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= psy8078
         (105 letters)

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

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



>pdb|2QL2|B Chain B, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
           The Heterodimer E47NEUROD1 BOUND TO DNA
 pdb|2QL2|D Chain D, Crystal Structure Of The Basic-Helix-Loop-Helix Domains Of
           The Heterodimer E47NEUROD1 BOUND TO DNA
          Length = 60

 Score = 30.0 bits (66), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 23/51 (45%)

Query: 55  RERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILRLAICYIAYLNNVLET 105
           RER R+   N+A                 SKIE LRLA  YI  L+ +L +
Sbjct: 9   RERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILRS 59


>pdb|1MDY|A Chain A, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
           Perspectives On Dna Recognition And Implications For
           Transcriptional Activation
          Length = 68

 Score = 29.3 bits (64), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 49  RTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILRLAICYIAYLNNVL 103
           R A   RER R+   N AF E               K+EILR AI YI  L  +L
Sbjct: 13  RKAATMRERRRLSKVNEAF-ETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL 66


>pdb|1MDY|B Chain B, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
           Perspectives On Dna Recognition And Implications For
           Transcriptional Activation
 pdb|1MDY|C Chain C, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
           Perspectives On Dna Recognition And Implications For
           Transcriptional Activation
 pdb|1MDY|D Chain D, Crystal Structure Of Myod Bhlh Domain Bound To Dna:
           Perspectives On Dna Recognition And Implications For
           Transcriptional Activation
          Length = 62

 Score = 29.3 bits (64), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 49  RTAHATRERVRVEAFNSAFGEXXXXXXXXXXXXXXSKIEILRLAICYIAYLNNVL 103
           R A   RER R+   N AF E               K+EILR AI YI  L  +L
Sbjct: 7   RKAATMRERRRLSKVNEAF-ETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL 60


  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
   0.320    0.130    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,862,751
Number of Sequences: 62578
Number of extensions: 36000
Number of successful extensions: 34
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 33
Number of HSP's gapped (non-prelim): 3
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
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)