RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780939|ref|YP_003065352.1| type I signal peptidase [Candidatus Liberibacter asiaticus str. psy62] (248 letters) >1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase, signal peptide processing, protein translocation, membrane bound proteinase; HET: 1PN; 1.95A {Escherichia coli} SCOP: b.87.1.2 PDB: 1t7d_A* 1kn9_A Length = 248 Score = 149 bits (377), Expect = 5e-37 Identities = 84/260 (32%), Positives = 127/260 (48%), Gaps = 55/260 (21%) Query: 30 IRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGD 89 +R+F+++P IPSGSM+PTLL+GD+I+V KF+YG + + I P+RGD Sbjct: 1 VRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKT------LIETGHPKRGD 54 Query: 90 VVVFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRH----------------- 132 +VVF+YP+DP +DY+KR +GLPGD+++ + + P Sbjct: 55 IVVFKYPEDPKLDYIKRAVGLPGDKVTYDPVSKELTIQPGCSSGQACENALPVTYSNVEP 114 Query: 133 ---------------MEGYFSYHYKEDWSSNVPIFQEKLSNG-----VLYNVLSQDFLA- 171 G+F E + + + + K + G +L ++QD + Sbjct: 115 SDFVQTFSRRNGGEATSGFFEVPKNETKENGIRLSERKETLGDVTHRILTVPIAQDQVGM 174 Query: 172 ----PSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVLFSIGGDT 227 P ++ ++VP G YFMMGDNRD S DSR+ GFVPE NLVGRA+ + S Sbjct: 175 YYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRY--WGFVPEANLVGRATAIWMSFDKQE 232 Query: 228 PFSKVWLWIPNMRWDRLFKI 247 W +R R+ I Sbjct: 233 -----GEWPTGLRLSRIGGI 247 >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 = 36.8 bits (85), Expect = 0.005 Identities = 43/252 (17%), Positives = 71/252 (28%), Gaps = 135/252 (53%) Query: 11 IFGSDTLKS-------ILQALFFAILI---------RTFLFQPSVI----------PSGS 44 I +D+ +S + LFF I T L PS++ PS Sbjct: 283 IAETDSWESFFVSVRKAITVLFF---IGVRCYEAYPNTSL-PPSILEDSLENNEGVPS-- 336 Query: 45 MIPTLLVGD--------YI-IVNKFSYGYSKYSFP----FSYNLFNGRIFNNQPRRGDVV 91 P L + + Y+ N P +L NG + ++V Sbjct: 337 --PMLSISNLTQEQVQDYVNKTNS--------HLPAGKQVEISLVNG------AK--NLV 378 Query: 92 V-------------FRYPKDPS------IDYVKR--VIG---LPGDRISLEKGIIYINGA 127 V R K PS I + +R LP ++ + Sbjct: 379 VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP---VA----------S 425 Query: 128 PVVRHMEGYFSYHY--------KED-------WSSN---VPIFQEKLSNGVLYNVLSQDF 169 P F H +D +++ +P++ +G D Sbjct: 426 P--------FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTF--DG-------SDL 468 Query: 170 LAPSSNISEFLV 181 S +ISE +V Sbjct: 469 RVLSGSISERIV 480 >3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: FDA; 2.10A {Mycobacterium thermoresistibile} Length = 393 Score = 28.6 bits (64), Expect = 1.2 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%) Query: 171 APSSNISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGR 215 ++ IS F+V K F +G K K S E+ F +P + ++G Sbjct: 189 KGANGISAFMVHKDDEGFTVGPKERKLGIKGSPTTELYFENCRIPGDRIIGE 240 >1fmj_A Retinol dehydratase; sulfotransferase, adenosine 3',5'- diphosphate; HET: A3P RTL; 2.00A {Spodoptera frugiperda} SCOP: c.37.1.5 PDB: 1fml_A* 1x8l_A* 1x8k_A* 1x8j_A* Length = 351 Score = 28.3 bits (62), Expect = 1.6 Identities = 15/91 (16%), Positives = 33/91 (36%), Gaps = 1/91 (1%) Query: 60 FSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLEK 119 G Y Y I+N R DV V Y + + + ++ L + ++ E Sbjct: 36 VKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTT-MTQELVWLIENDLNFEA 94 Query: 120 GIIYINGAPVVRHMEGYFSYHYKEDWSSNVP 150 Y++ + + +E+++ +P Sbjct: 95 AKTYMSLRYIYLDGFMIYDPEKQEEYNDILP 125 >2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A Length = 189 Score = 27.8 bits (61), Expect = 2.6 Identities = 8/74 (10%), Positives = 17/74 (22%), Gaps = 26/74 (35%) Query: 44 SMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDY 103 + G V+K + + SI Sbjct: 114 DGMAIRSEGKIYFVDK-----------------------QASLSDGLWLVDIKGAISI-- 148 Query: 104 VKRVIGLPGDRISL 117 + + LPG ++ + Sbjct: 149 -RELTKLPGRKLHV 161 >2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid metabolism, FAD, polymorphism, flavoprotein, mitochondrion, disease mutation; HET: FAD COS; 1.9A {Homo sapiens} PDB: 1jqi_A* Length = 391 Score = 27.5 bits (60), Expect = 2.9 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 7/55 (12%) Query: 168 DFLAPSSNISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGR 215 D + +IS FLVP +G DK + S + F +P+++++G Sbjct: 174 DRALQNKSISAFLVPMPTPGLTLGKKEDKLGIRGSSTANLIFEDCRIPKDSILGE 228 >2wnv_A C1Q chain A, complement C1Q subcomponent subunit A; immune system, secreted, collagen, recognition, disulfide bond, innate immunity; HET: NAG; 1.25A {Homo sapiens} PDB: 2jg8_A 2wnu_A* 2jg9_A* 1pk6_A Length = 134 Score = 26.6 bits (58), Expect = 5.1 Identities = 11/37 (29%), Positives = 17/37 (45%) Query: 42 SGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNG 78 SG M+ L GD + V K Y + ++F+G Sbjct: 91 SGGMVLQLQQGDQVWVEKDPKKGHIYQGSEADSVFSG 127 >2uxw_A VERY-long-chain specific acyl-COA dehydrogenase; alternative splicing, fatty acid metabolism, transit peptide, disease mutation, lipid metabolism; HET: FAD TH3; 1.45A {Homo sapiens} PDB: 3b96_A* Length = 607 Score = 26.8 bits (58), Expect = 5.3 Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 7/48 (14%) Query: 176 ISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVGRA 216 I+ F+V +G G K K S EV F VP EN++G Sbjct: 231 ITAFVVERGFGGITHGPPEKKMGIKASNTAEVFFDGVRVPSENVLGEV 278 >1ges_A Glutathione reductase; oxidoreductase(flavoenzyme); HET: FAD; 1.74A {Escherichia coli} SCOP: c.3.1.5 c.3.1.5 d.87.1.1 PDB: 1geu_A* 1ger_A* 1get_A* Length = 450 Score = 26.4 bits (57), Expect = 6.3 Identities = 15/114 (13%), Positives = 35/114 (30%), Gaps = 9/114 (7%) Query: 40 IPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDP 99 +P M + + I + YG+ F++ R Sbjct: 48 VPKKVMWHAAQIREAIHMYGPDYGFDTTINKFNWETLIASRTAYIDRIHTSYENVL-GKN 106 Query: 100 SIDYVK--------RVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDW 145 ++D +K + + + G+ I+ + +I G P + G + + Sbjct: 107 NVDVIKGFARFVDAKTLEVNGETITADHILIATGGRPSHPDIPGVEYGIDSDGF 160 >3muj_A Transcription factor COE3; immunoglobulin like fold, helix-loop-helix, structural genom consortium, SGC, DNA binding protein; 1.92A {Homo sapiens} PDB: 3mqi_A Length = 138 Score = 26.2 bits (57), Expect = 7.1 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 11/65 (16%) Query: 76 FNGRIFNNQPRRGDVVVFRY--PKDPSIDYV-----KRVIGLPGDRISLEKGIIYINGAP 128 + + F +G F Y +P+IDY K + PGD L K ++ A Sbjct: 73 YKSKQFC----KGAPGRFVYTALNEPTIDYGFQRLQKVIPRHPGDPERLPKEVLLKRAAD 128 Query: 129 VVRHM 133 +V + Sbjct: 129 LVEAL 133 >1q6z_A BFD, BFDC, benzoylformate decarboxylase; lyase, carbon-carbon, mandelate catabolism, thiamin thiazolone diphosphate, inhibitor; HET: TZD; 1.00A {Pseudomonas putida} SCOP: c.31.1.3 c.36.1.5 c.36.1.9 PDB: 1po7_A* 1pi3_A* 3fsj_X* 1mcz_A* 1bfd_A* 2fwn_A* 3fzn_A* 2fn3_A* 2v3w_A* 1yno_A* 3f6b_X* 3f6e_X* Length = 528 Score = 26.0 bits (56), Expect = 7.5 Identities = 6/34 (17%), Positives = 9/34 (26%), Gaps = 9/34 (26%) Query: 104 VKRVIGLPGDRI-----SLEKGIIYINGAPVVRH 132 + V G PG + YI + Sbjct: 17 IDTVFGNPGSNALPFLKDFPEDFRYI----LALQ 46 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 0.325 0.143 0.454 Gapped Lambda K H 0.267 0.0642 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,367,958 Number of extensions: 112273 Number of successful extensions: 375 Number of sequences better than 10.0: 1 Number of HSP's gapped: 371 Number of HSP's successfully gapped: 24 Length of query: 248 Length of database: 5,693,230 Length adjustment: 90 Effective length of query: 158 Effective length of database: 3,511,270 Effective search space: 554780660 Effective search space used: 554780660 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 (21.6 bits) S2: 55 (25.1 bits)