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= 040193
         (80 letters)

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

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



>pdb|1DEQ|A Chain A, The Crystal Structure Of Modified Bovine Fibrinogen (At
          ~4 Angstrom Resolution)
 pdb|1DEQ|D Chain D, The Crystal Structure Of Modified Bovine Fibrinogen (At
          ~4 Angstrom Resolution)
 pdb|1DEQ|N Chain N, The Crystal Structure Of Modified Bovine Fibrinogen (At
          ~4 Angstrom Resolution)
 pdb|1DEQ|Q Chain Q, The Crystal Structure Of Modified Bovine Fibrinogen (At
          ~4 Angstrom Resolution)
          Length = 390

 Score = 26.6 bits (57), Expect = 3.4,   Method: Composition-based stats.
 Identities = 12/27 (44%), Positives = 14/27 (51%)

Query: 24 RRVDAQVKRCEEKSNPNCSLEDCRAKC 50
          R V+ Q   C+E   P CS ED   KC
Sbjct: 22 RLVERQQSACKETGWPFCSDEDWNTKC 48


>pdb|1TLQ|A Chain A, Crystal Structure Of Protein Ypjq From Bacillus
          Subtilis, Pfam Duf64
          Length = 189

 Score = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 30 VKRCEEKSNPNCSLEDCRAKCINKYINKRGFGECIENG 67
          V++ +EK NPN  L  C  + + K +NKR     +  G
Sbjct: 33 VQKLQEKYNPNLPLSVC-XENVEKVLNKREIIHAVLTG 69


>pdb|1R4P|A Chain A, Shiga Toxin Type 2
 pdb|2GA4|A Chain A, Stx2 With Adenine
          Length = 297

 Score = 25.4 bits (54), Expect = 8.4,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 21/43 (48%)

Query: 1   MAKLSFNNIFVFLLILSAALMAVRRVDAQVKRCEEKSNPNCSL 43
           + ++SFNNI   L  ++  L    +    V+   E+S P C +
Sbjct: 220 VGRISFNNISAILGTVAVILNCHHQGARSVRAVNEESQPECQI 262


  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    0.140    0.469 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,216,841
Number of Sequences: 62578
Number of extensions: 67939
Number of successful extensions: 234
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 230
Number of HSP's gapped (non-prelim): 6
length of query: 80
length of database: 14,973,337
effective HSP length: 49
effective length of query: 31
effective length of database: 11,907,015
effective search space: 369117465
effective search space used: 369117465
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)