RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780140|ref|YP_003064553.1| putative ABC transporter, substrate-binding protein [Candidatus Liberibacter asiaticus str. psy62] (452 letters) >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 = 51.5 bits (123), Expect = 4e-07 Identities = 72/512 (14%), Positives = 127/512 (24%), Gaps = 241/512 (47%) Query: 4 KNYYTSVGL-------FVVSILF-------FSFFSIYWLSRSNQ-------------YD- 35 KNY T+ + S LF +I+ Q Y Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIF----GGQGNTDDYFEELRDLYQT 179 Query: 36 -GPMAEVIIRIPGSV-DGLSTDSSVRFNGIPVGRIVGLFLD----QEYPNHSLAKALIRP 89 + +I+ L + ++ L+ E P++ P Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAE------KVFTQGLNILEWLENPSN-------TP 226 Query: 90 DT----------PL--------Y----------PS------TTATIRTQGL---AGI--- 109 D PL Y P AT +QGL I Sbjct: 227 DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286 Query: 110 ----TYIELSTLRKEKKTIFQIATERNQRAMITA-TPSGINYFISNAENT-----SKKIS 159 ++ RK +F I + T+ PS + + N E S IS Sbjct: 287 DSWESFFVSV--RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS--IS 342 Query: 160 DSSR-HIQKIIENIEK--PLTTTIANIETISTVLANNISHIDKMMHTTQVT-PHSSDSKN 215 + ++ +Q + P + IS L N ++ V+ P S Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVE----IS--LVNGAKNL-------VVSGPPQS---- 385 Query: 216 TFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQ 275 L +N L + S DQ Sbjct: 386 --------------------LYGLNLTLRKAKAPSGL-----DQ---------------- 404 Query: 276 EVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISA------IREITDQRQKII 329 +I S+ K K ++ FL +++ + +D Sbjct: 405 ---SRIPF------SERKLKFSNRFL------------PVASPFHSHLLVPASDL----- 438 Query: 330 STINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRY 389 I +L ++ F +I ++ TF Sbjct: 439 --------INKDLVKNNVSFNAKDIQI----------PVY-------DTF--D------- 464 Query: 390 IPSIGNNLQNFSQSGLNDIQNLVRKL-QETVN 420 G++L+ S + + +V + + V Sbjct: 465 ----GSDLRVLSG---SISERIVDCIIRLPVK 489 Score = 49.2 bits (117), Expect = 2e-06 Identities = 42/303 (13%), Positives = 85/303 (28%), Gaps = 119/303 (39%) Query: 174 KPLTTTIANIET---ISTVLANNISHIDKMMHTTQVTPHSSDSKNTFN----TITDLITS 226 +PLT + ++E + T +Q+ + FN T+ + Sbjct: 7 RPLTLSHGSLEHVLLVPTAS-----FF----IASQL-------QEQFNKILPEPTEGFAA 50 Query: 227 LDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQT-FQEVGQKIDHLL 285 D+ +L V + L +V V + F +V ++ L Sbjct: 51 DDEPTTPAEL--VGKFLG--------YV---------SSLVEPSKVGQFDQV---LNLCL 88 Query: 286 SDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITD----QRQKIIST-INTIENITS 340 ++F + +LE +++ + + + + D + +++I I Sbjct: 89 TEF--------ENCYLEG-----NDIHALAAKLLQENDTTLVKTKELIKNYITAR----I 131 Query: 341 NLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPSI----GNN 396 K + SAL F+ +I GN Sbjct: 132 MAKRPFDKKSN--------SAL------FRAVG---------EGNAQLV--AIFGGQGNT 166 Query: 397 LQNFSQSGLNDIQN----LVRKLQETVNHFDDCLNNFERNPQ----------DIV-W--G 439 F + L D+ LV L + + L+ R +I+ W Sbjct: 167 DDYFEE--LRDLYQTYHVLVGDLIKFS---AETLSELIRTTLDAEKVFTQGLNILEWLEN 221 Query: 440 REK 442 Sbjct: 222 PSN 224 >1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane protein, oxidoreductase; HET: HEM HEO; 3.50A {Escherichia coli} SCOP: f.25.1.1 Length = 204 Score = 33.4 bits (76), Expect = 0.11 Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%) Query: 12 LFVVS--ILFFSFFSIYWLSRSNQYDGPMAEVIIRIP 46 ++++S ILF F+ Y + + GP + I +P Sbjct: 31 IYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELP 67 >2d4x_A Flagellar HOOK-associated protein 3; multi-domain protein, alpha-helical bundle, complex all- beta folds, structural protein; 1.90A {Salmonella typhimurium} Length = 248 Score = 32.4 bits (72), Expect = 0.18 Identities = 19/226 (8%), Positives = 53/226 (23%) Query: 131 RNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVL 190 +A + + +S + IQ E I T+++ + S Sbjct: 15 SQAQAQNSQYALARTFATQKVSLEESVLSQVTTAIQTAQEKIVYAGNGTLSDDDRASLAT 74 Query: 191 ANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSS 250 M + + T + Q+ + Sbjct: 75 DLQGIRDQLMNLANSTDGNGRYIFAGYKTEAAPFDQATGGYHGGEKSVTQQVDSARTMVI 134 Query: 251 NNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSN 310 + I + ++ + + A Sbjct: 135 GHTGAQIFNSITSNAVPEPDGSDSEKNLFVMLDTAIAALKTPVEGNNVEKEKAAAAIDKT 194 Query: 311 MRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356 R +++ + R ++ + ++ + + S +D + MS + Sbjct: 195 NRGLKNSLNNVLTVRAELGTQLSELSTLDSLGSDRALGQKLQMSNL 240 >3bh2_A ADC, AAD, acetoacetate decarboxylase; lyase, plasmid, schiff base; 2.40A {Clostridium acetobutylicum atcc 824} Length = 244 Score = 32.2 bits (73), Expect = 0.28 Identities = 11/54 (20%), Positives = 15/54 (27%), Gaps = 11/54 (20%) Query: 25 IYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQEYP 78 G E IP V FNG+ + ++LD E Sbjct: 61 EIMAMHDTSGLGCYTESGQAIP-----------VSFNGVKGDYLHMMYLDNEPA 103 >2ch7_A Methyl-accepting chemotaxis protein; receptor, four-helix bundle, signal transduction, methyl-accepting receptor; 2.5A {Thermotoga maritima} SCOP: h.4.5.1 PDB: 2ch7_B Length = 309 Score = 31.3 bits (69), Expect = 0.40 Identities = 36/281 (12%), Positives = 83/281 (29%), Gaps = 16/281 (5%) Query: 149 SNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTP 208 +N S +I S +Q+ E+ +++ NI + A+ ++ Sbjct: 37 KEMDNISTRIESISASVQETTAGSEE-ISSATKNIADSAQQAASFADQSTQLAKEAGDAL 95 Query: 209 HSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVR 268 + + +++ +E I + + Sbjct: 96 KKVIEVTRMISNSAKDVERVVESFQKGAEEITSFVETINAIAEQTNLLALNAAIEAARAG 155 Query: 269 ETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKI 328 E + F V +I + + A + A + ++ ++ Sbjct: 156 EAGRGFAVVADEIRK--------LAEESQQASENVRRVVNEIRSIAEDAGKVSSEITARV 207 Query: 329 ISTINTIENITSNLNDSSQKFAELMSKINNI-SALKENNSLFKDAQRAMHTFRDTSEKIN 387 + LN + + NI +A++E + + AM +E+I Sbjct: 208 EEGTKLADEADEKLNSIVGAVERINEMLQNIAAAIEEQTAAVDEITTAMTENAKNAEEIT 267 Query: 388 RYIPSIGNNLQNFSQS------GLNDIQNLVRKLQETVNHF 422 + + LQ S S + I+ V+ L+E V + Sbjct: 268 NSVKEVNARLQEISASTEEVTSRVQTIRENVQMLKEIVARY 308 >2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomography, contractIle protein/transport protein complex; 24.00A {Gallus gallus} Length = 1080 Score = 31.0 bits (69), Expect = 0.55 Identities = 41/293 (13%), Positives = 89/293 (30%), Gaps = 31/293 (10%) Query: 162 SRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTIT 221 R + E KP++ A + + + ++ HS+ +++F + Sbjct: 377 HRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVNKALHSTVKQHSFIGVL 436 Query: 222 DLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTF------Q 275 D+ I + + +N E +Q N V +Q + T F Sbjct: 437 DIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKEQIPWTLIDFYDNQPCI 496 Query: 276 EVGQKIDHLLS--DFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIIS--- 330 + + +L D KM + + + ++ N + R + II Sbjct: 497 NLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEKPR--LSNKAFIIKHFA 554 Query: 331 ---TINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKIN 387 + N + ++ +++ L E LF+D ++A+ T Sbjct: 555 DKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPE---LFQDEEKAISPTSATPSGRV 611 Query: 388 ------------RYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHFDDCLNN 428 R + + + N + L+ L T H+ C+ Sbjct: 612 PLSRTPVKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKP 664 >3l39_A Putative PHOU-like phosphate regulatory protein; BT4638, structural genomics, joint center for structural genomics, JCSG; 1.93A {Bacteroides thetaiotaomicron} Length = 227 Score = 31.1 bits (70), Expect = 0.58 Identities = 26/177 (14%), Positives = 59/177 (33%), Gaps = 9/177 (5%) Query: 145 NYFISNAENTSKKISDSSRHIQKIIENIEKPLTT---TIANIETISTVLANNISHIDKMM 201 + + + K+I D R ++ I L+T T + E I + S +D ++ Sbjct: 52 HDLPTERADYYKQIKDMEREGDRLTHLIFDELSTTFITPFDREDIHDL----ASCMDDVI 107 Query: 202 HTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVI 261 + N I++ L ++I + + ++ ++ N D Sbjct: 108 DGINSSAKRIVIYN-PRPISESGKELSRLIHEEA-INIGKAMDELETFRKNPKPLRDYCT 165 Query: 262 NTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAI 318 + ++ K+ D +K KE LE D+ ++ + + Sbjct: 166 QLHDIENQADDVYELFITKLFEEEKDCIELIKIKEIMHELEKTTDAAEHVGKILKNL 222 >2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer, structural genomics; 2.80A {Thermus thermophilus HB8} Length = 997 Score = 30.5 bits (68), Expect = 0.71 Identities = 12/46 (26%), Positives = 22/46 (47%) Query: 319 REITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKE 364 REI ++++ +N +E L D + + EL K ++L E Sbjct: 14 REIARYYKQVVEPVNRLEAEVEKLPDLAAAYRELKEKHEKGASLDE 59 >2x2e_A Dynamin-1; nitration, hydrolase, membrane fission, nucleotide-binding, endocytosis, motor protein; HET: GDP; 2.00A {Homo sapiens} PDB: 2x2f_A* Length = 341 Score = 30.6 bits (68), Expect = 0.74 Identities = 23/214 (10%), Positives = 68/214 (31%), Gaps = 3/214 (1%) Query: 147 FISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQV 206 + T + D I+ I ++ T + + +++++ D + +V Sbjct: 129 LVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKVAKEV 188 Query: 207 TPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHD 266 P + T DL+ ++ + + I V + + + T Sbjct: 189 DPQGQRT-IGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAAL 247 Query: 267 VRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISA-IREITDQR 325 E + F + ++ +I D+ +R+ + + + I + Sbjct: 248 AAER-KFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQLLSIEKEV 306 Query: 326 QKIISTINTIENITSNLNDSSQKFAELMSKINNI 359 ++ + S +++ + + L ++ I Sbjct: 307 EEYKNFRPDKHGTDSRVDEMLRMYHALKEALSII 340 >2wm9_A Dedicator of cytokinesis protein 9; polymorphism, cell membrane, phosphoprotein, nucleotide-binding, alternative splicing; 2.20A {Homo sapiens} PDB: 2wmn_A* 2wmo_A* Length = 428 Score = 30.4 bits (68), Expect = 0.95 Identities = 18/142 (12%), Positives = 39/142 (27%), Gaps = 19/142 (13%) Query: 254 VKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRS 313 V +V + ++ L S M L+ N + Sbjct: 296 VMYQHHTDLNPIEV--AIDEMSKKVAELRQLCSSAEVDMIK--LQLKLQGSVSVQVN--A 349 Query: 314 SISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQ 373 A + NT + + + F + + AL N L K+ Q Sbjct: 350 GPLAYARA------FLDDTNTKRYPDNKVKLLKEVFRQFVEACGQ--ALAVNERLIKEDQ 401 Query: 374 RAMHT-----FRDTSEKINRYI 390 +R+ +++++ + Sbjct: 402 LEYQEEMKANYREMAKELSEIM 423 >3c8w_A Acetoacetate decarboxylase ADC; YP_094708.1, structural genomics, joint center for structural genomics, JCSG; HET: LCK CIT; 1.60A {Legionella pneumophila subsp} SCOP: d.347.1.1 Length = 255 Score = 29.9 bits (67), Expect = 1.1 Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 15/62 (24%) Query: 17 ILFFSFFSIYWLSRSNQYDGPMAEVIIRIPGSVDGLSTDSSVRFNGIPVGRIVGLFLDQE 76 ++ F F + + Y E +P VR+ G G + +FLD Sbjct: 68 VVKFEFIRMPDSTGFGDYT----ESGQVVP-----------VRYKGEEGGFTISMFLDCH 112 Query: 77 YP 78 P Sbjct: 113 AP 114 >1dn1_B Syntaxin 1A, syntaxin binding protein 1; protein-protein complex, multi-subunit; 2.60A {Rattus norvegicus} SCOP: a.47.2.1 PDB: 3c98_B Length = 267 Score = 30.1 bits (67), Expect = 1.2 Identities = 34/269 (12%), Positives = 86/269 (31%), Gaps = 26/269 (9%) Query: 157 KISDSSRHIQKIIENIEKPLTTTIANIETISTVLA---NNISHIDKMMHTTQVTP-HSSD 212 + + ++ + +E I + N+ + + +P Sbjct: 11 AKDSXXXXXVTVTVDRDRFMDEFFEQVEEIRGFIDKIAENVEEVKRKHSAILASPNPDEK 70 Query: 213 SKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQ 272 +K + I +++ L+ + Q +E + + + + ++ T H ++ Sbjct: 71 TKEELEELMSDIKKTANKVRS-KLKSIEQSIEQEEGLNRS--SADLRIRKTQHST--LSR 125 Query: 273 TFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSNMRSSISAIREITDQRQKIISTI 332 F EV + + SD+ + K + +TS + II Sbjct: 126 KFVEVMSEYNATQSDYRERCKGRIQRQLEITGRTTTSEELEDMLESGNPAIFASGIIMDS 185 Query: 333 NTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPS 392 + + S + + +L + I E + +F D + E I+R Sbjct: 186 SISKQALSEIETRHSEIIKLENSIR------ELHDMFMDMAMLVE---SQGEMIDR---- 232 Query: 393 IGNNLQNFSQSGLNDIQNLVRKLQETVNH 421 I N+++ ++ V ++ V + Sbjct: 233 IEYNVEHAVD----YVERAVSDTKKAVKY 257 >1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ... Length = 269 Score = 30.0 bits (67), Expect = 1.2 Identities = 9/90 (10%), Positives = 29/90 (32%), Gaps = 5/90 (5%) Query: 285 LSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQRQKIISTINT-IENIT 339 + S + + ++ + + + + + R I ++ I Sbjct: 137 MRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKR 196 Query: 340 SNLNDSSQKFAELMSKINNISALKENNSLF 369 N S++F +L ++++ + F Sbjct: 197 KNPTSCSRRFYQLTKLLDSVQPIARELHQF 226 >1s94_A S-syntaxin; three helix bundle, structural plasticity, endocytosis/exocytosis complex; 3.34A {Loligo pealei} SCOP: a.47.2.1 Length = 180 Score = 29.9 bits (67), Expect = 1.3 Identities = 16/149 (10%), Positives = 49/149 (32%), Gaps = 8/149 (5%) Query: 285 LSDFSSKMKSKETSAFLE-NIADSTSNMRSSISAIREITDQRQKIISTINTIENITSNLN 343 L+ + + +E + + M + EI KI ++ ++ S++ Sbjct: 11 LAALKAAVSDEEDVEEVAVQVDSGGGFMEEFFEQVEEIRAMIDKISDNVDAVKKKHSDIL 70 Query: 344 DSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQS 403 + Q ++ ++ + + + + + T E+ S + +Q Sbjct: 71 SAPQTDDQMKEELEEL--MTDIKRTANKVRGKLKTIELNIEQEEHSNKSSADLRIRKTQ- 127 Query: 404 GLNDIQNLVRKLQETVNHFDDCLNNFERN 432 + RK E ++ ++ ++ Sbjct: 128 ----YSTISRKFVEVMSDYNTTQIDYRDR 152 >3cmg_A Putative beta-galactosidase; structural genomics, PSI-2, protein structure initiative; 1.90A {Bacteroides fragilis nctc 9343} Length = 667 Score = 29.9 bits (66), Expect = 1.3 Identities = 21/141 (14%), Positives = 48/141 (34%), Gaps = 6/141 (4%) Query: 50 DGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKA------LIRPDTPLYPSTTATIRT 103 DG+++ + V N +G G + + L K L+R + + Sbjct: 73 DGVNSIADVFINRKHIGEHRGGYGAFIFEITDLVKYGEKNSVLVRANNGEQLDIMPLVGD 132 Query: 104 QGLAGITYIELSTLRKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSR 163 G Y ++ L ++ I + ++ S + N S + +D + Sbjct: 133 FNFYGGIYRDVHLLITDETCISPLDYASPGVYLVQEVVSPQEAKVCAKVNLSNRAADGTA 192 Query: 164 HIQKIIENIEKPLTTTIANIE 184 +Q ++ + K + N+ Sbjct: 193 ELQVLVTDGTKVICKESRNVS 213 >3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, polymorphism, receptor, transcription, transcription regulation; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467 Score = 29.5 bits (65), Expect = 1.4 Identities = 38/237 (16%), Positives = 78/237 (32%), Gaps = 12/237 (5%) Query: 153 NTSKKISDSSRHIQKIIENIEKPLTTTIANIETI--STVLANNISHIDKMMHTTQVTPHS 210 N ++ S SS + +E I + ET + + N S D + + Q Sbjct: 221 NENEVESTSSANEDMPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQ 280 Query: 211 SDSKNTFNTITDLITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRET 270 + + + L + I L+ L S + ++ T V Sbjct: 281 LFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 340 Query: 271 TQTFQEVGQKIDHLLSDFSSKMKS----KETSAFLENIADSTSNMRSSISAIREITDQRQ 326 + VG D +L++ SKM+ K L I + +S E+ R+ Sbjct: 341 SAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPD-SKGLSNPAEVEALRE 399 Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTS 383 K+ +++ + +FA+L+ ++ + ++ + DT Sbjct: 400 KVYASLE--AYCKHKYPEQPGRFAKLLLRLPALRSI---GLKCLEHLFFFKLIGDTP 451 >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 = 29.2 bits (64), Expect = 2.1 Identities = 7/17 (41%), Positives = 11/17 (64%), Gaps = 2/17 (11%) Query: 409 QNLVRKLQETVNHF-DD 424 Q L +KLQ ++ + DD Sbjct: 20 QAL-KKLQASLKLYADD 35 >3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 3l0e_A* Length = 283 Score = 29.3 bits (65), Expect = 2.1 Identities = 27/230 (11%), Positives = 77/230 (33%), Gaps = 34/230 (14%) Query: 149 SNAENTSKKISDSSRHIQKIIENI-EKPLTTTIANIETISTVLANNISHIDKMMHTTQVT 207 A + + + S +IE + + V ++ Sbjct: 30 PRASSPPQILPQLSPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPMA---------PDP 80 Query: 208 PHSSDSKNTFNTITDLIT-SLDKMI---KAI----DLQKVNQI-------LENIQVSSNN 252 + F T+L S+ +++ K + L + +QI +E + + ++ Sbjct: 81 HSREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 140 Query: 253 FVKSSDQVINTVHDVRETTQTFQEVGQKIDHL--LSDFSSKMKS----KETSAFLENIAD 306 + I + D + F + G +++ + + +FS M A L I+ Sbjct: 141 RYNPGSESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISI 200 Query: 307 STSNMRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356 +++ R ++ ++ + + ++ ++ + F ++ K+ Sbjct: 201 FSAD-RPNVQDQLQVERLQHTYVEALH--AYVSIHHPHDRLMFPRMLMKL 247 >2zbi_A Flagellin homolog; flagellum, structural protein; 2.00A {Sphingomonas SP} Length = 292 Score = 28.9 bits (63), Expect = 2.5 Identities = 17/231 (7%), Positives = 58/231 (25%), Gaps = 7/231 (3%) Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT 177 R + QR + +G + +I ++ + + + Sbjct: 55 RDALQAEVTQLQSEIQRVAEQTSFNGQKLLDGSFNGVQFQIGANAGETIGVSKIMNAQTA 114 Query: 178 TTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQ 237 + ++ ++ + + + + ++ +AI+ Sbjct: 115 SLGGSLTRTTSTIDATDLTKYDTAMAAGDLTINGVDVGKIDAASTAQERAAQLTEAINRV 174 Query: 238 KVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKET 297 + + V + V + + + Sbjct: 175 SSQTNVGASYDKTTGQVTLTSNAAIAVAGAANDATVAGWANNATTGTATTTTGINSLTVS 234 Query: 298 SAFLENIADSTSNMRSSI-SAIREITDQRQKIISTINTIENITSNLNDSSQ 347 S + + I +A+++I R + + N + +NL ++ Sbjct: 235 SF------TNAQQTITQIDNALKDINTARADLGAVQNRFTSTVANLQSMTE 279 >1fio_A SSO1 protein; four helix bundle, alpha helix, membrane protein; 2.10A {Saccharomyces cerevisiae} SCOP: a.47.2.1 Length = 196 Score = 28.5 bits (63), Expect = 2.7 Identities = 20/167 (11%), Positives = 51/167 (30%), Gaps = 2/167 (1%) Query: 251 NNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTSN 310 ++FV +++ D+ + T +V LL++ + + S + +A +T Sbjct: 2 HDFVGFMNKISQINRDLDKYDHTINQVDSLHKRLLTEVNEEQASHLRHSLDNFVAQATDL 61 Query: 311 MRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFK 370 + I+ + EN Q + + S KE Sbjct: 62 QFKLKNEIKSAQRDGIHDTNKQAQAENSRQRFLKLIQDYRIVDSNYK--EENKEQAKRQY 119 Query: 371 DAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQE 417 + T + I+ + + + + + + ++Q Sbjct: 120 MIIQPEATEDEVEAAISDVGGQQIFSQALLNANRRGEAKTALAEVQA 166 >2ot3_A RAB5 GDP/GTP exchange factor; rabex-5, VPS9 domain, vesicular traffic, protein transport; 2.10A {Homo sapiens} SCOP: a.222.1.1 PDB: 1txu_A Length = 274 Score = 28.8 bits (64), Expect = 2.9 Identities = 10/73 (13%), Positives = 26/73 (35%), Gaps = 3/73 (4%) Query: 363 KENNSLFKDAQRAMHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHF 422 E + + K+ + TF T ++I + L+ I+ Q+ ++ Sbjct: 10 IETDRVSKEFIEFLKTFHKTGQEIYKQTKLF---LEGMHYKRDLSIEEQSECAQDFYHNV 66 Query: 423 DDCLNNFERNPQD 435 + + + P + Sbjct: 67 AERMQTRGKVPPE 79 >2je8_A Beta-mannosidase; glycoside hydrolase, hydrolase; HET: B3P; 1.7A {Bacteroides thetaiotaomicron} SCOP: b.1.4.1 b.1.4.1 b.1.4.1 b.18.1.5 c.1.8.3 PDB: 2vr4_A* 2vl4_A* 2vmf_A* 2vo5_A* 2vot_A* 2vqt_A* 2vjx_A* 2vqu_A* 2wbk_A* Length = 848 Score = 28.5 bits (62), Expect = 3.4 Identities = 24/223 (10%), Positives = 62/223 (27%), Gaps = 12/223 (5%) Query: 50 DGLSTDSSVRFNGIPVGRIVGLFLDQEYPNHSLAKA-----LIRPDTPLYPSTTATIRTQ 104 +GL T + V NG + + +F+ P S+ + I +P+ T+ Sbjct: 89 EGLDTYADVYLNGSLLLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQ----TLPQY 144 Query: 105 GLAGITYIELSTLRKEKKTIFQIATERNQRA--MITATPSGINYFISNAENTSKKISDSS 162 G Y + ++ ++F + I SG+ + Sbjct: 145 ASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGV-WRPVTLRFYDIATISDY 203 Query: 163 RHIQKIIENIEKPLTTTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITD 222 Q + + L+ + + + + + + TT + Sbjct: 204 YVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVTLQPGINHIT 263 Query: 223 LITSLDKMIKAIDLQKVNQILENIQVSSNNFVKSSDQVINTVH 265 L + ++ + L + + + + + Sbjct: 264 LPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHRIG 306 >2oo2_A Hypothetical protein AF_1782; structural genomics, unknown function, PSI-2, protein structure initiative; 1.80A {Archaeoglobus fulgidus dsm 4304} SCOP: a.8.11.1 Length = 86 Score = 28.2 bits (63), Expect = 4.2 Identities = 6/57 (10%), Positives = 16/57 (28%), Gaps = 5/57 (8%) Query: 376 MHTFRDTSEKINRYIPSIGNNLQNFSQSGLNDIQNLVRKLQETVNHF---DDCLNNF 429 M + + +++ I ++ G + +F D + F Sbjct: 1 MSLEEELRRETLKWLERIEERVKEI--EGDEGFMRNIEAYISDSRYFLEKGDLVRAF 55 >3k8w_A Flagellin homolog; flagellum, structural protein, bacterial flagellu; 1.70A {Sphingomonas SP} PDB: 2zbi_A 3k8v_A Length = 326 Score = 27.8 bits (60), Expect = 5.2 Identities = 23/235 (9%), Positives = 67/235 (28%), Gaps = 15/235 (6%) Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLT 177 R + QR + +G + +I ++ + + + Sbjct: 89 RDALQAEVTQLQSEIQRVAEQTSFNGQKLLDGSFNGVQFQIGANAGETIGVSKIMNAQTA 148 Query: 178 TTIANIETISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQ 237 + ++ ++ + + + + ++ +AI Sbjct: 149 SLGGSLTRTTSTIDATDLTKYDTAMAAGDLTINGVDVGKIDAASTAQERAAQLTEAI--- 205 Query: 238 KVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKET 297 N S N S D+ V ++ + T Sbjct: 206 -------NRVSSQTNVGASYDKTTGQVTLTSNAAIAVAGAANDATVAGWANNATTGTATT 258 Query: 298 SAFLENIADST-SNMRSSI----SAIREITDQRQKIISTINTIENITSNLNDSSQ 347 + + ++ S+ +N + +I +A+++I R + + N + +NL ++ Sbjct: 259 TTGINSLTVSSFTNAQQTITQIDNALKDINTARADLGAVQNRFTSTVANLQSMTE 313 >1ucu_A Phase 1 flagellin; flagellar filament, cryo-electron microscopy, helical reconstruction, structural protein; 4.00A {Salmonella typhimurium} SCOP: e.32.1.1 Length = 494 Score = 27.8 bits (60), Expect = 5.4 Identities = 24/233 (10%), Positives = 61/233 (26%), Gaps = 6/233 (2%) Query: 125 FQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEKPLTTTIANIE 184 + T + ++ + + + Sbjct: 226 TGKYYAKVTVTGGTGKDGYYEVSVDKTNGEVTLAGGATSPLTGGLPATATEDVKNVQVAN 285 Query: 185 TISTVLANNISHIDKMMHTTQVTPHSSDSKNTFNTITDLITSLDKMIKAIDLQKVNQILE 244 T ++ + V +D N TI + Q + + Sbjct: 286 ADLTEAKAALTAAGVTGTASVVKMSYTD--NNGKTIDGGLAVKVGDDYYSATQNKDGSIS 343 Query: 245 NIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENI 304 +S +N + T+ G+ ++ + + + E Sbjct: 344 INTTKYTADDGTSKTALNKLGGADGKTEVVSIGGKTYAASKAEGHNFKAQPDLA---EAA 400 Query: 305 ADSTSNMRSSI-SAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKI 356 A +T N I +A+ ++ R + + N + +NL ++ + S+I Sbjct: 401 ATTTENPLQKIDAALAQVDTLRSDLGAVQNRFNSAITNLGNTVNNLTSVRSRI 453 >2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P, hydrolase, tRNA processing; NMR {Pyrococcus furiosus} PDB: 2ki7_B Length = 123 Score = 27.9 bits (62), Expect = 5.4 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 12/57 (21%) Query: 118 RKEKKTIFQIATERNQRAMITATPSGINYFISNAENTSKKISDSSRHIQKIIENIEK 174 EKK +IA ER I+ S AE + ++ ++ +++ Sbjct: 4 YNEKKEKKRIAKER------------IDILFSLAERVFPYSPELAKRYVELALLVQQ 48 >3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, polymorphism, receptor, transcription, transcription regulation; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A Length = 419 Score = 27.6 bits (60), Expect = 5.5 Identities = 18/113 (15%), Positives = 43/113 (38%), Gaps = 3/113 (2%) Query: 250 SNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKSKETSAFLENIADSTS 309 + + S Q T ++ + F + + F++ A + S Sbjct: 278 KDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVI-ILS 336 Query: 310 NMRSSISAIREITDQRQKIISTINTIENITSNLNDSSQKFAELMSKINNISAL 362 R + ++ I D + ++ + + N +SSQ FA+L+ K+ ++ + Sbjct: 337 GDRPGLLNVKPIEDIQDNLLQALE--LQLKLNHPESSQLFAKLLQKMTDLRQI 387 >2j0o_A Invasin IPAD; type III secretion, cell invasion, T3SS, plasmid, virulence; 3.00A {Shigella flexneri} SCOP: a.250.1.1 Length = 318 Score = 27.6 bits (61), Expect = 6.4 Identities = 24/163 (14%), Positives = 54/163 (33%), Gaps = 17/163 (10%) Query: 235 DLQKVNQILENIQVSSNNFVKSSDQVINTVHDVRETTQTFQEVGQKIDHLLSDFSSKMKS 294 L +N L NI+ ++ K Q T + E ++ ++ + Sbjct: 29 SLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRH 88 Query: 295 KET------SAFLENIADSTSNMRSSISAIREITDQRQKIISTINT-----IENITSNLN 343 + ++ + IS RE+ + I+ IN E+ S+ Sbjct: 89 EYPINKDARELLHSAPKEAELDGDQMIS-HRELWAKIANSINDINEQYLKVYEHAVSSYT 147 Query: 344 DSSQKFAELMSKINN--ISALKENNSL---FKDAQRAMHTFRD 381 Q F+ ++S + + NS+ ++A+ ++ Sbjct: 148 QMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKE 190 >2nrj_A HBL B protein; enterotoxin, hemolysis, transmembrane, structural genomics, PSI-2, protein structure initiative; 2.03A {Bacillus cereus} SCOP: h.4.4.2 Length = 346 Score = 27.2 bits (60), Expect = 6.7 Identities = 14/111 (12%), Positives = 46/111 (41%), Gaps = 13/111 (11%) Query: 327 KIISTINTIENITSNLNDSSQKFAELMSKINNISALKENNSLFKDAQRAMHTFRDTSEKI 386 +++ T+N I + ++ + E ++ + + + L + Q+ + E++ Sbjct: 87 QLLDTLNGIVEYDTTFDNYYETMVEAINTGDGETLKEGITDLRGEIQQNQKYAQQLIEEL 146 Query: 387 NRYIPSIGNNLQNFS-------------QSGLNDIQNLVRKLQETVNHFDD 424 + SIG++++ F + ++ Q + ++ +VN++ Sbjct: 147 TKLRDSIGHDVRAFGSNKELLQSILKNQGADVDADQKRLEEVLGSVNYYKQ 197 >1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A Length = 922 Score = 26.9 bits (59), Expect = 9.5 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 15/80 (18%) Query: 292 MKSKETSAFLENIADS--------TSNMRSSISAIREITDQR-----QKIISTINTIENI 338 MK + F DS +M +S + + + R +K+ + T+ + Sbjct: 1 MKETAAAKFERQHMDSPDLGTLVPRGSMADILSKLLRLGEGRMVKRLKKVADYVGTLSDD 60 Query: 339 TSNLNDS--SQKFAELMSKI 356 L D+ K E ++ Sbjct: 61 VEKLTDAELRAKTDEFKRRL 80 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 0.314 0.129 0.350 Gapped Lambda K H 0.267 0.0494 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,445,661 Number of extensions: 153620 Number of successful extensions: 675 Number of sequences better than 10.0: 1 Number of HSP's gapped: 668 Number of HSP's successfully gapped: 73 Length of query: 452 Length of database: 5,693,230 Length adjustment: 96 Effective length of query: 356 Effective length of database: 3,365,806 Effective search space: 1198226936 Effective search space used: 1198226936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 58 (26.7 bits)