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= 018258
         (359 letters)

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

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



>pdb|2YFA|A Chain A, X-Ray Structure Of Mcps Ligand Binding Domain In Complex
           With Malate
 pdb|2YFA|B Chain B, X-Ray Structure Of Mcps Ligand Binding Domain In Complex
           With Malate
 pdb|2YFB|A Chain A, X-Ray Structure Of Mcps Ligand Binding Domain In Complex
           With Succinate
 pdb|2YFB|B Chain B, X-Ray Structure Of Mcps Ligand Binding Domain In Complex
           With Succinate
          Length = 258

 Score = 35.0 bits (79), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 26/107 (24%), Positives = 53/107 (49%), Gaps = 5/107 (4%)

Query: 190 ADQYALTEQQYAQKLKQKTLELQIGELKIKQHEEKLVQEQSQMKLYAEQVSQLLATEKNL 249
           AD   L + Q   K +Q+ L+++I +++    E     EQ+ ++    Q+   LA   NL
Sbjct: 136 ADSVRLAQYQLISKARQQLLQVRI-DVRGYIAENSSANEQAALR----QLDAALADTDNL 190

Query: 250 RLQLTADGEKFQQFQDALVKSNEVFETFKQEIEKMAKSIKELKKENA 296
           + QL ++  + QQF++A++   +    F+  +  +  S  E+  + A
Sbjct: 191 KRQLPSEDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGA 237


  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
   0.307    0.122    0.309 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,942,218
Number of Sequences: 62578
Number of extensions: 267358
Number of successful extensions: 1284
Number of sequences better than 100.0: 99
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 83
Number of HSP's that attempted gapping in prelim test: 1214
Number of HSP's gapped (non-prelim): 142
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 52 (24.6 bits)