN 451 Query: 453 --SLNYPLPIVDHKKACHHT 470 + P+ + T Sbjct: 452 AKDIQIPV---------YDT 462 Score = 48.8 bits (116), Expect = 3e-06 Identities = 58/320 (18%), Positives = 98/320 (30%), Gaps = 150/320 (46%) Query: 28 AACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLLQVQKSLSQKGIVFQY----HQ 83 A H S V AV IA + W F + +K+++ ++F ++ Sbjct: 270 ATGH-SQGLVTAVAIAETDSW---------ESFFVSV----RKAIT---VLFFIGVRCYE 312 Query: 84 C--------SNFDDSI---EWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL----Q 128 S +DS+ E + S L I+ + +++ ++ + Sbjct: 313 AYPNTSLPPSILEDSLENNEGVPSPMLS-------------ISNLTQEQ-VQDYVNKTNS 358 Query: 129 H----RVICKSF---DDSVLL--PPGSI--LNHALQMYKVYT-------PF--RKALIQN 168 H + + S ++++ PP S+ LN L+ K + PF RK N Sbjct: 359 HLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418 Query: 169 -------------------LVQADL--RSLPVPAIRLTGPV----TPSN--------IPR 195 L+ DL ++ A + PV S+ R Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISER 478 Query: 196 FFDYPFQAI--DPM-------FPIGEQNALHILRKFCKEKVYYYVEQRDI-PAIQGTSQL 245 D I P+ F A HIL D P G S Sbjct: 479 IVD----CIIRLPVKWETTTQFK-----ATHIL---------------DFGPG--GAS-- 510 Query: 246 SPYLSIGVLSPRQCWNRLKE 265 +GVL+ +R K+ Sbjct: 511 ----GLGVLT-----HRNKD 521 Score = 41.1 bits (96), Expect = 5e-04 Identities = 83/480 (17%), Positives = 136/480 (28%), Gaps = 219/480 (45%) Query: 25 ALYAACHNSDAKVIAVFIATPEQWRQHGISA-----RQSHFIYASLLQ--VQKS------ 71 AL+ A +A+++A+F Q R + Y L+ ++ S Sbjct: 144 ALFRAVGEGNAQLVAIFGG------QGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSE 197 Query: 72 LSQKGIVFQYHQCSNFDDSIEWLD--------SY-----------CLQQRVTKLFYNRQY 112 L + + + + +EWL+ Y + Q Y Sbjct: 198 LIRTTLDAEKVFTQGL-NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA-------HY 249 Query: 113 EINEVRRDKLLEKRLQHRVICKSFDDSVL-LPPGSILNH---------------ALQMYK 156 V K +L PG + ++ A+ Sbjct: 250 -----------------VVTAK-----LLGFTPGELRSYLKGATGHSQGLVTAVAIAETD 287 Query: 157 VYTPF----RKAL-----I----QNLVQADLR-SLPVPAIRLT----GPVTPSNIPRFFD 198 + F RKA+ I +A SLP P+I PS Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCY---EAYPNTSLP-PSILEDSLENNEGVPS------- 336 Query: 199 YPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQ--RDIPAIQGTSQLSPYLSIGVLSP 256 PM L I +E+V YV + +PA Q+ +S+ V Sbjct: 337 -------PM--------LSI-SNLTQEQVQDYVNKTNSHLPA---GKQVE--ISL-VNGA 374 Query: 257 RQCWNRLKEEFV------DLL--------IKPKSGA------FSWLNELIWR--EF-YRH 293 + V L K SG FS E R +F R Sbjct: 375 KN--------LVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS---E---RKLKFSNR- 419 Query: 294 LMAFYPSVCMGKPF-----IPWTEKIEWNKD---SHLLQAWKQGYTGFPIID----AAMR 341 F P + PF +P ++ I KD +++ ++ P+ D + +R Sbjct: 420 ---FLP---VASPFHSHLLVPASDLIN--KDLVKNNV--SFNAKDIQIPVYDTFDGSDLR 469 Query: 342 QL--NTIGWMHNRL-RMITASFLVKDLLVDWRIGEEYFMSQLLD---------GDLASNN 389 L + R+ I L V W ++ + +LD G L N Sbjct: 470 VLSGSISE----RIVDCIIR------LPVKWETTTQFKATHILDFGPGGASGLGVLTHRN 519 >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 = 34.6 bits (78), Expect = 0.047 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 7/29 (24%) Query: 162 RKALIQNLVQADLR-----SLPVPAIRLT 185 ++AL + L QA L+ S P AI+ T Sbjct: 19 KQAL-KKL-QASLKLYADDSAPALAIKAT 45 >2bas_A YKUI protein; EAL domain, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 2.61A {Bacillus subtilis} SCOP: c.1.33.1 d.110.6.2 PDB: 2w27_A* Length = 431 Score = 28.9 bits (64), Expect = 2.6 Identities = 5/41 (12%), Positives = 14/41 (34%), Gaps = 3/41 (7%) Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61 ++ A ++ I Q ++G Q +++ Sbjct: 217 YSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQGYYL 257 >3gfz_A Klebsiella pneumoniae BLRP1; TIM-barrel, EAL domain, BLUF domain, hydrolase, signaling protein; HET: C2E FMN; 2.05A {Klebsiella pneumoniae subsp} PDB: 3gfy_A* 3gfx_A* 3gg0_A* 3gg1_A* 2kb2_A* Length = 413 Score = 28.4 bits (63), Expect = 3.5 Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 3/41 (7%) Query: 24 KALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI 61 ++ C + V+A + T E+W + GI Q Sbjct: 351 ASVVRCCEDLGITVVAEGVETLEEWCWLQSVGIRLFQGFLF 391 >2ov8_A STAL; sulfotransferase, structural genomics, montreal-kingston bacterial structural genomics initiative, BSGI, unknown function; 2.58A {Streptomyces toyocaensis} PDB: 2ovb_A 2ovf_A* Length = 288 Score = 28.4 bits (62), Expect = 3.8 Identities = 17/149 (11%), Positives = 41/149 (27%), Gaps = 5/149 (3%) Query: 274 PKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPF----IPWTEKIEWNKDSHLLQAWKQG 329 PK+G WL ++ + +P + G P + E + D +L A Sbjct: 29 PKAGG-HWLRCMLTSYVTGEPVETWPGIQAGVPHLEGLLRDGEAPSADPDEQVLLATHFT 87 Query: 330 YTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNN 389 + + + N + + +K + + + + S+ Sbjct: 88 ADRPVLRFYRESTAKVVCLIRNPRDAMLSLMRMKGIPPEDVEACRKIAETFIADEGFSSV 147 Query: 390 GGWQWAASTGNDSVPYFRIFNPTIQGKRF 418 W S + + + + Sbjct: 148 RIWAGEGSWPENIRSWTDSVHESFPNAAV 176 >2r6o_A Putative diguanylate cyclase/phosphodiesterase (ggdef & EAL domains); ggdef and EAL domains, structural genomics, PSI-2; 1.80A {Thiobacillus denitrificans atcc 25259} PDB: 3ii8_A* Length = 294 Score = 28.1 bits (61), Expect = 4.8 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 11/74 (14%) Query: 13 WLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQW---RQHGISARQSHFI-------- 61 + + A +V+A I T +Q+ R G Q + + Sbjct: 212 IPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNLMSTPQAADA 271 Query: 62 YASLLQVQKSLSQK 75 +ASLL QK+ Q+ Sbjct: 272 FASLLDRQKASGQR 285 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 27.5 bits (60), Expect = 6.4 Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 9/48 (18%) Query: 146 SILNHA------LQMYKVYTPFRKALIQN-LVQADLRSLPVPAIRLTG 186 SIL H+ +++ Y P +K +IQ +V+ DL P A + T Sbjct: 897 SILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLE--PFEASKETA 942 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.324 0.138 0.444 Gapped Lambda K H 0.267 0.0529 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 4,551,054 Number of extensions: 216635 Number of successful extensions: 975 Number of sequences better than 10.0: 1 Number of HSP's gapped: 913 Number of HSP's successfully gapped: 33 Length of query: 483 Length of database: 5,693,230 Length adjustment: 96 Effective length of query: 387 Effective length of database: 3,365,806 Effective search space: 1302566922 Effective search space used: 1302566922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 59 (27.0 bits)