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= psy6232
         (100 letters)

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

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



>pdb|2RDY|A Chain A, Crystal Structure Of A Putative Glycoside Hydrolase Family
           Protein From Bacillus Halodurans
 pdb|2RDY|B Chain B, Crystal Structure Of A Putative Glycoside Hydrolase Family
           Protein From Bacillus Halodurans
          Length = 803

 Score = 26.2 bits (56), Expect = 5.4,   Method: Composition-based stats.
 Identities = 7/17 (41%), Positives = 9/17 (52%)

Query: 41  VWLLWLLSQTWITLHIW 57
           VW  W     W+T H+W
Sbjct: 442 VWAFWPXGGVWLTQHLW 458


>pdb|3H7N|A Chain A, Structure Of Nup120
 pdb|3H7N|B Chain B, Structure Of Nup120
 pdb|3H7N|C Chain C, Structure Of Nup120
 pdb|3H7N|D Chain D, Structure Of Nup120
          Length = 729

 Score = 25.0 bits (53), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 2/27 (7%)

Query: 8   DPCFFQNSIPDYLFFVSP--SIYFLDD 32
           +P  F   +P +LF+VSP  S+ FL+D
Sbjct: 154 NPYDFTVRVPHFLFYVSPQFSVVFLED 180


  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
   0.328    0.141    0.490 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,190,332
Number of Sequences: 62578
Number of extensions: 110338
Number of successful extensions: 212
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: 211
Number of HSP's gapped (non-prelim): 4
length of query: 100
length of database: 14,973,337
effective HSP length: 66
effective length of query: 34
effective length of database: 10,843,189
effective search space: 368668426
effective search space used: 368668426
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)