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= 027787
         (219 letters)

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

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



>pdb|4ABM|A Chain A, Crystal Structure Of Chmp4b Hairpin
 pdb|4ABM|B Chain B, Crystal Structure Of Chmp4b Hairpin
 pdb|4ABM|C Chain C, Crystal Structure Of Chmp4b Hairpin
 pdb|4ABM|D Chain D, Crystal Structure Of Chmp4b Hairpin
          Length = 79

 Score = 34.3 bits (77), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 15/23 (65%), Positives = 20/23 (86%)

Query: 54 KNKRAAIQCLKRKRLYEQQIEQL 76
          KNKRAA+Q LKRK+ YE+Q+ Q+
Sbjct: 42 KNKRAALQALKRKKRYEKQLAQI 64


>pdb|3UM3|B Chain B, Crystal Structure Of The Brox Bro1 Domain In Complex With
           The C- Terminal Tail Of Chmp4b
          Length = 104

 Score = 27.3 bits (59), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 118 NIDDVDKTMDEINEQTENMKQIQEALSTPIG 148
           +ID VD+ M +I +Q E  ++I  A+S P+G
Sbjct: 4   DIDKVDELMQDIADQQELAEEISTAISKPVG 34


  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
   0.313    0.126    0.336 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,946,164
Number of Sequences: 62578
Number of extensions: 66477
Number of successful extensions: 141
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 4
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)