RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780468|ref|YP_003064881.1| sensory box/GGDEF family protein [Candidatus Liberibacter asiaticus str. psy62] (963 letters) >3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1} Length = 437 Score = 154 bits (390), Expect = 7e-38 Identities = 75/416 (18%), Positives = 162/416 (38%), Gaps = 7/416 (1%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVL 592 + QD +TG+ NR FLD + + A T+ I ++ Y + G++ D +L Sbjct: 13 SSQDPVTGLYNRSHFLDLMDAAVQ-QAVTARKPSTLAYIHLNGYPSLQADHGLSGIDLLL 71 Query: 593 VSLTRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPINLLEREI 652 L + E LAR + F + + A ++K L R Sbjct: 72 GQLAGLMREQFGEEADLARFGDSIFAALFKGKTPEQAQAALQRLLKKVENHLFELNGRSA 131 Query: 653 TVTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESFRVSSFRSDRVMIKEDLC 712 T SIG A + +++ A A +GG+ ++ + + + + + Sbjct: 132 QATLSIGVAGLDEKTAKAQDVMNRAHRCADDAARKGGSQIKQYNPAEELAAAAQRGDVIA 191 Query: 713 LA---VENSELYLVYHPIIRLMDEEIVGLEALIQWDHPKWGNISSSEFMLIAEELCMIKA 769 + +E + L++ P+I L + E L++ +P+ + +EF+ A+E + + Sbjct: 192 ILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHAAKEAGLAEK 251 Query: 770 INLFMLERIARDIISWRDQANMPPIFILINIASKDLLDNELCEGMQALISKTLYSPSRIK 829 I+ +++ + + R + + +F+ ++ AS D L + + P + Sbjct: 252 IDRWVILNSIKLLAEHRAKGHQTKLFVHLSSASLQ--DPGLLPWLGVALKAARLPPESLV 309 Query: 830 LSFSESVVMGNPERSRLLLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFDTVKFNGSLMT 889 SE+ ++++ L L + + FG + + L ++ +K +GS + Sbjct: 310 FQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQFIKIDGSFVQ 369 Query: 890 G-STEKRIAILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQDSHVASPL 944 + + IL+ +I + I + + L + G YIQ ++ P Sbjct: 370 DLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYYLQGPS 425 >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 = 147 bits (371), Expect = 2e-35 Identities = 47/277 (16%), Positives = 93/277 (33%), Gaps = 18/277 (6%) Query: 675 KNAELAMYHAKHRGGNHVESFRVSSFRSDRVMIKEDLCL----AVENSELYLVYHPIIRL 730 + + A G + R M+ + I+ Sbjct: 130 NDRMFRLLSAFIADGGRYCLPEP--LQPSRWMMMPASGTAAPQHLPGQPCQFALQAIVEP 187 Query: 731 MDEEIVGLEALIQWDHPKWGNISSSEFMLIAEELCMIKAINLFMLERIARDIISWRDQAN 790 + + EALI+ G F IA E + + Q Sbjct: 188 AKKRVSSFEALIRSPT---GGSPVEMFAAIAAEDRYRFDLESKAYA------FALAGQLP 238 Query: 791 MPPIFILINIASKDLLDNE-LCEGMQALISKTLYSPSRIKLSFSESVVMGNPERSRLLLG 849 + + IN+ L + + + P ++ + +E+ V+ ++ R +L Sbjct: 239 LGKHQLAINLLPGSLYHHPDAVGWLMDSLLAAGLRPDQVLIEVTETEVITCFDQFRKVLK 298 Query: 850 RLRKIGISLTLDDFGTKCSLLSYLGYIPFDTVKFNGSLMTG--STEKRIAILRSIIPMAK 907 LR G+ L +DDFG S LS L D +K + L+ + + AI+ S++ + Sbjct: 299 ALRVAGMKLAIDDFGAGYSGLSLLTRFQPDKIKVDAELVRDIHISGTKQAIVASVVRCCE 358 Query: 908 NIETTIIAKDIYGEIDIKELTRMGCDYIQDSHVASPL 944 ++ T++A+ + + L +G Q + P Sbjct: 359 DLGITVVAEGVETLEEWCWLQSVGIRLFQGFLFSRPC 395 >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 = 134 bits (337), Expect = 1e-31 Identities = 70/257 (27%), Positives = 132/257 (51%), Gaps = 3/257 (1%) Query: 703 DRVMIKEDLCLAVENSELYLVYHPIIRLMDEEIVGLEALIQWDHPKWGNISSSEFMLIAE 762 +R+ + L A+E +EL L Y PI+ L IVG EAL++W+ P+ G + S F+ AE Sbjct: 23 ERLTLDTRLRQALERNELVLHYQPIVELASGRIVGGEALVRWEDPERGLVMPSAFIPAAE 82 Query: 763 ELCMIKAINLFMLERIARDIISWRDQAN-MPPIFILINIASKDLLDNELCEGMQALISKT 821 + +I A++ ++LE + +W+ Q + + +NI+++ L + ++++ Sbjct: 83 DTGLIVALSDWVLEACCTQLRAWQQQGRAADDLTLSVNISTRQFEGEHLTRAVDRALARS 142 Query: 822 LYSPSRIKLSFSESVVMGNPERSRLLLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFDTV 881 P ++L +E+V++ + R L LR G+ L LDDFGT S LSYL +PF + Sbjct: 143 GLRPDCLELEITENVMLVMTDEVRTCLDALRARGVRLALDDFGTGYSSLSYLSQLPFHGL 202 Query: 882 KFNGSL--MTGSTEKRIAILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQDSH 939 K + S + I+ +I+ +A+ + ++A+ I L GC++ Q + Sbjct: 203 KIDQSFVRKIPAHPSETQIVTTILALARGLGMEVVAEGIETAQQYAFLRDRGCEFGQGNL 262 Query: 940 VASPLGFNSILKLLKER 956 +++P ++ LL + Sbjct: 263 MSTPQAADAFASLLDRQ 279 >1w25_A Stalked-cell differentiation controlling protein; two-component system, response regulator, diguanylate cyclase, ggdef domain; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* Length = 459 Score = 132 bits (334), Expect = 3e-31 Identities = 54/211 (25%), Positives = 94/211 (44%), Gaps = 3/211 (1%) Query: 484 RVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKSLEGILCNAFQDNLTGIPN 543 V+A + + ++ R + + I + +L+ L A D LTG+ N Sbjct: 239 MVKALEIGVNDILSRPIDPQELSARVKTQIQRKRYTDYLRNNLDHSLELAVTDQLTGLHN 298 Query: 544 RQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVLVSLTRRIGELL 603 R+ +L +++ AT + ++IDID +KKIND G +GD+VL R+ + Sbjct: 299 RRYMTGQLDSLVK-RATLGGDPVSALLIDIDFFKKINDTFGHDIGDEVLREFALRLASNV 357 Query: 604 KFPDILARLSGNRFGIIL--ISENNSLKIADFAIAMRKSIAMPINLLEREITVTASIGFA 661 + D+ R G F +I+ + ++L+IA+ + + VT SIG + Sbjct: 358 RAIDLPCRYGGEEFVVIMPDTALADALRIAERIRMHVSGSPFTVAHGREMLNVTISIGVS 417 Query: 662 SWTSSKITSSEMLKNAELAMYHAKHRGGNHV 692 + T +LK A+ +Y AK G N V Sbjct: 418 ATAGEGDTPEALLKRADEGVYQAKASGRNAV 448 >3mtk_A Diguanylate cyclase/phosphodiesterase; structural genomics, PSI-2, protein structure initiative; 2.24A {Caldicellulosiruptor saccharolyticus} Length = 178 Score = 131 bits (332), Expect = 5e-31 Identities = 43/164 (26%), Positives = 84/164 (51%), Gaps = 7/164 (4%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVL 592 AF D LTG+PN+ S + L + + D + ++ +++ +K+N G + D+++ Sbjct: 7 AFYDELTGLPNKNSLIRWLNLKV---SQMDCIDTYLIFLEVRDLEKLNVTYGYDLVDELI 63 Query: 593 VSLTRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPINLLEREI 652 + +++RI ++ + ++ +RF II SEN I+DF M + +P N+ I Sbjct: 64 IHISKRIKDIAGEGNKAFKIGFDRFAIICKSEN----ISDFIERMLSQLLLPYNVNGNLI 119 Query: 653 TVTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESFR 696 V +IG A +S ++ +++ +LA+ AK G N F+ Sbjct: 120 RVNFNIGAAQIENSNEAAANLMRRCDLALIKAKEEGLNEYVIFK 163 >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 = 129 bits (325), Expect = 3e-30 Identities = 43/247 (17%), Positives = 89/247 (36%), Gaps = 7/247 (2%) Query: 700 FRSDRVMIKEDLCLAVENSELYLVYHPIIRLMDEEIVGLEALIQWDHPKWGNISSSEFML 759 F+S+ ++ + L + ++ Y I ++++VG E L + F+ Sbjct: 20 FQSNAML--DPLDILTNIDDVLPYYQAIFSAEEQKVVGYEVLGRILADSEIQSLGPFFLD 77 Query: 760 IAEELCMIKAINLFMLERIARDIISWRDQANMPPIFILINIASKDLLDNELCEGMQALIS 819 ++ ++ + + IF+ + L E + Sbjct: 78 AGIPEEYKLEVDNRIIRQALDRFLEADSD---LLIFMNQDANLLMLDHGESFLELLKEYE 134 Query: 820 KTLYSPSRIKLSFSESVVMGNPERSRLLLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFD 879 R L +E G+ E+ +L R GI + +D+ G + S L + + D Sbjct: 135 AKGIELHRFVLEITEHNFEGDIEQLYHMLAYYRTYGIKIAVDNIGKESSNLDRIALLSPD 194 Query: 880 TVKFNGSLMTGSTEKRI--AILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQD 937 +K + + S +L SI +A+ I ++ +DI ++ R G Y Q Sbjct: 195 LLKIDLQALKVSQPSPSYEHVLYSISLLARKIGAALLYEDIEANFQLQYAWRNGGRYFQG 254 Query: 938 SHVASPL 944 ++ SP Sbjct: 255 YYLVSPS 261 >3ezu_A Ggdef domain protein; multidomain protein of unknown function with ggdef-domain, structural genomics; 1.95A {Geobacter sulfurreducens} Length = 342 Score = 124 bits (312), Expect = 9e-29 Identities = 53/305 (17%), Positives = 105/305 (34%), Gaps = 31/305 (10%) Query: 398 QGIFSDGERQSLAVLG--SGDIVWDWDIV-RDRVTTTPDIATILGLASGSMHGPIRNWLP 454 + + G R++L ++ + + + +++ + + + Sbjct: 56 ERLQERGGRENLPIIIYKPAETLEELEMIGKSIDEQVERYTEAPSSEAACL--------- 106 Query: 455 YIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIG 514 + R + +F R ++ R + G Sbjct: 107 ---LGFRLQLYLLHPAFASLCRLTRDASGEDLPDIGYGRYL----RRFIDGIGSCGLATA 159 Query: 515 ----IANDITEQKKSLEGILCNAFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMV 570 + + + + D LTG+ R F + ++ +A +M+ Sbjct: 160 ETELLGEALFRLWNEARQLAAQSHFDALTGVMTRAGFFKTVGSLAY-AAQRSGSNVGIML 218 Query: 571 IDIDKYKKINDVLGIAVGDDVLVSLTRRIGELLKFPDILARLSGNRFGIILISENNSLKI 630 ID+D +K + D G GD +L + I L+ D++ R G+ F + L S + Sbjct: 219 IDLDYFKLVGDNYGHQTGDRILQLVAETITSHLRRSDVVGRYDGDEFVVYL-SPVEPASL 277 Query: 631 ADFAIAMRKSIAMPINLLEREITVTASIGFASW---TSSKITSSEMLKNAELAMYHAKHR 687 A +R+SI R + VTASIG A T E+++ A+ + AK+ Sbjct: 278 RTVAENLRRSIEEESA---RMVPVTASIGVAQGILGTDVDGGIEELVRLADECLMQAKYT 334 Query: 688 GGNHV 692 G N V Sbjct: 335 GKNKV 339 >3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa PAO1} PDB: 3i5a_A* Length = 358 Score = 116 bits (292), Expect = 2e-26 Identities = 43/168 (25%), Positives = 77/168 (45%), Gaps = 6/168 (3%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVL 592 D LTG+ NR+ F + L S + + + ++++ID+D +K ND G GD+ L Sbjct: 171 MNSDGLTGLSNRRHFDEYLEMEWRRSLREQS-QLSLLMIDVDYFKSYNDTFGHVAGDEAL 229 Query: 593 VSLTRRIGE-LLKFPDILARLSGNRFGIIL--ISENNSLKIADFAIAMRKSIAMPINLLE 649 + I E + D+ AR G F ++L S + +A+ +S+ + + Sbjct: 230 RQVAGAIREGCSRSSDLAARYGGEEFAMVLPGTSPGGARLLAEKVRRTVESLQISHDQPR 289 Query: 650 REITVTASIGFASWTSSK--ITSSEMLKNAELAMYHAKHRGGNHVESF 695 +T SIG ++ T +++ A+ A+Y AK+ G N V Sbjct: 290 PGSHLTVSIGVSTLVPGGGGQTFRVLIEMADQALYQAKNNGRNQVGLM 337 >3pfm_A Ggdef domain protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics, EAL domain; 2.91A {Pseudomonas fluorescens} Length = 243 Score = 114 bits (287), Expect = 8e-26 Identities = 41/226 (18%), Positives = 91/226 (40%), Gaps = 11/226 (4%) Query: 714 AVENSELYLVYHPIIRLMD-EEIVGLEALIQWDHPKWGNISSSEFMLIAEELCMIKAINL 772 A+ L + P++ D ++ + L + + I + F+ E ++L Sbjct: 15 ALSEQHFQLYFQPVVAARDTHLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTSRLDL 74 Query: 773 FMLERIARDIISWRDQANMPPIFILINIASKDLLDNELCEGMQALISKTLYSPSRIKLSF 832 M + Q + +N+++ L D + ++ + R+ L Sbjct: 75 LM-------LEQVLRQMASHEDCLALNLSAATLADPHALNRVFEILRQHSDLGPRLTLEI 127 Query: 833 SESVVMGNPERSRLLLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFDTVKFNGSLMTGST 892 E + +L RLR++G SL+L FG + S++ L + +K +GS + Sbjct: 128 GEEQLPEQAMLEQLTR-RLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRDID 186 Query: 893 EKRI--AILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQ 936 ++ + +I A +I+ +IA+ + E +++ + MG +Q Sbjct: 187 QESDKRLFIEAIQRAAHSIDLPLIAERVETEGELQVIREMGLYGVQ 232 >3icl_A EAL/ggdef domain protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics, consortium, NESG; HET: MSE; 2.00A {Methylococcus capsulatus} Length = 171 Score = 110 bits (274), Expect = 2e-24 Identities = 58/160 (36%), Positives = 90/160 (56%), Gaps = 1/160 (0%) Query: 536 DNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVLVSL 595 D +TG+PNRQ F DRL L + D ++ +D+D +K IND LG VGD +L + Sbjct: 2 DTVTGLPNRQLFCDRLLQALA-AHERDGNPVVLLFLDVDNFKSINDSLGHLVGDRLLRAT 60 Query: 596 TRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPINLLEREITVT 655 RI ++ D +AR+ G++F I+L ++L A A + +A P ++I ++ Sbjct: 61 AERIRTAVRDGDTVARIGGDKFTILLNGAKDTLNGALVAQKILDGLAQPFVFGAQQIVIS 120 Query: 656 ASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESF 695 SIG A + T ++L+NA+ AMYHAK RG N+ + F Sbjct: 121 VSIGIAVSPADGETMEQLLRNADTAMYHAKSRGKNNYQFF 160 >3kzp_A LMO0111 protein, putative diguanylate cyclase/phosphodiesterase; EAL-domain, structural genomics, PSI-2, protein structure initiative; 2.00A {Listeria monocytogenes} Length = 235 Score = 109 bits (272), Expect = 4e-24 Identities = 37/241 (15%), Positives = 78/241 (32%), Gaps = 25/241 (10%) Query: 718 SELYLVYHPIIRLMDEEIVGLEALIQWDHPKWGNISSSEFMLIAEELCMIKAINLFMLER 777 + L P + ++ IV E L++ D SE + + + A + + E Sbjct: 4 MKFQLFIQPKLDVLQGNIVEYEILLRDDSAV-PRFPLSELEAVLADEELYLAFSEWFSEA 62 Query: 778 IARDIISWRDQANMPPIFILINIASKDLLDNELCEGMQALISKTLYSPSRIKLSFSESVV 837 + + + INIA + L E + L S+ RI + +E + Sbjct: 63 FLDVLKKYPNDR------FAINIAPQQLFYIETLHWLDKLKSE----SHRITVEMTEDIF 112 Query: 838 MGNPERSRL-----------LLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFDTVKFNGS 886 + L + + +G + +DD + L + ++ S Sbjct: 113 DVPGHKRHLNANDKNAFILNKIKVIHGLGYHIAIDDVSCGLNSLERVMSYLPYIIEIKFS 172 Query: 887 LMTGST---EKRIAILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQDSHVASP 943 L+ E + +++ A+ + + + I + + L G Q V P Sbjct: 173 LIHFKNIPLEDLLLFIKAWANFAQKNKLDFVVEGIETKETMTLLESHGVSIFQGYLVNKP 232 Query: 944 L 944 Sbjct: 233 F 233 >3hv8_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; HET: C2E; 1.45A {Pseudomonas aeruginosa PAO1} PDB: 3hv9_A Length = 268 Score = 103 bits (257), Expect = 2e-22 Identities = 43/245 (17%), Positives = 101/245 (41%), Gaps = 3/245 (1%) Query: 701 RSDRVMIKEDLCLAVENSELYLVYHPIIRLMDEEIVGLEALIQWDHPKWGNISSSEFMLI 760 + R + L A+E + L++ P+I L + E L++ +P+ + +EF+ Sbjct: 14 AAQRGDVIAILQQALETNSFRLLFQPVISLRGDSHENYEVLLRLLNPQGQEVPPAEFLHA 73 Query: 761 AEELCMIKAINLFMLERIARDIISWRDQANMPPIFILINIASKDLLDNELCEGMQALISK 820 A+E + + I+ +++ + + R + + +F ++++S L D L + + Sbjct: 74 AKEAGLAEKIDRWVILNSIKLLAEHRAKGHQTKLF--VHLSSASLQDPGLLPWLGVALKA 131 Query: 821 TLYSPSRIKLSFSESVVMGNPERSRLLLGRLRKIGISLTLDDFGTKCSLLSYLGYIPFDT 880 P + SE+ ++++ L L + + FG + + L ++ Sbjct: 132 ARLPPESLVFQISEADATSYLKQAKQLTQGLATLHCQAAISQFGCSLNPFNALKHLTVQF 191 Query: 881 VKFNGSLMTG-STEKRIAILRSIIPMAKNIETTIIAKDIYGEIDIKELTRMGCDYIQDSH 939 +K +GS + + + IL+ +I + I + + L + G YIQ + Sbjct: 192 IKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASVLATLWQAGATYIQGYY 251 Query: 940 VASPL 944 + P Sbjct: 252 LQGPS 256 >3hvw_A Diguanylate-cyclase (DGC); alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.70A {Pseudomonas aeruginosa} Length = 176 Score = 103 bits (258), Expect = 2e-22 Identities = 27/160 (16%), Positives = 54/160 (33%), Gaps = 5/160 (3%) Query: 534 FQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVLV 593 D TG+ NR + ++ L + ++ + I LG +D+++ Sbjct: 1 MIDEPTGLYNRLRLQEDVSLRLQRDGALTVI--AADLLPLALLNTIIRTLGYPFSNDLML 58 Query: 594 SLTRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPINLLEREIT 653 RI L L ++S RFG++L + + + ++ P+ I Sbjct: 59 EARDRIRAEL-PDFTLYKISPTRFGLLL-PRQQQEETESVCLRLLRAFESPVVCRGIPIK 116 Query: 654 VTASIGFASWTSSKITSSE-MLKNAELAMYHAKHRGGNHV 692 +G + + L+ A A+ RG Sbjct: 117 ANVGLGVLPLADDTLDGDQDWLRLVVSAADDARDRGVGWA 156 >3ign_A Diguanylate cyclase; ggdef domain, A1U3W3_marav, NESG, MQR89A, structural genomics, PSI-2, protein structure initiative; HET: C2E; 1.83A {Marinobacter aquaeolei VT8} Length = 177 Score = 101 bits (253), Expect = 6e-22 Identities = 41/162 (25%), Positives = 73/162 (45%), Gaps = 3/162 (1%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVL 592 + D LTG+ NR ++ + + + ++++ DID +K +ND G GD+V+ Sbjct: 8 SMTDRLTGLLNRGTWENLVDAEYE-RFRRYGQATSLVMFDIDHFKPVNDTYGHLAGDEVI 66 Query: 593 VSLTRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIA-MPINLLERE 651 ++ D R G FGIIL E ++ +R++I ++ + Sbjct: 67 RHTADVTRNNIRQSDSAGRYGGEEFGIIL-PETDAESARVICERIREAIEKSTVSTSAGD 125 Query: 652 ITVTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVE 693 I T S+G A T + + ++ A+ A+Y AK G N V Sbjct: 126 IQYTVSMGIAQLTETPENYMQWMQKADEALYKAKESGRNKVV 167 >3nja_A Probable ggdef family protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 2.37A {Chromobacterium violaceum} Length = 125 Score = 88.7 bits (220), Expect = 5e-18 Identities = 25/120 (20%), Positives = 44/120 (36%), Gaps = 1/120 (0%) Query: 405 ERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNF 464 + A +G W + R+ + + I G S + + +H +DR Sbjct: 7 KLLHTAESDAGIGSWVLHMESGRLEWSQAVHDIFGTDSATFDATEDAYFQRVHPDDRARV 66 Query: 465 RTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKK 524 R LD V E+R+ D Q ++ R ++G + G D+TE K+ Sbjct: 67 RRELDRHV-LGDRPFDVEYRIVRPDGQVRELLERNHIQRQASGQVDHLWGTVIDMTEHKQ 125 >3mr0_A Sensory box histidine kinase/response regulator; PAS fold, structural genomics, PSI-2; HET: PG5; 1.49A {Burkholderia thailandensis} Length = 142 Score = 76.5 bits (188), Expect = 2e-14 Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 1/120 (0%) Query: 405 ERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNF 464 ER LAV G+ +WDW+ + +P I+G + I IH +DR Sbjct: 9 ERFQLAVSGASAGLWDWNPKTGAMYLSPHFKKIMGYEDHELPDEITGHRESIHPDDRARV 68 Query: 465 RTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKK 524 L + + +R E+RVR F W+ R + + NS G+ R +G D+T++K+ Sbjct: 69 LAALKAHLEHRDTY-DVEYRVRTRSGDFRWIQSRGQALWNSAGEPYRMVGWIMDVTDRKR 127 >3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; 1.90A {Marinobacter aquaeolei VT8} Length = 115 Score = 71.5 bits (174), Expect = 9e-13 Identities = 19/110 (17%), Positives = 39/110 (35%), Gaps = 3/110 (2%) Query: 414 SGDIVWDWDIVRDRVT-TTPDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFV 472 + I W + P I +LG GS +W +H D++ Sbjct: 2 TKAIPWKINWQTMAFEYIGPQIEALLGWPQGSWKSV-EDWATRMHPEDQEWVVNFCVKQS 60 Query: 473 GYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQ 522 + ++R D + W+ + + + +G++ IG DI+ + Sbjct: 61 E-CGVDHEADYRALHRDGHYVWIRDVVHVVRDDSGEVEALIGFMFDISLE 109 >3hva_A Protein FIMX; ggdef diguanylate cyclase, biofilm, C-DI-GMP, transferase; 2.04A {Pseudomonas aeruginosa PAO1} Length = 177 Score = 67.8 bits (164), Expect = 1e-11 Identities = 35/164 (21%), Positives = 62/164 (37%), Gaps = 1/164 (0%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGDDVL 592 + QD +TG+ NR FLD + + A T+ I ++ Y + G++ D +L Sbjct: 13 SSQDPVTGLYNRSHFLDLMDAAVQ-QAVTARKPSTLAYIHLNGYPSLQADHGLSGIDLLL 71 Query: 593 VSLTRRIGELLKFPDILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPINLLEREI 652 L + E LAR + F + + A ++K L R Sbjct: 72 GQLAGLMREQFGEEADLARFGDSIFAALFKGKTPEQAQAALQRLLKKVENHLFELNGRSA 131 Query: 653 TVTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESFR 696 T SIG A + +++ A A +GG+ ++ + Sbjct: 132 QATLSIGVAGLDEKTAKAQDVMNRAHRCADDAARKGGSQIKQYN 175 >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 = 66.1 bits (161), Expect = 3e-11 Identities = 82/549 (14%), Positives = 165/549 (30%), Gaps = 238/549 (43%) Query: 557 LSATDDNLRPTVM-------VIDI------------DKYKK-INDVLGIAVGDDVLVSLT 596 + A + RP + V+ + +++ K + + DD + Sbjct: 1 MDAY--STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA 58 Query: 597 RRIGELL-KFPD-ILARLSGNRFGIILISENNSLKIA------DFAIAMRKSIAMPINLL 648 EL+ KF + + + ++ G + L + + L Sbjct: 59 ----ELVGKFLGYVSSLVEPSKVG----QFDQVLNLCLTEFENCY-------------LE 97 Query: 649 EREI-TVTASIGFASWTSSKITSSEMLKNAEL--AMYHAKHRGGNHVESFRVSS-FRS-- 702 +I + A + + + ++K EL A+ + S+ FR+ Sbjct: 98 GNDIHALAAKL-------LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVG 150 Query: 703 -DRVMI---------KEDLCLAVENSELYLVYHP----IIRLMDE---EIV--------- 736 + +D E +LY YH +I+ E E++ Sbjct: 151 EGNAQLVAIFGGQGNTDD-YFE-ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKV 208 Query: 737 ---GLEALIQW-DHPKWGNISSSEFMLIAE---------ELC--MIKAINL-----FMLE 776 GL +++W ++P N +++L +L ++ A L + Sbjct: 209 FTQGLN-ILEWLENPS--NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRS 265 Query: 777 RIA------RDII---------SWRD--------------------QA----NMPPIFIL 797 + + ++ SW +A ++PP + Sbjct: 266 YLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSIL- 324 Query: 798 INIASKDLLDNELCEG----M-----------QALISKT---LYSPSRIKLSFSES---- 835 +D L+N EG M Q ++KT L + ++++S Sbjct: 325 -----EDSLENN--EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL 377 Query: 836 VVMGNPERSRLLLG---RLRKIGISLTLDDFGTKCSLLSYLGYIPFD------------- 879 VV G P+ S L G LRK LD ++ IPF Sbjct: 378 VVSGPPQ-S--LYGLNLTLRKAKAPSGLDQ--SR---------IPFSERKLKFSNRFLPV 423 Query: 880 TVKFNGSLMTGSTEKRIAILRSIIPMAKNIETTIIAKD----IY----GEIDIKE----- 926 F+ L+ +++ I + + + N+ AKD +Y G D++ Sbjct: 424 ASPFHSHLLVPASDL---INKDL--VKNNVS--FNAKDIQIPVYDTFDGS-DLRVLSGSI 475 Query: 927 ---LTRMGC 932 + Sbjct: 476 SERIVDCII 484 Score = 61.5 bits (149), Expect = 8e-10 Identities = 112/701 (15%), Positives = 191/701 (27%), Gaps = 309/701 (44%) Query: 77 VSASSIRHRGDWAVFALANTSDSQLERLIVVPHYRLVGSHF--------FSPDLGSRRII 128 + A S R L S LE +++VP S F F+ L Sbjct: 1 MDAYSTRP------LTL---SHGSLEHVLLVPT----ASFFIASQLQEQFNKILPE---- 43 Query: 129 SVTPSEGFSLDRIPNSDSDVFRITINPGAVVTFIMEISTPNLPQIYLWEPNFYKDTVNSF 188 P+EGF+ D P + +++ G + ++ + P+ + + F Sbjct: 44 ---PTEGFAADDEPTTPAELV------GKFLGYVSSLVEPSKVGQF---DQVLNLCLTEF 91 Query: 189 --TLYRGIIIG--VASLLAIFLTIFYMVNRSSMLIPTFAMAWVVLGYISIDFGFLSKLVN 244 G I A LL T LI + A ++ Sbjct: 92 ENCYLEGNDIHALAAKLLQENDTTLVKTKE---LIKNYITARIMAK-------------- 134 Query: 245 LPSGELLIWRACSEIALSSSLIIFLFMYLHWNRWHAKVGYITFSGIACI-------AILF 297 R + + S+ LF +A++ F G L+ Sbjct: 135 ---------RPFDKKSNSA-----LFR--AVGEGNAQL-VAIFGGQGNTDDYFEELRDLY 177 Query: 298 CMSFYYPMVTASIARI--TLASIVL-------YYTYFIIYHGMKGYERAVLLIPAWILIF 348 Y+ +V I TL+ ++ +T G+ I W Sbjct: 178 QT--YHVLVGDLIKFSAETLSELIRTTLDAEKVFT-----QGLN--------ILEW---- 218 Query: 349 IWFIGLWMAITKRLDNDIIQPALVGGLVLIVI---LIG------FTVIQHVL-------- 391 L+N P L+ I I LIG + V +L Sbjct: 219 -------------LENPSNTPD-KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELR 264 Query: 392 -----ATGYFSQGIFSDGERQSLAVLGSGDIVWD--WDIVRDRVT-----------TTPD 433 ATG+ SQG+ + ++A+ + W+ + VR +T P+ Sbjct: 265 SYLKGATGH-SQGLVT-----AVAIAETDS--WESFFVSVRKAITVLFFIGVRCYEAYPN 316 Query: 434 IATILGLASGSM------HG---P-----IRN---------------WLP---YIHI--- 458 + L S+ + P I N LP + I Sbjct: 317 TS----LPP-SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV 371 Query: 459 NDRDNFRTIL----DSFVGYRRGRLQYEFRVRAAD--NQFHWMIIRIRPMSNSNGDILRY 512 N N ++ S G L+ + +A +Q RI P S Sbjct: 372 NGAKNL--VVSGPPQSLYGLNL-TLR---KAKAPSGLDQ-----SRI-PFS--------- 410 Query: 513 IGIANDITEQKKSLEGILCNAFQDNLTGI--PNRQSFLDRLTTIL--DLSATDDNLRPTV 568 ++K F + + P L + ++ DL + + Sbjct: 411 ---------ERKL-------KFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA-- 452 Query: 569 MVIDIDKYKKINDVLGIAV-----GDD-------VLVSLTRRIGEL-------LKFP--D 607 D + I V G D + + I L +F Sbjct: 453 -----------KD-IQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATH 500 Query: 608 IL----ARLSG-------NRFG----IIL-----ISENNSL 628 IL SG N+ G +I+ I+ ++ Sbjct: 501 ILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDY 541 Score = 38.0 bits (88), Expect = 0.011 Identities = 42/276 (15%), Positives = 75/276 (27%), Gaps = 119/276 (43%) Query: 2 LLSNSLRSHFEKAFL----ILVLFLLWMVSPSFAIEPINISSSDRVLDLTSITRIYVNQG 57 +L+ L FE +L I L + + + ++ + Y Sbjct: 83 VLNLCLT-EFENCYLEGNDIHAL-----AAKLLQENDTTLVKTKELI------KNY---- 126 Query: 58 EDFQVFTAADIDGISRRIEVSASSIRHRGDWAVFALANTSDSQL--------------ER 103 TA ++ + + A+F ++QL E Sbjct: 127 -----ITA---------RIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEE 172 Query: 104 LIVVPH-YR-LVGS--HFFSPDLGSRRIISVTP-------SEGFSL-------DRIPNSD 145 L + Y LVG F + L + T ++G ++ P+ D Sbjct: 173 LRDLYQTYHVLVGDLIKFSAETLSE---LIRTTLDAEKVFTQGLNILEWLENPSNTPDKD 229 Query: 146 ----SDV------------FRIT-----INPGA--------------VVT--FIMEISTP 168 + + +T PG +VT I E + Sbjct: 230 YLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDS- 288 Query: 169 NLPQIYLWEPNFYKDTVNSFT-LYRGIIIGVASLLA 203 WE +F+ + T L+ IGV A Sbjct: 289 -------WE-SFFVSVRKAITVLFF---IGVRCYEA 313 Score = 29.5 bits (66), Expect = 4.1 Identities = 28/93 (30%), Positives = 39/93 (41%), Gaps = 24/93 (25%) Query: 75 IEVSASSIRHR-GDWAVFALANTSD-SQLERLIVVPHYRLVGSHFFSPDLGSRRIISVTP 132 I A+ H G++A ALA+ +D +E L+ V YR G ++V Sbjct: 1753 IPADATFAGHSLGEYA--ALASLADVMSIESLVEVVFYR-----------GMTMQVAVPR 1799 Query: 133 SEGFSLDRIPNSDSDVFRITINPGAV-VTFIME 164 E L R S+ I INPG V +F E Sbjct: 1800 DE---LGR-----SNYGMIAINPGRVAASFSQE 1824 >3i5c_A Fusion of general control protein GCN4 and WSPR response regulator protein; C-DI-GMP, ggdef, leucine zipper, signaling protein; HET: C2E; 1.94A {Pseudomonas aeruginosa PAO1} PDB: 3i5b_A* Length = 206 Score = 56.3 bits (134), Expect = 3e-08 Identities = 35/168 (20%), Positives = 61/168 (36%), Gaps = 6/168 (3%) Query: 533 AFQDNLTGIPNRQSFLDRLTTILDLSATDDNLRPTVMVIDIDKYKKINDVLGIAVGD-DV 591 D LTG+ NR+ F + L + + + ++++ID+D +K ND G GD + Sbjct: 30 VNSDGLTGLSNRRHFDEYLEMEWR-RSLREQSQLSLLMIDVDYFKSYNDTFGHVAGDEAL 88 Query: 592 LVSLTRRIGELLKFPDILARLSGNRFGI----ILISENNSLKIADFAIAMRKSIAMPINL 647 + D+ AR G F + L I+ Sbjct: 89 RQVAGAIREGCSRSSDLAARYGGEEFAMVLPGTSPGGARLLAEKVRRTVESLQISHDQPR 148 Query: 648 LEREITVTASIGFASWTSSKITSSEMLKNAELAMYHAKHRGGNHVESF 695 +TV+ + T +++ A+ A+Y AK+ G N V Sbjct: 149 PGSHLTVSIGVSTLVPGGGGQTFRVLIEMADQALYQAKNNGRNQVGLM 196 >3eeh_A Putative light and redox sensing histidine kinase; structural genomics, PSI, MCSG, protein structure initiative; HET: PG5; 1.95A {Haloarcula marismortui} Length = 125 Score = 52.8 bits (125), Expect = 4e-07 Identities = 28/117 (23%), Positives = 46/117 (39%), Gaps = 3/117 (2%) Query: 405 ERQSLAVLGSGDIVWDWDIVRDRVTTT-PDIATILGLASGSMHGPIRNWLPYIHINDRDN 463 R + DI+W++ V I G + + ++L IH DR+ Sbjct: 11 RRVRELTEATNDILWEFTADLSEVLVINSAYEDIWGRSVAKLRENPHDFLNGIHPEDREL 70 Query: 464 FRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDIT 520 + + S E RV A + W+ I+ P++N G+ +R G A DIT Sbjct: 71 MKDTMQSL--MDGESADVECRVNATEEYQRWVWIQGEPITNDAGETVRVAGFARDIT 125 >3icy_A Sensor protein; sensory box histidine kinase/response regulator domain, kinase, chlorobium tepidum TLS, PSI-2; 2.68A {Chlorobaculum tepidum} Length = 118 Score = 51.9 bits (123), Expect = 6e-07 Identities = 21/119 (17%), Positives = 36/119 (30%), Gaps = 1/119 (0%) Query: 402 SDGERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDR 461 S+ E V ++ D+ A + L S N L IH +DR Sbjct: 1 SNAEELQALVDNIPAAIYHLDVSGQATIRFRPPAFLKTLVSEHAGTTRLNTLSMIHHDDR 60 Query: 462 DNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDIT 520 + V + + HW+ +R + +G GI ++T Sbjct: 61 HMLSNAYSKLREAKHSLTLVYRIVTP-EGKLHWIEDHMRSSFSDDGLFSGIDGILCEVT 118 >3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2, protein structure initiative, northeast structural genomics consortium; 2.00A {Colwellia psychrerythraea} Length = 124 Score = 46.1 bits (109), Expect = 3e-05 Identities = 22/121 (18%), Positives = 42/121 (34%), Gaps = 6/121 (4%) Query: 406 RQSLAVL-GSGDIVWDWDIVRDRVTTT-PDIATILGLASGSMHGPIRNWLPYIHINDRDN 463 +Q D + D+ + + T+ G + G + +H+ Sbjct: 7 KQRAKAFDYVFDAIVVTDL-QGFIIDWNKGSETLYGYSKEQAIG---QPVNMLHVPGDTE 62 Query: 464 FRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQK 523 T +G+ E R+ D W+ P+ N ++ +GI DIT++K Sbjct: 63 HITSEVISAVENQGKWTGEIRMLHKDGHIGWIESMCVPIYGENYQMVGALGINRDITKRK 122 Query: 524 K 524 K Sbjct: 123 K 123 >3f1p_B ARYL hydrocarbon receptor nuclear translocator; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_B* 3f1n_B 3h7w_B* 3h82_B* 1x0o_A 2hv1_A 2b02_A* 2k7s_A 2a24_B Length = 121 Score = 45.9 bits (108), Expect = 5e-05 Identities = 15/94 (15%), Positives = 31/94 (32%), Gaps = 3/94 (3%) Query: 432 PDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQ 491 +G + +N + + H D+ R V + L FR R+ + + Sbjct: 29 HRCVATVGYQPQELL--GKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQE 86 Query: 492 FHWMIIRIRPMSNS-NGDILRYIGIANDITEQKK 524 + WM N + +I I ++ + Sbjct: 87 WLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQ 120 >3gdi_A Period circadian protein homolog 2; tandem PAS domains, biological rhythms, cytoplasm, nucleus, phosphoprotein, transcription; 2.40A {Mus musculus} Length = 309 Score = 45.1 bits (105), Expect = 8e-05 Identities = 17/202 (8%), Positives = 46/202 (22%), Gaps = 1/202 (0%) Query: 355 WMAITKRLDNDIIQPALVGGLVLIVILIGFTVIQHVLATGYFSQGIFSDGERQSLAVLGS 414 + + L+ Q + + Sbjct: 103 SFFCRVSVGKHHENEIRYQPFRMTPYLVKVQEQQGAESQLCCLLLAERVHSGYEAPRIPP 162 Query: 415 GDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGY 474 ++ + + D + L L +H +DR I + Sbjct: 163 EKRIFTTTHTPNCLFQAVDERAVPLLGYLPQDLIETPVLVQLHPSDRPLMLAIHKKILQA 222 Query: 475 RRG-RLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKSLEGILCNA 533 R R + ++ + N + +I + + + + Sbjct: 223 GGQPFDYSPIRFRTRNGEYITLDTSWSSFINPWSRKISFIIGRHKVRVGPLNEDVFAAPP 282 Query: 534 FQDNLTGIPNRQSFLDRLTTIL 555 + T P+ Q +++ +L Sbjct: 283 CPEEKTPHPSVQELTEQIHRLL 304 >3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; 2.60A {Desulfitobacterium hafniense} Length = 126 Score = 42.0 bits (98), Expect = 7e-04 Identities = 8/112 (7%), Positives = 26/112 (23%), Gaps = 6/112 (5%) Query: 414 SGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVG 473 D++ + + + LG + + Sbjct: 8 IEDMILIINREGRLLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKIL----AEL 63 Query: 474 YRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKS 525 + + + + RI N I D+++++++ Sbjct: 64 FAGKKESLPLSLEKKEGTSIPAKARIWQGKWHNEPC--LFAIIKDLSKEERA 113 >1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin, electron transport; HET: FMN; 1.90A {Chlamydomonas reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A* Length = 109 Score = 42.0 bits (98), Expect = 7e-04 Identities = 13/89 (14%), Positives = 30/89 (33%), Gaps = 3/89 (3%) Query: 432 PDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQ 491 + G + G +L D + I D+ + D Sbjct: 23 EGFYAMTGYGPDEVLGHNCRFLQGEG-TDPKEVQKIRDAI--KKGEACSVRLLNYRKDGT 79 Query: 492 FHWMIIRIRPMSNSNGDILRYIGIANDIT 520 W ++ + P+ +G + +++G+ D+T Sbjct: 80 PFWNLLTVTPIKTPDGRVSKFVGVQVDVT 108 >1wa9_A Period circadian protein; PAS domain, circadian rhythm, clock protein, phosphorylation, polymorphism; 3.15A {Drosophila melanogaster} PDB: 3gec_A Length = 368 Score = 41.2 bits (95), Expect = 0.001 Identities = 14/149 (9%), Positives = 34/149 (22%), Gaps = 3/149 (2%) Query: 405 ERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHIND--RD 462 + S + LG + G + ++ Sbjct: 148 VPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKE 207 Query: 463 NFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQ 522 + T++ +R + + + N L ++ + + + Sbjct: 208 TYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQG 267 Query: 523 KKSLEGILCNAFQDNLTGIPNRQSFLDRL 551 K + A L QS R+ Sbjct: 268 PK-QCNVFEAAPTCKLKISEEAQSRNTRI 295 Score = 30.0 bits (66), Expect = 2.4 Identities = 18/135 (13%), Positives = 44/135 (32%), Gaps = 10/135 (7%) Query: 432 PDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQ----YEFRVRA 487 P I +LG G R+++ ++H+ DR F + + + + R + Sbjct: 25 PSITDVLGYPRDMWLG--RSFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCV 82 Query: 488 ADNQFHWMIIRIRPMSN--SNGDILRYIGIANDITEQKKSLEGILCNAFQDNL--TGIPN 543 ++ + + + + R + E+ + ++ N L P Sbjct: 83 MLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPI 142 Query: 544 RQSFLDRLTTILDLS 558 + S+ + S Sbjct: 143 KSSYKVPDEILSQKS 157 >3cax_A Uncharacterized protein PF0695; structural genomics, unknown function, PSI-2, protein structure initiative; 2.43A {Pyrococcus furiosus dsm 3638} Length = 369 Score = 41.0 bits (95), Expect = 0.001 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 5/75 (6%) Query: 450 RNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDI 509 R IL +F + GR + + ++ I+ P+ N G+ Sbjct: 280 RPVQLCHPPKSVYVVNKILKAF---KEGRKKEATFWLRLREK--YVYIKYVPLFNEKGEY 334 Query: 510 LRYIGIANDITEQKK 524 + + + DI KK Sbjct: 335 IGTLEMTMDIAPYKK 349 >3f1p_A Endothelial PAS domain-containing protein 1; PAS domain, heterodimer, internal cavity, activator, angiogenesis, congenital erythrocytosis; 1.17A {Homo sapiens} PDB: 3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A Length = 117 Score = 40.9 bits (95), Expect = 0.001 Identities = 11/95 (11%), Positives = 31/95 (32%), Gaps = 4/95 (4%) Query: 432 PDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQ 491 I ++G + G + T + + + ++R+ A Sbjct: 26 DRITELIGYHPEELLGRSAYEF---YHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGG 82 Query: 492 FHWMIIRIRPMSNS-NGDILRYIGIANDITEQKKS 525 + W+ + + N N + + ++E +K+ Sbjct: 83 YVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN 117 >2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing, ATP-binding, chromophore, flavoprotein, FMN, kinase, membrane, nucleotide-binding; HET: FMN; 2.00A {Arabidopsis thaliana} PDB: 2z6c_A* Length = 130 Score = 40.3 bits (93), Expect = 0.002 Identities = 15/123 (12%), Positives = 44/123 (35%), Gaps = 4/123 (3%) Query: 406 RQSLAVLGSGDIVWDWDIVRDRVT-TTPDIATILGLASGSMHGPIRNWLPYIHINDRDNF 464 + +L+ L +V D + + T+ G +S + G +L + + Sbjct: 9 KTALSTLQQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEIVGRNCRFLQGPDTDKNEVA 68 Query: 465 RTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKK 524 + D W ++ + P+ + G+ +++IG+ ++++ + Sbjct: 69 KIR---DCVKNGKSYCGRLLNYKKDGTPFWNLLTVTPIKDDQGNTIKFIGMQVEVSKYTE 125 Query: 525 SLE 527 + Sbjct: 126 GVN 128 >2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase, cell adhesion, nucleotide-binding, protein engineering, RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena sativa} PDB: 2wkr_A* 2wkp_A* Length = 332 Score = 40.2 bits (93), Expect = 0.002 Identities = 10/81 (12%), Positives = 26/81 (32%) Query: 475 RRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKSLEGILCNAF 534 + + + + W + ++PM + GD+ +IG+ D TE + Sbjct: 81 NQTEVTVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAAEREGVML 140 Query: 535 QDNLTGIPNRQSFLDRLTTIL 555 + + ++ Sbjct: 141 IKKTAENIDEAAKELIKCVVV 161 >3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG, structural genomics, center for structural genomics; 1.65A {Burkholderia thailandensis} PDB: 3mqo_A Length = 120 Score = 40.0 bits (93), Expect = 0.002 Identities = 9/80 (11%), Positives = 25/80 (31%), Gaps = 1/80 (1%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 R++ +D S V G + ++ A + W + R + + Sbjct: 40 ADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRAL-D 98 Query: 505 SNGDILRYIGIANDITEQKK 524 + + D++ ++ Sbjct: 99 RTAPLAAGVWTFEDLSATRR 118 >3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Length = 258 Score = 40.0 bits (93), Expect = 0.003 Identities = 20/135 (14%), Positives = 42/135 (31%), Gaps = 18/135 (13%) Query: 407 QSLAVLGSGDIVWDWDIVRDR-VTTTPDIATILGLASGSMHGPIRN------WLPYIHIN 459 +SL + +G D+ + T A LGL + + IH Sbjct: 36 RSLTEV-NGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPE 94 Query: 460 DRDNFRTILDSFV---------GYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN-SNGDI 509 D R + F + R + R+ + ++ ++ M N G++ Sbjct: 95 DLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNV 154 Query: 510 LRYIGIANDITEQKK 524 + + +Q+ Sbjct: 155 WLIFCLYSLSADQRP 169 >3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: PGE; 2.49A {Geobacter sulfurreducens} Length = 114 Score = 39.5 bits (91), Expect = 0.003 Identities = 18/116 (15%), Positives = 33/116 (28%), Gaps = 4/116 (3%) Query: 405 ERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATILGLASGSMHGPIRNWLPYIHINDRDNF 464 ER L + + +D + + GL G + G + + + Sbjct: 3 ERLRLFTEHAPAALAMFDREMRYLAVSRRWREDYGLGDGDILGMSHYDIFPEIGEEWKSV 62 Query: 465 RTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDIT 520 + E AD + W+ +RP G + + DIT Sbjct: 63 HRRGLA----GEVIRVEEDCFVRADGRTQWLRWEVRPWYEGEGRVGGVVIFTEDIT 114 >3mxq_A Sensor protein; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.78A {Vibrio cholerae o1 biovar el tor} Length = 152 Score = 39.6 bits (92), Expect = 0.004 Identities = 13/97 (13%), Positives = 29/97 (29%), Gaps = 8/97 (8%) Query: 437 ILGLASGSMHGPIRNWL-----PYIHINDRDNFRTILDSFVGYRRGRLQYEFR---VRAA 488 + +M G L Y+ SF + + F+ + Sbjct: 54 RVIFDGETMQGKNILELFPESADYLKRKIDTALVIESSSFSSWEQKPHLLPFKSSRPVSG 113 Query: 489 DNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKS 525 + + + + + P+ + +G I D+T Q Sbjct: 114 EEEQMYQNLEVIPIHSEDGTIEHVCLCVYDVTIQASQ 150 >2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox sensor, atomic resolution, transferase; HET: FAD; 1.04A {Azotobacter vinelandii} Length = 120 Score = 37.7 bits (86), Expect = 0.012 Identities = 9/77 (11%), Positives = 22/77 (28%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 + + ++ R D + + + P+ N Sbjct: 42 SEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLN 101 Query: 505 SNGDILRYIGIANDITE 521 G+ + Y+G+ D +E Sbjct: 102 EAGETIYYLGMHRDTSE 118 >1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A {Escherichia coli K12} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A* 1s67_L* 1s66_L* Length = 167 Score = 37.6 bits (86), Expect = 0.015 Identities = 10/83 (12%), Positives = 22/83 (26%), Gaps = 2/83 (2%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 + I +P + R + E ++ D W + +S Sbjct: 81 IGNNIDMLIPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSA 140 Query: 505 SNGDILRYIGIANDITEQKKSLE 527 Y+ + D + + E Sbjct: 141 EGKVY--YLALVRDASVEMAQKE 161 >3kx0_X Uncharacterized protein RV1364C/MT1410; PAS domain, sensory domain, mycobacteium tuberculos molecule binding domain; 2.30A {Mycobacterium tuberculosis} Length = 185 Score = 37.0 bits (85), Expect = 0.020 Identities = 8/79 (10%), Positives = 24/79 (30%), Gaps = 4/79 (5%) Query: 450 RNWLPYIHINDRDNFRTILDSFVGYRRGR----LQYEFRVRAADNQFHWMIIRIRPMSNS 505 + + +LD + + + + + + + P + Sbjct: 79 QPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWRLQTDYDGSGVEERYFDFVVTPRRRA 138 Query: 506 NGDILRYIGIANDITEQKK 524 +G I I +D+T + + Sbjct: 139 DGSIEGVQLIVDDVTSRVR 157 >2rh1_A Beta-2-adrenergic receptor/T4-lysozyme chimera; GPCR, 7TM, fusion, lipidic cubic phase, lipidic, mesophase, cholesterol, membrane protein; HET: MAL CAU CLR PLM 12P; 2.40A {Homo sapiens} PDB: 3d4s_A* Length = 500 Score = 36.9 bits (84), Expect = 0.023 Identities = 32/208 (15%), Positives = 67/208 (32%), Gaps = 47/208 (22%) Query: 154 NPGAVVTFIMEISTPNLPQIYLWEPNFYKDTVNSFTLYRGIIIGVASLLAIF---LTIFY 210 PG F++ + + P + + + + + GI++ + L +F L I Sbjct: 10 QPGNGSAFLLAPNRSHAP-----DHDVTQQRDEVWVVGMGIVMSLIVLAIVFGNVLVITA 64 Query: 211 MVNRSSMLIPTFAMAWVVLGYISIDFGFLSKLVNLPSGELLIWRACSEIALSSSLIIFLF 270 + + T + +L AC+++ + +++ F Sbjct: 65 IAKFERLQTVTNYF-----------------ITSL---------ACADLVMGLAVVPFGA 98 Query: 271 MYLHWNRWHAKVGYITFSGIACIAILFCMSFYYPMVTASIARITLASIVLYYTYFIIYHG 330 ++ W TF C F S VTASI + + ++ YF I Sbjct: 99 AHILMKMW-------TFGNFWCE---FWTSIDVLCVTASIETLCVIAV---DRYFAITSP 145 Query: 331 MKGYERAVLLIPAWILIFIWFIGLWMAI 358 K I++ +W + + Sbjct: 146 FKYQSLLTKNKARVIILMVWIVSGLTSF 173 >2qkp_A Uncharacterized protein; structural genomics, unknown function, PSI-2, protein structure initiative; 1.75A {Streptococcus mutans UA159} Length = 151 Score = 36.0 bits (81), Expect = 0.045 Identities = 8/80 (10%), Positives = 21/80 (26%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 P + + + F R G+ ++ ++ + + + Sbjct: 56 KRTPSQVGRNVELCHPPKVLDKVKKVFELLRNGQRDKVNMWFQSERLGKFVYVTYAAVRD 115 Query: 505 SNGDILRYIGIANDITEQKK 524 GD + DI + Sbjct: 116 QAGDFQGVLEYVQDIKPFFE 135 >3k3c_A Protein RV1364C/MT1410; sensor, PAS, signal transduction, fatty-acid binding, sigma regulator, signaling protein; HET: PLM; 1.62A {Mycobacterium tuberculosis} PDB: 3k3d_A Length = 158 Score = 35.6 bits (81), Expect = 0.054 Identities = 7/93 (7%), Positives = 23/93 (24%) Query: 432 PDIATILGLASGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQ 491 L + + + + + + + + Sbjct: 45 AAYRGFSPLLDTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWRLQTDYDGSGVE 104 Query: 492 FHWMIIRIRPMSNSNGDILRYIGIANDITEQKK 524 + + P ++G I I +D+T + + Sbjct: 105 ERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVR 137 >3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV, signaling protein; HET: FAD; 1.65A {Neurospora crassa} PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A* 3hji_A* Length = 149 Score = 35.4 bits (81), Expect = 0.066 Identities = 7/44 (15%), Positives = 16/44 (36%) Query: 475 RRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIAND 518 R +Q E + Q + + P+ + G+ +G + Sbjct: 106 RNAEVQVEVVNFKKNGQRFVNFLTMIPVRDETGEYRYSMGFQCE 149 >2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase, phosphoprotein, nitrogen fixation, PER-ARNT-SIM, metal-binding, PAS, iron; HET: HEM; 1.5A {Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A* 2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A* 1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A* 2owj_A* Length = 119 Score = 35.0 bits (79), Expect = 0.082 Identities = 10/80 (12%), Positives = 26/80 (32%), Gaps = 2/80 (2%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 + + +P + D++ + + + + D M + I M + Sbjct: 34 IGQNVNILMPEPDRSRHDSYISRYRTTSDPHIIGIGRIVTGKRRDGTTFPMHLSIGEMQS 93 Query: 505 SNGDILRYIGIANDITEQKK 524 + G D+TE ++ Sbjct: 94 GGEPY--FTGFVRDLTEHQQ 111 >2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory system, two-component signal transduction, transferase, phosphorylation, SCOD; 1.7A {Bacillus subtilis} Length = 111 Score = 35.1 bits (79), Expect = 0.083 Identities = 8/80 (10%), Positives = 27/80 (33%) Query: 444 SMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMS 503 + ++ + + +++S+ + FR D+ W+ + ++ Sbjct: 32 LGYLQGEMIGSFLKTFLHEEDQFLVESYFYNEHHLMPCTFRFIKKDHTIVWVEAAVEIVT 91 Query: 504 NSNGDILRYIGIANDITEQK 523 R I + + E++ Sbjct: 92 TRAERTEREIILKMKVLEEE 111 >1oj5_A Steroid receptor coactivator 1A; transcriptional coactivator, complex, LXXLL motif, transcriptional regulation; 2.2A {Mus musculus} SCOP: d.110.3.8 Length = 132 Score = 34.6 bits (79), Expect = 0.095 Identities = 9/76 (11%), Positives = 15/76 (19%), Gaps = 2/76 (2%) Query: 450 RNWLPYIHINDRDNFRTILDSFVGYRRGR-LQYEFRVRAADNQFHWMIIRIRPMSNS-NG 507 + + R+ RG +R D R + Sbjct: 41 KCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTRCKLCYPQSPD 100 Query: 508 DILRYIGIANDITEQK 523 +GI E Sbjct: 101 MQPFIMGIHIIDREHS 116 >1byw_A Protein (human ERG potassium channel); PAS domain, potassium channel domain; 2.60A {Homo sapiens} SCOP: d.110.3.6 Length = 110 Score = 33.5 bits (75), Expect = 0.21 Identities = 8/71 (11%), Positives = 22/71 (30%) Query: 452 WLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDILR 511 ++H + + E D ++ + P+ N +G ++ Sbjct: 40 TCDFLHGPCTQRRAAAQIAQALLGAEERKVEIAFYRKDGSCFLCLVDVVPVKNEDGAVIM 99 Query: 512 YIGIANDITEQ 522 +I + E+ Sbjct: 100 FILNFEVVMEK 110 >3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase, phosphoprotein, transferase, flavoprotein; HET: FAD; 2.34A {Methylococcus capsulatus} Length = 227 Score = 33.4 bits (74), Expect = 0.23 Identities = 9/74 (12%), Positives = 19/74 (25%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 I + + R + D + +W I P+ Sbjct: 154 QSPSILDSPLADQETLAAMQEALQAGQPWSGRLLNRRRTGPAPHDAEDYWAEISTTPIHT 213 Query: 505 SNGDILRYIGIAND 518 ++ Y+ I +D Sbjct: 214 DGNGLVGYVQIQHD 227 >3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain, HTR-like protein, PSI-2, protein structure initiative; HET: MSE I3A; 1.73A {Haloarcula marismortui atcc 43049} Length = 126 Score = 32.8 bits (73), Expect = 0.33 Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 4/71 (5%) Query: 450 RNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSNSNGDI 509 R+ + + D ++ +T L F R ++E D + + + + D Sbjct: 60 RSIWEFDLMFDAEDVQTQLSGFS--VDERRKFEGLYERRDGSTMSVEVHLLRFNLEGED- 116 Query: 510 LRYIGIANDIT 520 R++ I+ DIT Sbjct: 117 -RFLAISRDIT 126 >1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1 Length = 222 Score = 32.5 bits (73), Expect = 0.42 Identities = 14/129 (10%), Positives = 32/129 (24%), Gaps = 7/129 (5%) Query: 389 HVLATGYFSQGIFSDGERQSLAVLGSGDIVWDWDIVRDRVTTTPDIATI-------LGLA 441 V+ G + + SL L SGD+ T ++ Sbjct: 45 FVVVDGRLRVYLVGEEREISLFYLTSGDMFCMHSGCLVEATERTEVRFADIRTFEQKLQT 104 Query: 442 SGSMHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRP 501 SM + L + ++ + R + +I+ + Sbjct: 105 CPSMAWGLIAILGRALTSCMRTIEDLMFHDIKQRIAGFFIDHANTTGRQTQGGVIVSVDF 164 Query: 502 MSNSNGDIL 510 +++ Sbjct: 165 TVEEIANLI 173 >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 = 32.3 bits (72), Expect = 0.53 Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 3/27 (11%) Query: 544 RQSFLDRLTTILDLSATDDNLRPTVMV 570 +Q+ L +L L L A DD+ P + + Sbjct: 19 KQA-LKKLQASLKLYA-DDS-APALAI 42 Score = 30.0 bits (66), Expect = 2.4 Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 6/25 (24%) Query: 851 LRKIGISLTL--DD----FGTKCSL 869 L+K+ SL L DD K ++ Sbjct: 22 LKKLQASLKLYADDSAPALAIKATM 46 >2hk2_A Diphosphomevalonate decarboxylase; mevalonate diphosphate decarboxylase, lyase; 2.30A {Staphylococcus aureus} PDB: 2hk3_A Length = 331 Score = 32.1 bits (72), Expect = 0.62 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 1/55 (1%) Query: 856 ISLTLDDFGTKCSLLSYLGYIPFDTVKFNGSLMTGSTEKRIAILRSIIPMAKNIE 910 IS+TL+ F T+ +++ + D NG ++G ++I+ I+ I+ Sbjct: 38 ISVTLEKFYTETK-VTFNDQLTQDQFWLNGEKVSGKELEKISKYMDIVRNRAGID 91 >2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding, serine/threonine-protein kinase, light-induced signal transduction, phototropin1; HET: FMN; 1.40A {Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A* 1g28_A* Length = 146 Score = 31.9 bits (71), Expect = 0.68 Identities = 10/48 (20%), Positives = 20/48 (41%) Query: 480 QYEFRVRAADNQFHWMIIRIRPMSNSNGDILRYIGIANDITEQKKSLE 527 + + W + ++PM + GD+ +IG+ D TE + Sbjct: 77 TVQLINYTKSGKKFWNLFHLQPMRDQKGDVQYFIGVQLDGTEHVRDAA 124 >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 = 31.7 bits (71), Expect = 0.77 Identities = 42/165 (25%), Positives = 75/165 (45%), Gaps = 33/165 (20%) Query: 783 ISWRDQANMPPIFILINIASKDLLDNELCEGMQALISKTLYSPSRIKLSFSESVVMGNPE 842 ++++D+ ++LI A K + E+ +G+ +K + + SR FS+ V + Sbjct: 472 VTFKDK------YVLITGAGKGSIGAEVLQGLLQGGAKVVVTTSR----FSKQVT----D 517 Query: 843 RSRLLLGRLRKIGISLTLDDF--GTKCSLLSYLGYIPFDTVKFNGSLMTGSTEKRIAILR 900 + + + G +L + F G+K + + + +I +DT K NG L G L Sbjct: 518 YYQSIYAKYGAKGSTLIVVPFNQGSKQDVEALIEFI-YDTEK-NGGL--GWD------LD 567 Query: 901 SIIPMA----KNIETT-IIAKDIYG-EIDIKELTR-MGCDYIQDS 938 +IIP A + IE I +K + I + + R MGC Q S Sbjct: 568 AIIPFAAIPEQGIELEHIDSKSEFAHRIMLTNILRMMGCVKKQKS 612 >3eml_A Human adenosine A2A receptor/T4 lysozyme chimera; caffeine, GPCR, membrane protein, LCP, mesophase, structural genomics, PSI-2; HET: ZMA STE; 2.60A {Homo sapiens} Length = 488 Score = 31.1 bits (69), Expect = 1.2 Identities = 24/166 (14%), Positives = 49/166 (29%), Gaps = 41/166 (24%) Query: 194 IIIGVASLLAIFLTIFYMVNRSSMLIPTFAMAWVVLGYISIDFGFLSKLVNLPSGELLIW 253 + I V ++L L + + S++ T +V+L Sbjct: 29 LAIAVLAILGNVLVCWAVWLNSNLQNVTNYF-----------------VVSL-------- 63 Query: 254 RACSEIALSSSLIIFLFMYLHWNRWHAKVGYITFSGIACIAILFCMSFYYPMVTASIARI 313 A ++I L I + + + C LF F + +SI Sbjct: 64 -AAADI-AVGVLAIPFAITISTGFC--------AACHGC---LFIACFVLVLTQSSI--F 108 Query: 314 TLASIVLYYTYFIIYHGMKGYERAVLLIPAWILIFIWFIGLWMAIT 359 +L +I + I ++ I+ W + + +T Sbjct: 109 SLLAIAIDRYIAIRIP-LRYNGLVTGTRAKGIIAICWVLSFAIGLT 153 >2ei4_A AR 2, archaerhodopsin-2; membrane protein, retinal, bacterioruberin, proton pump, transport protein; HET: GLC RET 22B L2P; 2.10A {Halobacterium SP} PDB: 1vgo_A* 2z55_A* 1uaz_A* Length = 253 Score = 30.8 bits (69), Expect = 1.5 Identities = 19/173 (10%), Positives = 44/173 (25%), Gaps = 18/173 (10%) Query: 196 IGVASLLAIFLTIFYMVN-------RSSMLIPTFAMAWVVLGYISIDFGFLSKLVNLPSG 248 IG +L R I Y+++ FG V L SG Sbjct: 19 IGTLLMLIGTFYFIARGWGVTDKEAREYYAITILVPGIASAAYLAMFFGIGVTEVELASG 78 Query: 249 EL--LIWRACSEIALSSSLIIFLFMYLHWNRWHAKVGYITFSGIACIAILFCMSFYYPMV 306 + + + ++ ++ L++ L I + + L Sbjct: 79 TVLDIYYARYADWLFTTPLLLLDLALLAKVDRVTIGTLIGVDALMIVTGLIG--ALSKTP 136 Query: 307 TASIARITLASIVLYYTYFIIYHGMKGYERAV-------LLIPAWILIFIWFI 352 A ++I + + + ++ ++ +W Sbjct: 137 LARYTWWLFSTIAFLFVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTA 189 >1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor, histidine kinase, PAS, high-resolution, two- component system; HET: HEM; 1.40A {Rhizobium meliloti} SCOP: d.110.3.2 PDB: 1ew0_A* Length = 130 Score = 30.4 bits (67), Expect = 1.8 Identities = 10/76 (13%), Positives = 25/76 (32%), Gaps = 2/76 (2%) Query: 445 MHGPIRNWLPYIHINDRDNFRTILDSFVGYRRGRLQYEFRVRAADNQFHWMIIRIRPMSN 504 + +R +P + ++ D + + R + + D M + + M + Sbjct: 57 IGQNLRILMPEPYRHEHDGYLQRYMATGEKRIIGIDRVVSGQRKDGSTFPMKLAVGEMRS 116 Query: 505 SNGDILRYIGIANDIT 520 + G D+T Sbjct: 117 GGERF--FTGFIRDLT 130 >1zxu_A AT5G01750 protein; PFAM PF01167, TULP, structural genomics, protein structure initiative, center for eukaryotic structural genomics, CESG; 1.70A {Arabidopsis thaliana} SCOP: d.23.1.2 PDB: 2q4m_A Length = 217 Score = 30.3 bits (68), Expect = 2.4 Identities = 21/108 (19%), Positives = 33/108 (30%), Gaps = 12/108 (11%) Query: 60 FQVFTAADIDGISRRIEVSASSI-RHRGDWAVFALANTSDSQLERLIVVPHYRLVGSHF- 117 +QVF D V SS+ + + VF N + +R+ GS Sbjct: 102 WQVFRGGSTDQRDLLYTVKRSSMLQLKTKLDVFLGHNKDEK-------RCDFRVKGSWLE 154 Query: 118 --FSPDLGSRRIISVTPSEGFSLDRIPNSDSDVFRITINPGAVVTFIM 163 G I ++ + D F +T+ P FI Sbjct: 155 RSCVVYAGESDAIVAQMHRKHTVQSVFLGK-DNFSVTVYPNVDYAFIA 201 >3gia_A Uncharacterized protein MJ0609; membrane protein, transporter, cell membrane, membrane, transmembrane, transport protein; HET: D10 BCN; 2.32A {Methanocaldococcus jannaschii} PDB: 3gi9_C* 3gi8_C Length = 444 Score = 30.0 bits (66), Expect = 2.5 Identities = 16/121 (13%), Positives = 39/121 (32%), Gaps = 13/121 (10%) Query: 209 FYMVNRSSMLIPTFAMAWVVLGYISIDFGFLSKLVNLPSGELLIWRACSEIALSSSLIIF 268 V S A VL + + ++ + + + + L + Sbjct: 313 ERKVWFKSTEGLYITSALGVLFALLFNMEGVASITSA-------------VFMVIYLFVI 359 Query: 269 LFMYLHWNRWHAKVGYITFSGIACIAILFCMSFYYPMVTASIARITLASIVLYYTYFIIY 328 L Y+ + + + FS I + + + +Y + + +A+ + + IIY Sbjct: 360 LSHYILIDEVGGRKEIVIFSFIVVLGVFLLLLYYQWITNRFVFYGIIATFIGVLIFEIIY 419 Query: 329 H 329 Sbjct: 420 R 420 >3g2f_A Bone morphogenetic protein receptor type-2; kinase, structural genomics, structural genomics consortium, SGC, ATP-binding, disease mutation; HET: ADP; 2.35A {Homo sapiens} Length = 336 Score = 29.7 bits (66), Expect = 3.3 Identities = 8/46 (17%), Positives = 22/46 (47%) Query: 620 ILISENNSLKIADFAIAMRKSIAMPINLLEREITVTASIGFASWTS 665 +L+ + + I+DF ++MR + + E + + +G + + Sbjct: 151 VLVKNDGTCVISDFGLSMRLTGNRLVRPGEEDNAAISEVGTIRYMA 196 >2gs8_A Mevalonate pyrophosphate decarboxylase; structural genomics, PSI, protein structure initiative; HET: MSE; 1.50A {Streptococcus pyogenes m1 gas} Length = 317 Score = 29.4 bits (65), Expect = 4.4 Identities = 12/58 (20%), Positives = 19/58 (32%) Query: 856 ISLTLDDFGTKCSLLSYLGYIPFDTVKFNGSLMTGSTEKRIAILRSIIPMAKNIETTI 913 ISLTL++ T S+ D NG L +I+ + + Sbjct: 38 ISLTLENMFTTTSVSFLPDTATSDQFYINGILQNDEEHTKISAIIDQFRQPGQAFVKM 95 >3kvc_A Retinoid isomerohydrolase; 7-bladed beta-propeller, monotopic membrane protein, sensory transduction, vision, isomerase, non-heme iron protein; 1.90A {Bos taurus} PDB: 3fsn_A Length = 533 Score = 29.4 bits (65), Expect = 4.6 Identities = 17/131 (12%), Positives = 40/131 (30%), Gaps = 6/131 (4%) Query: 211 MVNRSSMLIPTFAMAWVV-----LGYISID-FGFLSKLVNLPSGELLIWRACSEIALSSS 264 + N + F++A+ + L D +V P + L+ + Sbjct: 189 VYNIGNCFGKNFSIAYNIVKIPPLQADKEDPISKSEIVVQFPCSDRFKPSYVHSFGLTPN 248 Query: 265 LIIFLFMYLHWNRWHAKVGYITFSGIACIAILFCMSFYYPMVTASIARITLASIVLYYTY 324 I+F+ + N + + + + + A R + + Sbjct: 249 YIVFVETPVKINLFKFLSSWSLWGANYMDCFESNETMGVWLHIADKKRKKYINNKYRTSP 308 Query: 325 FIIYHGMKGYE 335 F ++H + YE Sbjct: 309 FNLFHHINTYE 319 >3jui_A Translation initiation factor EIF-2B subunit epsilon; heat repeat, guanine nucleotide exchange factor, disease mutation, leukodystrophy; 2.00A {Homo sapiens} Length = 182 Score = 29.1 bits (65), Expect = 4.9 Identities = 21/127 (16%), Positives = 40/127 (31%), Gaps = 19/127 (14%) Query: 621 LISENNSLKIADFAIAMRKSIAMPINLLE-REITVTASIGFASW-TSSKITSSEMLKNAE 678 L+ E NSLK A I+L E ++ + F S + SS Sbjct: 35 LVLEINSLKYA-----------YNISLKEVMQVLSHVVLEFPLQQMDSPLDSSRYCALLL 83 Query: 679 LAMYHAKHRGGNHVESFRVSSFRSDRVMIKEDLCLAVENSELYLVYHPIIRLM-DEEIVG 737 + K ++ + + +E+ L + ++ EI+ Sbjct: 84 PLL---KAWSP-VFRNY-IKRAADHLEALAAIEDFFLEHEALGISMAKVLMAFYQLEILA 138 Query: 738 LEALIQW 744 E ++ W Sbjct: 139 GETILSW 145 >3m73_A Tellurite resistance protein TEHA homolog; anion channel, alpha helical integral membrane protein, STRU genomics, PSI-2; HET: BOG; 1.15A {Haemophilus influenzae} PDB: 3m75_A* 3m74_A* 3m77_A* 3m71_A* 3m7b_A* 3m7c_A* 3m7e_A* 3m7l_A* 3m78_A* 3m76_A* 3m72_A* Length = 314 Score = 28.5 bits (63), Expect = 6.5 Identities = 20/219 (9%), Positives = 47/219 (21%), Gaps = 22/219 (10%) Query: 194 IIIGVASLLAIFLTIFYMV---------------NRSSMLIPTFAMAWVVLGYISIDFGF 238 ++ VAS + I + Y I + +++G I + Sbjct: 43 VLGIVASAVWILFILMYAYKLRYYFEEVRAEYHSPVRFSFIALIPITTMLVGDILYRWNP 102 Query: 239 LSKLVNLPSGELLIWRACSEIALSSSLIIFLFMYLHWNRWHAKVGYITFSGIACIAILFC 298 E+LIW L S+L + + +A Sbjct: 103 -------LIAEVLIWIGTIGQLLFSTLRVSELWQGGVFEQKSTHPSFYLPAVAANFTSAS 155 Query: 299 MSFYYPMVTASIARITLASIVLYYTYFIIYHGMKGYERAVLLIPAWILIFIWFIGLWMAI 358 I ++ ++ ++ A Sbjct: 156 SLALLGYHDLGYLFFGAGMIAWIIFEPVLLQHLRISSLEPQFRATMGIVLAPAFVCVSAY 215 Query: 359 TKRLDNDIIQPALVGGLVLIVILIGFTVIQHVLATGYFS 397 ++ A + + L + + + Sbjct: 216 LSINHGEVDTLAKILWGYGFLQLFFLLRLFPWIVEKGLN 254 >1dqu_A Isocitrate lyase; beta barrel; 2.80A {Emericella nidulans} SCOP: c.1.12.7 Length = 538 Score = 28.7 bits (64), Expect = 7.2 Identities = 9/27 (33%), Positives = 16/27 (59%), Gaps = 1/27 (3%) Query: 402 SDGERQSLA-VLGSGDIVWDWDIVRDR 427 S+ E +++A + DI +DW+ R R Sbjct: 339 SNLEARAIAKEIAGTDIYFDWEAPRTR 365 >3pbl_A D(3) dopamine receptor, lysozyme chimera; structural genomics, PSI-2, protein structure initiative, AC technologies center for gene to 3D structure; HET: ETQ MAL; 2.89A {Homo sapiens} Length = 481 Score = 28.6 bits (63), Expect = 7.5 Identities = 20/118 (16%), Positives = 42/118 (35%), Gaps = 18/118 (15%) Query: 242 LVNLPSGELLIWRACSEIALSSSLIIFLFMYLHWNRWHAKVGYITFSGIACIAILFCMSF 301 +V+L A +++ L ++L++ +YL G FS I C + Sbjct: 77 VVSL---------AVADL-LVATLVMPWVVYLEVTG-----GVWNFSRICCDVFVTLDVM 121 Query: 302 YYPMVTASIARITL---ASIVLYYTYFIIYHGMKGYERAVLLIPAWILIFIWFIGLWM 356 ++ I++ ++V+ Y A+++ W+L F L Sbjct: 122 MCTASIWNLCAISIDRYTAVVMPVHYQHGTGQSSCRRVALMITAVWVLAFAVSCPLLF 179 >1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding site, hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A* Length = 507 Score = 28.4 bits (63), Expect = 8.4 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 4/52 (7%) Query: 598 RIGELLKFPD----ILARLSGNRFGIILISENNSLKIADFAIAMRKSIAMPI 645 GEL++F + I L N G++L+ + ++ A + +P+ Sbjct: 49 MAGELVEFEEGTIGIALNLESNNVGVVLMGDGLMIQEGSSVKATGRIAQIPV 100 >3og7_A AKAP9-BRAF fusion protein; proto-oncogene, V600E, kinase, transferase; HET: 032; 2.45A {Homo sapiens} PDB: 3c4c_A* 3c4d_A* 3idp_A* 3ii5_A* 3d4q_A* 2fb8_A* 1uwj_A* 1uwh_A* Length = 289 Score = 28.1 bits (63), Expect = 9.5 Identities = 10/21 (47%), Positives = 15/21 (71%) Query: 620 ILISENNSLKIADFAIAMRKS 640 I + E+N++KI DF +A KS Sbjct: 151 IFLHEDNTVKIGDFGLATEKS 171 >3lb7_A RAF proto-oncogene serine/threonine-protein kinas; kinase domain, alternative splicing, ATP-binding, disease MU kinase, metal-binding; 4.00A {Homo sapiens} PDB: 3omv_A* Length = 307 Score = 28.1 bits (63), Expect = 9.9 Identities = 9/21 (42%), Positives = 13/21 (61%) Query: 620 ILISENNSLKIADFAIAMRKS 640 I + E ++KI DF +A KS Sbjct: 163 IFLHEGLTVKIGDFGLATVKS 183 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 0.326 0.141 0.420 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: 8,523,232 Number of extensions: 416948 Number of successful extensions: 1729 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1672 Number of HSP's successfully gapped: 114 Length of query: 963 Length of database: 5,693,230 Length adjustment: 101 Effective length of query: 862 Effective length of database: 3,244,586 Effective search space: 2796833132 Effective search space used: 2796833132 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 61 (27.7 bits)