RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254781170|ref|YP_003065583.1| deoxyribodipyrimidine photolyase [Candidatus Liberibacter asiaticus str. psy62] (483 letters) >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* (A:317-525) Length = 209 Score = 209 bits (533), Expect = 6e-55 Identities = 65/208 (31%), Positives = 108/208 (51%), Gaps = 4/208 (1%) Query: 276 SGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPI 335 + + L ELIWR+++R L + P + +W++D L ++W+ TG+P+ Sbjct: 1 NSTYWVLFELIWRDYFRFLSIKCGNSLF-HLGGPRNVQGKWSQDQKLFESWRDAKTGYPL 59 Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395 IDA M++L+T G+M NR R I SFLV+D+ +DWR+G E+F + LLD D SN G W + Sbjct: 60 IDANMKELSTTGFMSNRGRQIVCSFLVRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYG 119 Query: 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPHSWLDKNDLSLN 455 A GND R F+ Q + +DP+G ++ WL +L +P + H P + + + Sbjct: 120 AGVGNDP-REDRYFSIPKQAQNYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPL 178 Query: 456 --YPLPIVDHKKACHHTLNQYYAAKKQS 481 P+ K+ + + + Sbjct: 179 KHGNGPMAGGSKSGGGFRGSHSGRRSRH 206 >1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} (A:264-426) Length = 163 Score = 201 bits (512), Expect = 2e-52 Identities = 113/161 (70%), Positives = 136/161 (84%) Query: 276 SGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKIEWNKDSHLLQAWKQGYTGFPI 335 WLNELIWREFYRHL+ ++PS+C +PFI WT++++W + LQAW++G TG+PI Sbjct: 3 GAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPI 62 Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDGDLASNNGGWQWA 395 +DAAMRQLN+ GWMHNRLRMITASFLVKDLL+DWR GE YFMSQL+DGDLA+NNGGWQWA Sbjct: 63 VDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWA 122 Query: 396 ASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVP 436 ASTG D+ PYFRIFNPT QG++FD +G FIR WLPEL +VP Sbjct: 123 ASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVP 163 >2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} (A:222-395) Length = 174 Score = 199 bits (507), Expect = 7e-52 Identities = 77/181 (42%), Positives = 106/181 (58%), Gaps = 8/181 (4%) Query: 255 SPRQCWNRLKEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGKPFIPWTEKI 314 SPR + + GA W+ EL+WR+F HL+ +P + +P P + Sbjct: 1 SPRLAAWEAER-------RGGEGARKWVAELLWRDFSYHLLYHFPWMAE-RPLDPRFQAF 52 Query: 315 EWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEE 374 W +D L QAW +G TG P++DAAMR+L+ G++ NR RM A F VK LL+ W+ EE Sbjct: 53 PWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVKHLLLPWKRCEE 112 Query: 375 YFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNN 434 F LLDGD A N GWQWA G D+ PYFR+FNP +QG+R DP+G +++ W PE + Sbjct: 113 AFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPS 172 Query: 435 V 435 Sbjct: 173 Y 173 >1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} (A:318-446) Length = 129 Score = 164 bits (416), Expect = 2e-41 Identities = 58/127 (45%), Positives = 83/127 (65%) Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370 + W D + +AW+QG TG+P++DA MR+L GW+H+R+R++ +SF VK L + WR Sbjct: 2 LKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVVSSFFVKVLQLPWR 61 Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430 G +YF LLD DL S+ GWQ+ T DS + RI NP +G +FDP G ++R WLP Sbjct: 62 WGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGYKFDPNGEYVRRWLP 121 Query: 431 ELNNVPT 437 EL+ +PT Sbjct: 122 ELSRLPT 128 >1u3d_A Cryptochrome 1 apoprotein; photolyase, AMPPNP, signaling protein; HET: FAD ANP NDS; 2.45A {Arabidopsis thaliana} (A:1-259) Length = 259 Score = 161 bits (408), Expect = 2e-40 Identities = 57/260 (21%), Positives = 98/260 (37%), Gaps = 11/260 (4%) Query: 1 MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHF 60 + + +VW R DLR+ DN AL AA VIA+F+ PE+ + + Sbjct: 5 VSGCGSGGCSIVWFRRDLRVEDNPALAAAVRA--GPVIALFVWAPEEEGHYHPGRVSRWW 62 Query: 61 IYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRD 120 + SL Q+ SL G + DS+ L +++F+N Y+ + RD Sbjct: 63 LKNSLAQLDSSLRSLGTCLITKRS---TDSVASLLDVVKSTGASQIFFNHLYDPLSLVRD 119 Query: 121 KLLEKRLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPV 179 + L + I +SF+ +L P + + + + ++ F + + + LP Sbjct: 120 HRAKDVLTAQGIAVRSFNADLLYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPP 179 Query: 180 PAIRLTGPVTPSNIPRFFDYPFQA-----IDPMFPIGEQNALHILRKFCKEKVYYYVEQR 234 I P F+ + + + G N L F + Y + R Sbjct: 180 KKIISGDVSKCVADPLVFEDDSEKGSNALLARAWSPGWSNGDKALTTFINGPLLEYSKNR 239 Query: 235 DIPAIQGTSQLSPYLSIGVL 254 TS LSP+L G + Sbjct: 240 RKADSATTSFLSPHLHFGEV 259 >1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} (A:308-448) Length = 141 Score = 161 bits (408), Expect = 2e-40 Identities = 73/135 (54%), Positives = 92/135 (68%), Gaps = 1/135 (0%) Query: 312 EKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRI 371 ++ W L AW Q TG+PI+DAAMRQL GWMHNR RMI ASFL KDL++DWR Sbjct: 3 QQFPWENREALFTAWTQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTKDLIIDWRR 62 Query: 372 GEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPE 431 GE++FM L+DGDLA+NNGGWQW+AS+G D RIFNP Q K+FD T+I+ WLPE Sbjct: 63 GEQFFMQHLVDGDLAANNGGWQWSASSGMDP-KPLRIFNPASQAKKFDATATYIKRWLPE 121 Query: 432 LNNVPTQYIHAPHSW 446 L +V + + + Sbjct: 122 LRHVHPKDLISGEIT 136 >1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} (A:314-441) Length = 128 Score = 159 bits (403), Expect = 7e-40 Identities = 61/127 (48%), Positives = 83/127 (65%), Gaps = 1/127 (0%) Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370 + W +D + W+ G TG+P++DA MR+LN G+M NR R ASFL K+L +DWR Sbjct: 2 NKNFPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCKNLGIDWR 61 Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430 G E+F S L+D D+ SN G W + A GND+ FR FN Q +++DPQGT++RHWLP Sbjct: 62 WGAEWFESCLIDYDVCSNWGNWNYTAGIGNDA-RDFRYFNIPKQSQQYDPQGTYLRHWLP 120 Query: 431 ELNNVPT 437 EL N+P Sbjct: 121 ELKNLPG 127 >2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} (A:268-406) Length = 139 Score = 158 bits (401), Expect = 1e-39 Identities = 68/136 (50%), Positives = 91/136 (66%), Gaps = 2/136 (1%) Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWR 370 + I W + +AWK+G TG+PIIDA MR LN+ G+++ R+RM+ A FLVK L VDWR Sbjct: 2 YDNISWENNESYFEAWKEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKVLFVDWR 61 Query: 371 IGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLP 430 GE YF ++L+D D A NNG WQW ASTG D FR+FNP Q ++FDP+ FI+ W+ Sbjct: 62 WGERYFATKLVDYDPAINNGNWQWIASTGVD--YMFRVFNPWKQQEKFDPEAKFIKEWVE 119 Query: 431 ELNNVPTQYIHAPHSW 446 EL +VP IH+ + Sbjct: 120 ELKDVPPSIIHSIYKT 135 >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* (A:347-475) Length = 129 Score = 153 bits (388), Expect = 4e-38 Identities = 53/129 (41%), Positives = 74/129 (57%), Gaps = 2/129 (1%) Query: 310 WTEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVK-DLLVD 368 + +I W + L+AW G TG+P IDA MRQL GW+H+ R A FL + DL + Sbjct: 1 YCMQIPWQEHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWIS 60 Query: 369 WRIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHW 428 W G+ F LLD D A N G W W +++ YFR+++P GK+ DPQG +IR + Sbjct: 61 WEEGQRVFEQLLLDQDWALNAGNWMWLSASAFFH-QYFRVYSPVAFGKKTDPQGHYIRKY 119 Query: 429 LPELNNVPT 437 +PEL+ P Sbjct: 120 VPELSKYPA 128 >3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} (A:323-451) Length = 129 Score = 153 bits (387), Expect = 6e-38 Identities = 54/129 (41%), Positives = 76/129 (58%), Gaps = 2/129 (1%) Query: 311 TEKIEWNKDSHLLQAWKQGYTGFPIIDAAMRQLNTIGWMHNRLRMITASFLVKDLL-VDW 369 ++I WN+D +L AW+ G TG+P IDA M QL GWMH+ R A FL + L + W Sbjct: 2 CKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGDLFIHW 61 Query: 370 RIGEEYFMSQLLDGDLASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWL 429 G + F L+D D A NNG W W + + + RI++P GK++DP G +IRH+L Sbjct: 62 EQGRDVFERLLIDSDWAINNGNWMWLSCSSFFY-QFNRIYSPISFGKKYDPDGKYIRHFL 120 Query: 430 PELNNVPTQ 438 P L ++P Q Sbjct: 121 PVLKDMPKQ 129 >1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} (A:1-140) Length = 140 Score = 133 bits (337), Expect = 4e-32 Identities = 68/141 (48%), Positives = 97/141 (68%), Gaps = 1/141 (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 QHRVICKSFDDSVLLPPGSIL 148 ++ V+C+ FDDSV+LPPG+++ Sbjct: 121 RN-VVCEGFDDSVILPPGAVM 140 >1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} (A:1-196) Length = 196 Score = 124 bits (311), Expect = 4e-29 Identities = 42/196 (21%), Positives = 72/196 (36%), Gaps = 9/196 (4%) Query: 7 MS-VHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASL 65 M+ L W R DLR++DN L AA S ++I +F P+ + ++ + ++ L Sbjct: 1 MAAPILFWHRRDLRLSDNIGLAAARAQSA-QLIGLFCLDPQILQSADMAPARVAYLQGCL 59 Query: 66 LQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEK 125 ++Q+ Q G Q D + Q + +++N+ E RD + Sbjct: 60 QELQQRYQQAGSRLLLLQG----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAA 115 Query: 126 RLQHRVI-CKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRL 184 L+ I D +L P IL+ + Y VY PF K + + Sbjct: 116 ALKTAGIRAVQLWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPVA--TPTELVD 173 Query: 185 TGPVTPSNIPRFFDYP 200 P + I Sbjct: 174 LSPEQLTAIAPLLLSE 189 >1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} (A:147-313) Length = 167 Score = 120 bits (303), Expect = 3e-28 Identities = 34/162 (20%), Positives = 62/162 (38%), Gaps = 12/162 (7%) Query: 153 QMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPR-----FFDYPFQAIDP- 206 + ++T FRK + + + P+ L P + F F Sbjct: 6 DLPDLFTKFRKDIEKKKISI-RPCFFAPSQLLPSPNIKLELTAPPPEFFPQINFDHRSVL 64 Query: 207 MFPIGEQNALHILRKFCKEK--VYYYVEQRD-IPAIQGTSQLSPYLSIGVLSPRQCWNRL 263 F GE L L+ + + Y E R+ + +S+ SP+L++G LSPR + + Sbjct: 65 AFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSKFSPWLALGCLSPRFIYQEV 124 Query: 264 KEEFVDLLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCMGK 305 K + + EL+WR+F+R + Y + + Sbjct: 125 KRYEQE--RVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNR 164 >2j07_A Deoxyribodipyrimidine photo-lyase; chromophore, DNA binding protein, flavoprotein, nucleotide- binding, antenna chromophore; HET: FAD HDF; 1.95A {Thermus thermophilus} (A:1-149) Length = 149 Score = 113 bits (283), Expect = 6e-26 Identities = 28/164 (17%), Positives = 57/164 (34%), Gaps = 16/164 (9%) Query: 7 MSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHGISARQSHFIYASLL 66 M LVW R DLR+ D+ AL A V+ + + P + R+ + ++ Sbjct: 1 MGPLLVWHRGDLRLHDHPALLEALAR--GPVVGLVVLDPNNLKTT---PRRRAWFLENVR 55 Query: 67 QVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKR 126 ++++ +G + E + + + ++ + RD + + Sbjct: 56 ALREAYRARGGALWVLEG----LPWEKVPEAARRLKAKAVYALTSHTPYGRYRDGRVREA 111 Query: 127 LQHRVICKSFDDSVLLPPGSILNHALQMYKVYTPFRKALIQNLV 170 L +L P + + Y+VYTPF + Sbjct: 112 L-------PVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAP 148 >2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} (A:133-267) Length = 135 Score = 112 bits (282), Expect = 9e-26 Identities = 33/151 (21%), Positives = 59/151 (39%), Gaps = 25/151 (16%) Query: 153 QMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDP-MFPIG 211 ++ +T F + + V+ P S++ F F+ I+ +F G Sbjct: 3 FHHRNFTSFYNEVSKVKVRE-----PETMEGSFDVT-DSSMNVDFLLTFKKIESPLFRGG 56 Query: 212 EQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLL 271 + L++L + +RD PA +LSP+L G +S R+ + K Sbjct: 57 RREGLYLLHRNV------DFRRRDYPAENNNYRLSPHLKFGTISMREAYYTQK------- 103 Query: 272 IKPKSGAFSWLNELIWREFYRHLMAFYPSVC 302 G ++ EL WR+F+ L + P V Sbjct: 104 -----GKEEFVRELYWRDFFTLLAYYNPHVF 129 >1np7_A DNA photolyase; protein with FAD cofactor; HET: DNA FAD; 1.90A {Synechocystis SP} (A:1-146) Length = 146 Score = 111 bits (279), Expect = 2e-25 Identities = 35/153 (22%), Positives = 63/153 (41%), Gaps = 13/153 (8%) Query: 1 MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG-----ISA 55 MK LVW RNDLR+ D++ L+ A + + AV+ P Q+ Q Sbjct: 1 MKHVPP--TVLVWFRNDLRLHDHEPLHRALKSGL-AITAVYCYDPRQFAQTHQGFAKTGP 57 Query: 56 RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115 +S+F+ S+ + +SL + G + + Q ++Y+R+ Sbjct: 58 WRSNFLQQSVQNLAESLQKVGNKLLVTTG----LPEQVIPQIAKQINAKTIYYHREVTQE 113 Query: 116 EVRRDKLLEKRL-QHRVICKSFDDSVLLPPGSI 147 E+ ++ L K+L + K + S L P + Sbjct: 114 ELDVERNLVKQLTILGIEAKGYWGSTLCHPEDL 146 >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* (A:34-183) Length = 150 Score = 110 bits (275), Expect = 5e-25 Identities = 32/154 (20%), Positives = 61/154 (39%), Gaps = 14/154 (9%) Query: 3 ATTAMSVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH------GISAR 56 V ++W RNDLR+ DN ALY A +SD ++ V+ P + A Sbjct: 2 KRKGKGVTILWFRNDLRVLDNDALYKAWSSSD-TILPVYCLDPRLFHTTHFFNFPKTGAL 60 Query: 57 QSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINE 116 + F+ L+ ++K+L ++G+ E L S +F +++ E Sbjct: 61 RGGFLMECLVDLRKNLMKRGLNLLIRSG----KPEEILPSLAKDFGARTVFAHKETCSEE 116 Query: 117 VRRDKLLEKRLQHR---VICKSFDDSVLLPPGSI 147 V ++L+ + L+ + S + + Sbjct: 117 VDVERLVNQGLKRVGNSTKLELIWGSTMYHKDDL 150 >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* (A:1-163) Length = 163 Score = 106 bits (266), Expect = 5e-24 Identities = 27/146 (18%), Positives = 47/146 (32%), Gaps = 10/146 (6%) Query: 1 MKATTAMSVHLVWLRNDLRITDNKALYAACHNSDAK-----VIAVFIATPEQWRQHGISA 55 + S + W R LR+ DN AL ++A V +FI P + A Sbjct: 22 GLMDSQRSTLVHWFRKGLRLHDNPALSHIFTAANAAPGRYFVRPIFILDPGILDWMQVGA 81 Query: 56 RQSHFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEIN 115 + F+ +L + L + + E RV L + E Sbjct: 82 NRWRFLQQTLEDLDNQLRKLNSRLFVVRG----KPAEVFPRIFKSWRVEMLTFETDIEPY 137 Query: 116 EVRRDKLLEKRLQHRVI-CKSFDDSV 140 V RD ++K + + ++ Sbjct: 138 SVTRDAAVQKLAKAEGVRVETHCSHT 163 >1owl_A Photolyase, deoxyribodipyrimidine photolyase; DNA repair, flavin enzyme, photoreactivating enzyme; HET: FAD; 1.80A {Synechococcus elongatus pcc 6301} (A:197-307) Length = 111 Score = 104 bits (262), Expect = 2e-23 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 1/97 (1%) Query: 208 FPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEF 267 GE A+ L++FC + Y QR+ PA GTS LSP L G + RQ W Sbjct: 10 VEPGETAAIARLQEFCDRAIADYDPQRNFPAEAGTSGLSPALKFGAIGIRQAWQAASAAH 69 Query: 268 VD-LLIKPKSGAFSWLNELIWREFYRHLMAFYPSVCM 303 + ++ W EL WREFY+H + +PS+ Sbjct: 70 ALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLAD 106 >3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} (A:1-142) Length = 142 Score = 101 bits (254), Expect = 1e-22 Identities = 27/142 (19%), Positives = 46/142 (32%), Gaps = 15/142 (10%) Query: 8 SVHLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQHG---------ISARQS 58 S L+W R LR+ DN AL A S+ + VF+ P + Sbjct: 5 SGSLIWFRKGLRVHDNPALEYASKGSE-FMYPVFVIDPHYMESDPSAFSPGSSRAGVNRI 63 Query: 59 HFIYASLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVR 118 F+ SL + SL + G + + E L + +V +L + + Sbjct: 64 RFLLESLKDLDSSLKKLGSRLLVFKG----EPGEVLVRCLQEWKVKRLCFEYDTDPYYQA 119 Query: 119 RDKLLEKRLQHRVI-CKSFDDS 139 D ++ + S Sbjct: 120 LDVKVKDYASSTGVEVFSPVSH 141 >2e0i_A 432AA long hypothetical deoxyribodipyrimidine photolyase; FAD, DNA repair; HET: FAD; 2.80A {Sulfolobus tokodaii str} (A:1-132) Length = 132 Score = 101 bits (252), Expect = 3e-22 Identities = 35/136 (25%), Positives = 61/136 (44%), Gaps = 9/136 (6%) Query: 10 HLVWLRNDLRITDNKALYAACHNSDAKVIAVFIATPEQWRQH-GISARQSHFIYASLLQV 68 + R DLR+ DN L A D +VI VFIA P Q + S F+ SLL++ Sbjct: 3 CIFIFRRDLRLEDNTGLNYALSECD-RVIPVFIADPRQLINNPYKSEFAVSFMINSLLEL 61 Query: 69 QKSLSQKGIVFQYHQCSNFDDSIEWLDSYCLQQRVTKLFYNRQYEINEVRRDKLLEKRL- 127 L +KG ++ + + + +V ++ N Y + RD+ + K Sbjct: 62 DDELRKKGSRLNVFFG----EAEKVVSRFF--NKVDAIYVNEDYTPFSISRDEKIRKVCE 115 Query: 128 QHRVICKSFDDSVLLP 143 ++ + K+++D +L P Sbjct: 116 ENGIEFKAYEDYLLTP 131 >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* (A:1-33,A:184-316) Length = 166 Score = 98.3 bits (244), Expect = 2e-21 Identities = 23/133 (17%), Positives = 46/133 (34%), Gaps = 7/133 (5%) Query: 142 LPPGSILNHALQMYKVYTPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPF 201 LP S + VYT FRK++ +P+ ++P Sbjct: 28 LPSSSSPFDVFDLPDVYTQFRKSVEAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGV 87 Query: 202 ----QAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRD---IPAIQGTSQLSPYLSIGVL 254 F GE + + ++ +K V + + +++ SP+L+ G + Sbjct: 88 EPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCI 147 Query: 255 SPRQCWNRLKEEF 267 SPR + ++ Sbjct: 148 SPRFIYEEVQRYE 160 >1dnp_A DNA photolyase; DNA repair, electron transfer, excitation energy transfer, carbon-carbon; HET: DNA FAD MHF; 2.30A {Escherichia coli} (A:184-263) Length = 80 Score = 74.9 bits (184), Expect = 2e-14 Identities = 34/72 (47%), Positives = 47/72 (65%), Gaps = 1/72 (1%) Query: 197 FDYPFQAIDP-MFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLS 255 +YP Q+ D FP+ E+ A+ LR+FC+ Y +QRD PA++GTS+LS L+ G LS Sbjct: 5 LNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLS 64 Query: 256 PRQCWNRLKEEF 267 PRQC +RL E Sbjct: 65 PRQCLHRLLAEQ 76 >3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} (A:196-290) Length = 95 Score = 73.8 bits (181), Expect = 4e-14 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 7/89 (7%) Query: 184 LTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEK--VYYYVEQRDIPAI-- 239 ++ + + + QA F GE AL L K +K V + + + P+ Sbjct: 1 ISEVPSLEELG--YKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFL 58 Query: 240 -QGTSQLSPYLSIGVLSPRQCWNRLKEEF 267 T+ +SPYL G LS R + L+ + Sbjct: 59 KPATTVMSPYLKFGCLSSRYFYQCLQNIY 87 >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* (A:220-313) Length = 94 Score = 68.8 bits (168), Expect = 1e-12 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 5/82 (6%) Query: 190 PSNIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEK--VYYYVEQRDIPAI--QGTSQL 245 P+ + FP GE AL + + K++ V + + P T+ L Sbjct: 7 PTMKQLVKRPE-ELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVL 65 Query: 246 SPYLSIGVLSPRQCWNRLKEEF 267 SPYL G LS R +LKE Sbjct: 66 SPYLKFGCLSARLFNQKLKEII 87 >3fy4_A 6-4 photolyase; DNA repair, clock cryptochrome; HET: MES FAD; 2.70A {Arabidopsis thaliana} (A:452-537) Length = 86 Score = 42.7 bits (100), Expect = 1e-04 Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 6/49 (12%) Query: 439 YIHAPHSWLDKN------DLSLNYPLPIVDHKKACHHTLNQYYAAKKQS 481 YI+ P + + +YP P+V H A + A + Sbjct: 1 YIYEPWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALN 49 >1aua_A Phosphatidylinositol transfer protein SEC14P; phospholipid-binding protein, peripheral golgi membrane protein, phospholipid exchange; HET: BOG; 2.50A {Saccharomyces cerevisiae} (A:94-296) Length = 203 Score = 30.3 bits (67), Expect = 0.55 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 6/82 (7%) Query: 192 NIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSI 251 N P F F+ P + + IL ++++ + ++P G Sbjct: 120 NAPFGFSTAFRLFKPFLDPVTVSKIFILGSSYQKELLKQIPAENLPVKFGGKSEVDESKG 179 Query: 252 GVLSPRQCWNRLKEEFVDLLIK 273 G + + D Sbjct: 180 G------LYLSDIGPWRDPKYI 195 >3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation termination, ATP-binding, cytoplasm, hydrolase, membrane; 2.80A {Schizosaccharomyces pombe} (A:1-326) Length = 326 Score = 29.7 bits (66), Expect = 0.81 Identities = 7/100 (7%), Positives = 19/100 (19%), Gaps = 28/100 (28%) Query: 40 VFIATPEQWRQHGISARQSHFIYA---SLLQVQKSLSQKGIVFQYHQCSNFDDSIEWLDS 96 + I TP + ++ + D + Sbjct: 238 IVIGTPG---------TVMDLMKRRQLDARDIKVFVLD--EADNMLDQQGLGDQSMRIKH 286 Query: 97 YCLQQRVTKLF--------------YNRQYEINEVRRDKL 122 + LF + ++ ++L Sbjct: 287 LLPRNTQIVLFSATFSERVEKYAERFAPNANEIRLKTEEL 326 >1r31_A 3-hydroxy-3-methylglutaryl-coenzyme A reductase; 4-electron oxido-reductase, oxidoreductase; HET: COA MEV; 2.10A {Pseudomonas mevalonii} (A:56-109,A:219-428) Length = 264 Score = 29.8 bits (67), Expect = 0.87 Identities = 11/82 (13%), Positives = 23/82 (28%), Gaps = 9/82 (10%) Query: 4 TTAMSVHLVWLRNDLRITDNKALYAACHNSDAK--VIAVFIATPEQWRQ-----HGISAR 56 + + + D HN + + +AT WR H + R Sbjct: 76 SGEAVIEGILDAYAFAAVDPYRAAT--HNKGIMNGIDPLIVATGNDWRAVEAGAHAYACR 133 Query: 57 QSHFIYASLLQVQKSLSQKGIV 78 H+ + + + G + Sbjct: 134 SGHYGSLTTWEKDNNGHLVGTL 155 >1xsz_A Guanine nucleotide exchange protein; ARF guanine nucleotide exchange factor, signaling protein; 1.41A {Legionella pneumophila} (A:198-356) Length = 159 Score = 29.6 bits (66), Expect = 1.0 Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 6/65 (9%) Query: 385 LASNNGGWQWAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHWLPELNNVPTQYIHAPH 444 + G++ ++T N F+ + + + F P + + + P Sbjct: 1 FVKTSPGYELTSTTLNKD-STFKKLDSFLHSTDVNINTVF-----PGIGDNVKTTVDQPK 54 Query: 445 SWLDK 449 SWL Sbjct: 55 SWLSF 59 >3b7n_A Uncharacterized protein YKL091C; SEC14, golgi, phospholipid, phosphatidylinositol, signaling protein; HET: B7N; 1.86A {Saccharomyces cerevisiae} PDB: 3b74_A* 3b7q_A* 3b7z_A* (A:95-320) Length = 226 Score = 28.7 bits (63), Expect = 1.6 Identities = 11/86 (12%), Positives = 27/86 (31%), Gaps = 6/86 (6%) Query: 192 NIPRFFDYPFQAIDPMFPIGEQNALHILRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSI 251 + P F F+ + P + + IL K+++ + ++P G + + Sbjct: 134 HSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHN--- 190 Query: 252 GVLSPRQCWNRLKEEFVDLLIKPKSG 277 + + + D G Sbjct: 191 ---PNDKFYYSDIGPWRDPRYIGPEG 213 >3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown function, ATP-binding, isomerase, nucleotide-binding, topoisomerase; HET: DNA; 1.95A {Myxococcus xanthus dk 1622} (A:1-206) Length = 206 Score = 27.8 bits (61), Expect = 3.0 Identities = 13/102 (12%), Positives = 28/102 (27%), Gaps = 12/102 (11%) Query: 279 FSWLNELIWREFYRHLMAFYPSVCMGKPFIPWT-EKIEWNKDSHLLQAWKQGYTGFPIID 337 S IW + + + G+ E + + + + + T F ++ Sbjct: 109 SSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLA 168 Query: 338 AAMRQLNTIGWMHNRLRMITASFLVKDL---LVDWRIGEEYF 376 + R + + L L D + GE Sbjct: 169 FDRA------RLSRRCNEL--AALAPGLRVSFADLQRGERTL 202 >2ix5_A Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4, flavin, peroxisome, glyoxysome, fatty acid metabolism, lipid metabolism; HET: CAA FAD; 2.7A {Arabidopsis thaliana} PDB: 2ix6_A* (A:1-164,A:273-436) Length = 328 Score = 27.1 bits (59), Expect = 5.2 Identities = 8/74 (10%), Positives = 25/74 (33%) Query: 162 RKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHILRK 221 R + + + + P+ TP++ + + + EQ +R+ Sbjct: 9 RASNEKKVKSSYFDLPPMEMSVAFPQATPASTFPPCTSDYYHFNDLLTPEEQAIRKKVRE 68 Query: 222 FCKEKVYYYVEQRD 235 +++V + + Sbjct: 69 CMEKEVAPIMTEYW 82 >2qe8_A Uncharacterized protein; YP_324691.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE UNL PG4; 1.35A {Anabaena variabilis atcc 29413} (A:117-167,A:195-289) Length = 146 Score = 26.9 bits (59), Expect = 5.3 Identities = 9/99 (9%), Positives = 22/99 (22%), Gaps = 15/99 (15%) Query: 336 IDAAMRQLNTIGWMHNRLRMITASFLVKDLLVDWRIGEEYFMSQLLDG--DLASNNGGWQ 393 +DA L I ++ L L D +G + ++ + Sbjct: 59 LDAENEWLYLSPXHSTSXYRIKSADLSNLQLTDAELGSKIERYSEKPICDGISIDKDHNI 118 Query: 394 WAASTGNDSVPYFRIFNPTIQGKRFDPQGTFIRHW-LPE 431 + + ++ + E Sbjct: 119 YVGDLAHSAI------------GVITSADRAYKLLVTDE 145 >3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A* (A:) Length = 244 Score = 27.0 bits (58), Expect = 5.3 Identities = 5/145 (3%), Positives = 28/145 (19%), Gaps = 8/145 (5%) Query: 159 TPFRKALIQNLVQADLRSLPVPAIRLTGPVTPSNIPRFFDYPFQAIDPMFPIGEQNALHI 218 + + ++ + D + + + + Sbjct: 6 SEKDLKELDSIRDSFQCMNEPLDNDQQASTLAKKEHNPTD--------ILNVMDITMRRL 57 Query: 219 LRKFCKEKVYYYVEQRDIPAIQGTSQLSPYLSIGVLSPRQCWNRLKEEFVDLLIKPKSGA 278 ++ + + + + ++ + GV + + Sbjct: 58 VKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQISFNMF 117 Query: 279 FSWLNELIWREFYRHLMAFYPSVCM 303 ++ + L F Sbjct: 118 DKLRPDIKDTQKKGFLHFFNLLHSD 142 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.324 0.138 0.444 Gapped Lambda K H 0.267 0.0480 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 4,048,323 Number of extensions: 192019 Number of successful extensions: 761 Number of sequences better than 10.0: 1 Number of HSP's gapped: 717 Number of HSP's successfully gapped: 44 Length of query: 483 Length of database: 4,956,049 Length adjustment: 92 Effective length of query: 391 Effective length of database: 1,845,989 Effective search space: 721781699 Effective search space used: 721781699 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: 56 (26.0 bits)