RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

Searching..................................................done

Query= psy16739
         (129 letters)



>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
            acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
            synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 30.4 bits (68), Expect = 0.18
 Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 4/42 (9%)

Query: 57   YVISGLLDAID--GHAARYFN-QSTKFGAMLDQLT-DRVGTM 94
            YV +G L A+D   +   +   Q      +   L+ + V   
Sbjct: 1853 YVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGH 1894



 Score = 28.5 bits (63), Expect = 0.70
 Identities = 6/11 (54%), Positives = 8/11 (72%)

Query: 12   YVISGLLDAID 22
            YV +G L A+D
Sbjct: 1853 YVAAGDLRALD 1863



 Score = 25.4 bits (55), Expect = 8.0
 Identities = 24/124 (19%), Positives = 43/124 (34%), Gaps = 37/124 (29%)

Query: 21  IDGHAARYFNQSYGRIVLALISFYFMPTHYAIACWCYV-------ISGLLDAIDGHAARY 73
           +D ++ R    S+G +   L+    +PT    A +             L +  +G AA  
Sbjct: 1   MDAYSTRPLTLSHGSLEHVLL----VPT----ASFFIASQLQEQFNKILPEPTEGFAADD 52

Query: 74  FNQS-----TKFGAMLDQLTD--RVGTM--CLCVTLSTFYPKYQFLFQLSMAIDIACHWI 124
              +      KF   +  L +  +VG     L + L+ F  +  +L       DI     
Sbjct: 53  EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEF--ENCYLEG----NDI----- 101

Query: 125 YLHS 128
             H+
Sbjct: 102 --HA 103


>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A
          {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1
          PDB: 1sc5_A
          Length = 239

 Score = 28.7 bits (65), Expect = 0.50
 Identities = 9/43 (20%), Positives = 13/43 (30%), Gaps = 16/43 (37%)

Query: 61 GLLDAIDGHAARY-FNQSTKF---------GAMLDQL--TDRV 91
          GL+ A+D            +          GA+ D L   D  
Sbjct: 52 GLIKAVD----NLSTENPKRAEAYIKLRIKGAIYDYLRSLDFG 90


>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase,
           ATP binding site, hydro; HET: ADP; 2.15A {Escherichia
           coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A*
           1ii9_A*
          Length = 589

 Score = 28.0 bits (62), Expect = 1.0
 Identities = 13/66 (19%), Positives = 16/66 (24%), Gaps = 2/66 (3%)

Query: 61  GLLDAIDGHAARYFNQSTKFGAMLDQLTDRVGTMCLCVTLSTFYPKY--QFLFQLSMAID 118
               A     A+   +   F   +  L D   T  L VTL    P      L        
Sbjct: 459 DATGAYHREIAKKMGEKGHFTTPMMLLQDPERTKVLLVTLPETTPVLEAANLQADLERAG 518

Query: 119 IACHWI 124
           I     
Sbjct: 519 IHPWGW 524


>2et6_A (3R)-hydroxyacyl-COA dehydrogenase; MFE-2, beta-oxidation,
           peroxisome, SDR, oxido; 2.22A {Candida tropicalis}
          Length = 604

 Score = 25.8 bits (57), Expect = 4.5
 Identities = 9/15 (60%), Positives = 9/15 (60%), Gaps = 1/15 (6%)

Query: 24  HAARYF-NQSYGRIV 37
            A  YF  Q YGRIV
Sbjct: 132 AAWPYFQKQKYGRIV 146



 Score = 25.4 bits (56), Expect = 6.2
 Identities = 6/16 (37%), Positives = 9/16 (56%), Gaps = 1/16 (6%)

Query: 24  HAARYF-NQSYGRIVL 38
            A  YF  + +GRI+ 
Sbjct: 436 LAWPYFVEKQFGRIIN 451


>3s95_A LIMK-1, LIM domain kinase 1; structural genomics, structural
           genomics consortium, SGC, PR kinase,
           transferase-antibiotic complex; HET: STU GOL; 1.65A
           {Homo sapiens}
          Length = 310

 Score = 25.8 bits (57), Expect = 5.2
 Identities = 9/18 (50%), Positives = 11/18 (61%)

Query: 112 QLSMAIDIACHWIYLHSN 129
           ++S A DIA    YLHS 
Sbjct: 110 RVSFAKDIASGMAYLHSM 127


>1gz6_A Estradiol 17 beta-dehydrogenase 4; 17BETA-HSD4, MFE-2,
           beta-oxidation, peroxisome, SDR, steroid biosynthesis,
           oxidoreductase, NADP; HET: NAI; 2.38A {Rattus
           norvegicus} SCOP: c.2.1.2 PDB: 1zbq_A*
          Length = 319

 Score = 25.8 bits (57), Expect = 5.3
 Identities = 6/15 (40%), Positives = 9/15 (60%), Gaps = 1/15 (6%)

Query: 24  HAARYF-NQSYGRIV 37
            A  +   Q+YGRI+
Sbjct: 133 AAWDHMKKQNYGRII 147


>2jlj_A YSCU, YOP proteins translocation protein U; cell membrane,
          transmembrane, yersinia pesits, protein trans type III
          secretion system, membrane; 1.3A {Yersinia pestis} PDB:
          2jlh_A* 2v5g_A 2w0r_A
          Length = 144

 Score = 25.2 bits (56), Expect = 5.9
 Identities = 4/7 (57%), Positives = 4/7 (57%)

Query: 2  PTHYAIA 8
           TH AI 
Sbjct: 54 ATHIAIG 60



 Score = 25.2 bits (56), Expect = 5.9
 Identities = 4/7 (57%), Positives = 4/7 (57%)

Query: 47 PTHYAIA 53
           TH AI 
Sbjct: 54 ATHIAIG 60


>2jli_A YSCU, YOP proteins translocation protein; cell membrane,
          transmembrane, protein transport, type III secretion
          system, plasmid, membrane; 1.13A {Yersinia pestis}
          Length = 123

 Score = 24.8 bits (55), Expect = 6.0
 Identities = 5/7 (71%), Positives = 5/7 (71%)

Query: 2  PTHYAIA 8
          PTH AI 
Sbjct: 45 PTHIAIG 51



 Score = 24.8 bits (55), Expect = 6.0
 Identities = 5/7 (71%), Positives = 5/7 (71%)

Query: 47 PTHYAIA 53
          PTH AI 
Sbjct: 45 PTHIAIG 51


>3b0z_B Flagellar biosynthetic protein FLHB; type III secretion system,
         protein transport, MEMB protein; 2.45A {Salmonella
         enterica subsp}
          Length = 114

 Score = 24.9 bits (55), Expect = 6.4
 Identities = 5/7 (71%), Positives = 7/7 (100%)

Query: 2 PTHYAIA 8
         PTHY++A
Sbjct: 1 PTHYSVA 7



 Score = 24.9 bits (55), Expect = 6.4
 Identities = 5/7 (71%), Positives = 7/7 (100%)

Query: 47 PTHYAIA 53
          PTHY++A
Sbjct: 1  PTHYSVA 7


>3bzs_A ESCU; auto cleavage protein, intein, T3SS, TTSS, asparagine
          cycliz membrane, membrane protein, protein transport;
          1.48A {Escherichia coli} PDB: 3bzr_A 3bzp_A 3bzt_A
          3c03_A
          Length = 137

 Score = 24.8 bits (55), Expect = 6.7
 Identities = 5/7 (71%), Positives = 5/7 (71%)

Query: 2  PTHYAIA 8
          PTH AI 
Sbjct: 55 PTHIAIC 61



 Score = 24.8 bits (55), Expect = 6.7
 Identities = 5/7 (71%), Positives = 5/7 (71%)

Query: 47 PTHYAIA 53
          PTH AI 
Sbjct: 55 PTHIAIC 61


>3c01_E Surface presentation of antigens protein SPAS; auto cleavage
         protein, flagella, ESCU, YSCU, intein, T3SS, M inner
         membrane, transmembrane; 2.60A {Salmonella
         typhimurium} SCOP: d.367.1.1
          Length = 98

 Score = 24.1 bits (53), Expect = 9.8
 Identities = 4/7 (57%), Positives = 4/7 (57%)

Query: 2 PTHYAIA 8
         PTH  I 
Sbjct: 1 PTHITIG 7



 Score = 24.1 bits (53), Expect = 9.8
 Identities = 4/7 (57%), Positives = 4/7 (57%)

Query: 47 PTHYAIA 53
          PTH  I 
Sbjct: 1  PTHITIG 7


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.333    0.142    0.488 

Gapped
Lambda     K      H
   0.267   0.0726    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,120,760
Number of extensions: 116085
Number of successful extensions: 461
Number of sequences better than 10.0: 1
Number of HSP's gapped: 459
Number of HSP's successfully gapped: 43
Length of query: 129
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,384,350
Effective search space: 201680100
Effective search space used: 201680100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 52 (23.8 bits)