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= 012303
         (466 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 = 30.0 bits (66), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 3/38 (7%)

Query: 148 RSLHHIG---DDQNPYEQAISIIGKTLSSFDEDNLIPC 182
           R+L++IG   + Q+ YE AI    + ++ F+E N++P 
Sbjct: 225 RTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPS 262


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

 Score = 28.9 bits (63), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 11/84 (13%)

Query: 282 VKASEYPLSIILVGVGDGPWDMMREFDDNIPARAFDNFQFVNFTEIMSKNVDR-SRKEAE 340
           V  ++    +I+V   D    +      N+P          NF E M+K V +   K   
Sbjct: 86  VSVADLNRGVIVVSGNDATVALAEHISGNVP----------NFVETMNKYVQQFGLKNTN 135

Query: 341 FALAALMEIPSQYKAALEFNILGA 364
           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
   0.319    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: 12,639,001
Number of Sequences: 62578
Number of extensions: 474869
Number of successful extensions: 1064
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: 1063
Number of HSP's gapped (non-prelim): 3
length of query: 466
length of database: 14,973,337
effective HSP length: 102
effective length of query: 364
effective length of database: 8,590,381
effective search space: 3126898684
effective search space used: 3126898684
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)