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= 003940
         (784 letters)

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

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



>pdb|3IRA|A Chain A, The Crystal Structure Of One Domain Of The Conserved
           Protein From Methanosarcina Mazei Go1
          Length = 173

 Score =  177 bits (449), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 78/154 (50%), Positives = 104/154 (67%)

Query: 103 NRLAAEHSPYLLQHAHNPVDXXXXXXXXXXXXRKRDVPIFLSIGYSTCHWCHVMEVESFE 162
           NRL  E SPYLLQHA+NPVD            RK + P+FLSIGYSTCHWCH+M  ESFE
Sbjct: 4   NRLIKEKSPYLLQHAYNPVDWYPWGEEAFEKARKENKPVFLSIGYSTCHWCHMMAHESFE 63

Query: 163 DEGVAKLLNDWFVSIKVDREERPDVDKVYMTYVQALYGGGGWPLSVFLSPDLKPLMGGTY 222
           DE VA L+N+ FVSIKVDREERPD+D +YMT  Q + G GGWPL++ ++P  KP   GTY
Sbjct: 64  DEEVAGLMNEAFVSIKVDREERPDIDNIYMTVCQIILGRGGWPLNIIMTPGKKPFFAGTY 123

Query: 223 FPPEDKYGRPGFKTILRKVKDAWDKKRDMLAQSG 256
            P   ++ + G   ++ ++K+ W+++ + +  S 
Sbjct: 124 IPKNTRFNQIGMLELVPRIKEIWEQQHEEVLDSA 157


  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    0.135    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,168,658
Number of Sequences: 62578
Number of extensions: 984156
Number of successful extensions: 1890
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1889
Number of HSP's gapped (non-prelim): 4
length of query: 784
length of database: 14,973,337
effective HSP length: 107
effective length of query: 677
effective length of database: 8,277,491
effective search space: 5603861407
effective search space used: 5603861407
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)