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= psy2587
         (210 letters)

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

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



>pdb|1MKC|A Chain A, C-Terminal Domain Of Midkine
          Length = 43

 Score = 29.3 bits (64), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 60  CKYDKSSWSECDPNTHMKNRTLTLKKGSPTT-CEATKSISRKC 101
           CKY   +W  CD  T  K R  TLKK      C+ T  +++ C
Sbjct: 1   CKYKFENWGACDGGTGTKVRQGTLKKARYNAQCQETIRVTKPC 43



 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 105 CRYEKGSWSQCSVA-GDMTRTDMLKEANSDANCEKSRTLTKKC 146
           C+Y+  +W  C    G   R   LK+A  +A C+++  +TK C
Sbjct: 1   CKYKFENWGACDGGTGTKVRQGTLKKARYNAQCQETIRVTKPC 43


>pdb|1IO4|D Chain D, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN-
           Cbfbeta Core Domain Heterodimer And CEBPBETA BZIP
           Homodimer Bound To A Dna Fragment From The Csf-1r
           Promoter
 pdb|1ILF|A Chain A, Nmr Structure Of Apo Cbfb
          Length = 141

 Score = 28.9 bits (63), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 32/71 (45%)

Query: 135 NCEKSRTLTKKCKAKNSGRKNKANNDCLTDLGLGLSDGRTCVVYKARHLGLSGSLIDRHT 194
           N E  R L+++C+ K +G +++ + +  T       DGR+ + + A    LS        
Sbjct: 14  NEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVATGTNLSLQFFPASW 73

Query: 195 RSNGRPTRSSE 205
           +   R T S E
Sbjct: 74  QGEQRQTPSRE 84


>pdb|2JHB|A Chain A, Core Binding Factor Beta
          Length = 143

 Score = 28.9 bits (63), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 32/71 (45%)

Query: 135 NCEKSRTLTKKCKAKNSGRKNKANNDCLTDLGLGLSDGRTCVVYKARHLGLSGSLIDRHT 194
           N E  R L+++C+ K +G +++ + +  T       DGR+ + + A    LS        
Sbjct: 16  NEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVATGTNLSLQFFPASW 75

Query: 195 RSNGRPTRSSE 205
           +   R T S E
Sbjct: 76  QGEQRQTPSRE 86


>pdb|1CL3|A Chain A, Molecular Insights Into Pebp2CBF-Smmhc Associated Acute
           Leukemia Revealed From The Three-Dimensional Structure
           Of Pebp2CBF BETA
          Length = 138

 Score = 28.9 bits (63), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 32/71 (45%)

Query: 135 NCEKSRTLTKKCKAKNSGRKNKANNDCLTDLGLGLSDGRTCVVYKARHLGLSGSLIDRHT 194
           N E  R L+++C+ K +G +++ + +  T       DGR+ + + A    LS        
Sbjct: 11  NEEFFRKLSRECEIKYTGFRDRPHEERQTRFQNACRDGRSEIAFVATGTNLSLQFFPASW 70

Query: 195 RSNGRPTRSSE 205
           +   R T S E
Sbjct: 71  QGEQRQTPSRE 81


  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
   0.316    0.130    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,052,090
Number of Sequences: 62578
Number of extensions: 208478
Number of successful extensions: 360
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 355
Number of HSP's gapped (non-prelim): 6
length of query: 210
length of database: 14,973,337
effective HSP length: 95
effective length of query: 115
effective length of database: 9,028,427
effective search space: 1038269105
effective search space used: 1038269105
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)