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= 035414
         (57 letters)

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

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



>pdb|3COL|A Chain A, Crystal Structure Of Putative Transcription Regulator
          From Lactobacillus Plantarum
 pdb|3COL|B Chain B, Crystal Structure Of Putative Transcription Regulator
          From Lactobacillus Plantarum
          Length = 196

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 20/31 (64%)

Query: 26 IGVVLPVGYMMFRNKRVPSTSSYSKQTNKVL 56
          +G+     Y+ F+NK+    S Y+++TN++L
Sbjct: 40 VGIAQSNVYLYFKNKQALIDSVYARETNRIL 70


>pdb|2BG9|C Chain C, Refined Structure Of The Nicotinic Acetylcholine Receptor
           At 4a Resolution
          Length = 369

 Score = 25.8 bits (55), Expect = 6.8,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 24/41 (58%)

Query: 16  RYLMGAVIMMIGVVLPVGYMMFRNKRVPSTSSYSKQTNKVL 56
           +YLM  + ++ GVV+  G ++  + R PST S    TN ++
Sbjct: 275 KYLMFIMSLVTGVVVNCGIVLNFHFRTPSTHSGIDSTNYIV 315


  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
   0.325    0.139    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,438,495
Number of Sequences: 62578
Number of extensions: 36183
Number of successful extensions: 101
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 98
Number of HSP's gapped (non-prelim): 3
length of query: 57
length of database: 14,973,337
effective HSP length: 29
effective length of query: 28
effective length of database: 13,158,575
effective search space: 368440100
effective search space used: 368440100
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)