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= 014115
         (430 letters)

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

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



>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
          Length = 602

 Score = 28.1 bits (61), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 10/100 (10%)

Query: 199 CILYQLICYLHLVKMEDLAQFFQKEAEVVSILHEHLRIRRNLRIISHRYRAFILLSLILV 258
           CILY+++  LH +  E LA+F   +   V   +E      N +I S   + F+     L 
Sbjct: 74  CILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDE--LP 131

Query: 259 TASQFVSLLTITRSSAHNNI--FEAGELALCSISLVTGLF 296
           TA +F            NN+  +E+ + AL    +V   +
Sbjct: 132 TAEEFYDY------GERNNVCPYESMKAALPDADIVIAPY 165


  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
   0.326    0.137    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,997,833
Number of Sequences: 62578
Number of extensions: 470226
Number of successful extensions: 968
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 968
Number of HSP's gapped (non-prelim): 2
length of query: 430
length of database: 14,973,337
effective HSP length: 102
effective length of query: 328
effective length of database: 8,590,381
effective search space: 2817644968
effective search space used: 2817644968
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)