BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 012592
         (460 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|3ULQ|A Chain A, Crystal Structure Of The Anti-Activator Rapf Complexed
           With The Response Regulator Coma Dna Binding Domain
          Length = 383

 Score = 29.6 bits (65), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 24/37 (64%), Gaps = 3/37 (8%)

Query: 142 RSLHHIG---DDQNPYEQAISIIGKTLSSFDEDNLIP 175
           R+L++IG   + Q+ YE AI    + ++ F+E N++P
Sbjct: 225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILP 261


>pdb|3A3J|A Chain A, Crystal Structures Of Penicillin Binding Protein 5 From
           Haemophilus Influenzae
          Length = 344

 Score = 28.9 bits (63), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 11/84 (13%)

Query: 276 VKASEYPLSIILVGVGDGPWDMMREFDDNIPARAFDNFQFVNFTEIMSKNVDR-SRKEAE 334
           V  ++    +I+V   D    +      N+P          NF E M+K V +   K   
Sbjct: 86  VSVADLNRGVIVVSGNDATVALAEHISGNVP----------NFVETMNKYVQQFGLKNTN 135

Query: 335 FALAALMEIPSQYKAALEFNILGA 358
           F     ++ P+QY +A +  I+GA
Sbjct: 136 FTTPHGLDDPNQYSSARDMAIIGA 159


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.318    0.134    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,764,261
Number of Sequences: 62578
Number of extensions: 480528
Number of successful extensions: 1036
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1035
Number of HSP's gapped (non-prelim): 3
length of query: 460
length of database: 14,973,337
effective HSP length: 102
effective length of query: 358
effective length of database: 8,590,381
effective search space: 3075356398
effective search space used: 3075356398
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)