RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11264
         (50 letters)



>1t90_A MMSDH, probable methylmalonate-semialdehyde dehydrogenase;
           oxidoreductase, NAD; HET: NAD; 2.50A {Bacillus subtilis}
          Length = 486

 Score = 26.0 bits (58), Expect = 0.49
 Identities = 7/22 (31%), Positives = 12/22 (54%), Gaps = 2/22 (9%)

Query: 16  DRIGDYLYETASRDISRKRTQC 37
             +G+Y+Y+  S   + KR Q 
Sbjct: 229 KPVGEYVYKKGSE--NLKRVQS 248


>4e4g_A Methylmalonate-semialdehyde dehydrogenase; structural genomics,
           protein structure INI nysgrc, PSI-biology; 2.90A
           {Sinorhizobium meliloti}
          Length = 521

 Score = 25.3 bits (56), Expect = 0.73
 Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)

Query: 16  DRIGDYLYETASRDISRKRTQC 37
             I  Y+Y TA+   + KR QC
Sbjct: 250 TPIARYVYGTAAM--NGKRAQC 269


>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 = 24.8 bits (53), Expect = 1.2
 Identities = 5/25 (20%), Positives = 12/25 (48%), Gaps = 6/25 (24%)

Query: 8   ALSSPEKLDRIGDYLYETASRDISR 32
           AL + +      + ++E A + + R
Sbjct: 571 ALMAED------EAIFEEAHKQVQR 589


>1t94_A Polymerase (DNA directed) kappa; replication, DNA repair, Y-family
           DNA polymerase, translesion DNA synthesis, lesion
           bypass; 2.40A {Homo sapiens} SCOP: d.240.1.1 e.8.1.7
           PDB: 2oh2_A* 2w7o_A* 2w7p_A* 3hed_A* 3in5_A*
          Length = 459

 Score = 23.0 bits (49), Expect = 5.9
 Identities = 6/30 (20%), Positives = 15/30 (50%)

Query: 5   TFYALSSPEKLDRIGDYLYETASRDISRKR 34
           TF  ++  E+   +   L    ++D+ ++R
Sbjct: 354 TFSEINKAEEQYSLCQELCSELAQDLQKER 383


  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
   0.316    0.128    0.358 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 689,275
Number of extensions: 24625
Number of successful extensions: 60
Number of sequences better than 10.0: 1
Number of HSP's gapped: 60
Number of HSP's successfully gapped: 4
Length of query: 50
Length of database: 6,701,793
Length adjustment: 23
Effective length of query: 27
Effective length of database: 6,059,610
Effective search space: 163609470
Effective search space used: 163609470
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 (21.7 bits)
S2: 51 (23.4 bits)