RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3977
         (99 letters)



>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics,
          NPPSFA, N project on protein structural and functional
          analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19
          Length = 253

 Score = 26.4 bits (59), Expect = 1.4
 Identities = 6/41 (14%), Positives = 16/41 (39%), Gaps = 5/41 (12%)

Query: 61 IRGNADYPPEAVQSFHEKPVPS-----VEKSHHNKPNMIQQ 96
          + G        +++F E  +       +  + + +P  IQ+
Sbjct: 11 VTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQK 51


>3soo_A LINE-1 type transposase domain-containing protein; alpha/beta
          protein, structural genomics, joint center for ST
          genomics, JCSG; 2.73A {Homo sapiens}
          Length = 88

 Score = 24.3 bits (52), Expect = 5.2
 Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 58 GAPIRGNADYPPEAVQ-SFHEKPVPSVEKSHHNKPNMI 94
          GA +   AD     +  S     V ++ + +  +P  +
Sbjct: 7  GAVLTLAADLSSATLDISXQWSNVFNILRENDFEPXFL 44


>3v39_A D-alanyl-D-alanine carboxypeptidase; peptidoglycan transpeptidase
           fold, endopeptidase, serine MOD hepes buffer molecule,
           hydrolase; HET: PGE; 1.45A {Bdellovibrio bacteriovorus}
          Length = 418

 Score = 24.3 bits (52), Expect = 10.0
 Identities = 9/32 (28%), Positives = 17/32 (53%)

Query: 68  PPEAVQSFHEKPVPSVEKSHHNKPNMIQQPRK 99
            P+A++   + P+P  + S+  K N I   +K
Sbjct: 379 GPKAIKYTEQLPLPFDKYSYLTKANTITTEKK 410


  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
   0.305    0.123    0.355 

Gapped
Lambda     K      H
   0.267   0.0515    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,412,416
Number of extensions: 65581
Number of successful extensions: 45
Number of sequences better than 10.0: 1
Number of HSP's gapped: 45
Number of HSP's successfully gapped: 8
Length of query: 99
Length of database: 6,701,793
Length adjustment: 65
Effective length of query: 34
Effective length of database: 4,886,928
Effective search space: 166155552
Effective search space used: 166155552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 51 (23.9 bits)