RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13897
         (86 letters)



>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 29.1 bits (64), Expect = 0.16
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 11/90 (12%)

Query: 7   SILSDAHLAAIVNAKEESTSLLRNFY----KSEDI---FL-DMFQFEYDQIQKKPLNVEY 58
           SILS   +  I+ +K+  +  LR F+    K E++   F+ ++ +  Y  +   P+  E 
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL-MSPIKTEQ 102

Query: 59  L--MMDSKMLLPPAGTPLTGNNPLTALTVS 86
               M ++M +         N       VS
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132


>4duh_A DNA gyrase subunit B; structure-based drug design, antibacterial,
           DNA gyrase B, GY isomerase-isomerase inhibitor complex;
           HET: DNA RLI; 1.50A {Escherichia coli} PDB: 1aj6_A*
           1kzn_A* 3g7e_A*
          Length = 220

 Score = 27.9 bits (63), Expect = 0.31
 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 11  DAHLAAIVNAKEESTSLLRNFYKSEDIFLDMFQFEYDQIQK 51
            A LA     ++  T +   F+ S + F ++ +FEY+ + K
Sbjct: 151 QAPLAVTGETEKTGTMV--RFWPSLETFTNVTEFEYEILAK 189


>2o0b_A 3-phosphoshikimate 1-carboxyvinyltransferase; shikimate pathway,
          EPSP synthase, structural genomics; HET: S3P; 1.15A
          {Mycobacterium tuberculosis} PDB: 2o0d_A* 2o0e_A*
          2o0x_A* 2o0z_A* 2o15_A 2bjb_A
          Length = 450

 Score = 25.6 bits (57), Expect = 2.2
 Identities = 7/24 (29%), Positives = 11/24 (45%)

Query: 14 LAAIVNAKEESTSLLRNFYKSEDI 37
          LAA+  A+    S +    +S D 
Sbjct: 32 LAALAAAQGRGASTISGALRSRDT 55


>1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP;
           2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2
          Length = 391

 Score = 24.7 bits (55), Expect = 4.1
 Identities = 7/21 (33%), Positives = 14/21 (66%)

Query: 31  FYKSEDIFLDMFQFEYDQIQK 51
           F+ S + F ++ +FEY+ + K
Sbjct: 168 FWPSLETFTNVTEFEYEILAK 188


>3n0q_A Putative aromatic-ring hydroxylating dioxygenase; rieske [2Fe-2S]
          domain, structural genomics, joint center FO structural
          genomics, JCSG; HET: MSE; 1.80A {Ruegeria SP}
          Length = 409

 Score = 24.3 bits (53), Expect = 5.6
 Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 4/38 (10%)

Query: 12 AHLAAIVNAKEESTSLLRNFYKSEDIFLDMFQFEYDQI 49
          +++  ++       +L + FY   ++    FQ +  +I
Sbjct: 4  SNINTLIANHRAGHALDQAFYTDAEV----FQTDLQEI 37


>3ltl_A Brefeldin A-inhibited guanine nucleotide-exchange 1; all alpha,
           guanine-nucleotide releasing factor, signaling PR; 2.20A
           {Homo sapiens} PDB: 3l8n_A 3swv_A
          Length = 211

 Score = 24.3 bits (53), Expect = 6.4
 Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 4/56 (7%)

Query: 3   LCFHSIL--SDAHLAAIVN--AKEESTSLLRNFYKSEDIFLDMFQFEYDQIQKKPL 54
           L +  I+  +D H   + N   KE+   + R    S+D+  +     Y++I  K +
Sbjct: 147 LAYSIIMLTTDLHSPQVKNKMTKEQYIKMNRGINDSKDLPEEYLSAIYNEIAGKKI 202


>1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES cluster,
           transferase; HET: SAM DTB; 3.40A {Escherichia coli}
           SCOP: c.1.28.1
          Length = 369

 Score = 23.8 bits (52), Expect = 8.4
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 65  MLLPPAGTPLTGNNPLTAL 83
           ML+   GTPL  N+ + A 
Sbjct: 246 MLVKVKGTPLADNDDVDAF 264


  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
   0.319    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0829    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,217,189
Number of extensions: 57333
Number of successful extensions: 75
Number of sequences better than 10.0: 1
Number of HSP's gapped: 75
Number of HSP's successfully gapped: 10
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.2 bits)