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= 042988
         (255 letters)

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

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



>pdb|1E6Y|B Chain B, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
 pdb|1E6Y|E Chain E, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
          Length = 433

 Score = 28.5 bits (62), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 22/44 (50%)

Query: 17  VISLGLFLSPIPTMAAIVRQKSVENFKADPYIATVLNCFVWTFY 60
           +I+   F+S     AA V Q  ++ F  DPY A ++   VW  Y
Sbjct: 117 IIAGADFMSATTVGAAAVTQTIMDMFGTDPYDAPIVKSAVWGSY 160


>pdb|2B2F|A Chain A, Ammonium Transporter Amt-1 From A.Fulgidus (Native)
 pdb|2B2H|A Chain A, Ammonium Transporter Amt-1 From A. Fulgidus (as)
 pdb|2B2I|A Chain A, Ammonium Transporter Amt-1 From A. Fulgidus (Ma)
 pdb|2B2J|A Chain A, Ammonium Transporter Amt-1 From A. Fulgidus (xe)
          Length = 399

 Score = 27.7 bits (60), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 31 AAIVRQKSVENFKADPYIATVLNCFVWTFYG--LPFVHPDSTLVVTIN 76
          A +VR+K+  N  A  +I+ ++   +W FYG  + F +  S ++  +N
Sbjct: 28 AGMVRRKNAVNMIALSFISLIITVLLWIFYGYSVSFGNDISGIIGGLN 75


  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
   0.331    0.144    0.432 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,505,421
Number of Sequences: 62578
Number of extensions: 184362
Number of successful extensions: 363
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 361
Number of HSP's gapped (non-prelim): 3
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 bits)