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= psy9898
         (82 letters)

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

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



>pdb|3E4B|A Chain A, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|B Chain B, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|C Chain C, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
 pdb|3E4B|D Chain D, Crystal Structure Of Algk From Pseudomonas Fluorescens
           Wcs374r
          Length = 452

 Score = 28.9 bits (63), Expect = 0.69,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 23/48 (47%)

Query: 6   RTQAEVVEFLVHKSGVTIEEKIDALELLGASFANDKENYCLTSAFKYL 53
           R QA +   L  K G T  E  +A  LL  +FAN + N  +  A  YL
Sbjct: 70  RAQARLGRLLAAKPGATEAEHHEAESLLKKAFANGEGNTLIPLAMLYL 117


>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core
 pdb|1W63|N Chain N, Ap1 Clathrin Adaptor Core
 pdb|1W63|O Chain O, Ap1 Clathrin Adaptor Core
 pdb|1W63|P Chain P, Ap1 Clathrin Adaptor Core
 pdb|1W63|R Chain R, Ap1 Clathrin Adaptor Core
 pdb|1W63|V Chain V, Ap1 Clathrin Adaptor Core
          Length = 423

 Score = 26.2 bits (56), Expect = 5.5,   Method: Composition-based stats.
 Identities = 9/22 (40%), Positives = 15/22 (68%)

Query: 38 ANDKENYCLTSAFKYLYKTMQL 59
          A  K+N C++  F +LYK +Q+
Sbjct: 69 ATSKKNACVSLVFSFLYKVVQV 90


  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
   0.322    0.135    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,951,153
Number of Sequences: 62578
Number of extensions: 58549
Number of successful extensions: 127
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 125
Number of HSP's gapped (non-prelim): 2
length of query: 82
length of database: 14,973,337
effective HSP length: 51
effective length of query: 31
effective length of database: 11,781,859
effective search space: 365237629
effective search space used: 365237629
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)