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)