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= psy15318
         (566 letters)

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

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



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

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 44/60 (73%), Positives = 50/60 (83%)

Query: 446 RRQANNVRERIRIRDINEALKELGRMCMAHLKTDKPQTKLGILNMAVEVIMSLEQQVRER 505
           RR ANN RER+R+RDINEA +ELGRMC  HLK+DK QTKL IL  AV+VI+ LEQQVRER
Sbjct: 1   RRMANNARERVRVRDINEAFRELGRMCQLHLKSDKAQTKLLILQQAVQVILGLEQQVRER 60


>pdb|3U5V|A Chain A, Crystal Structure Of Max-E47
          Length = 76

 Score = 92.4 bits (228), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 44/65 (67%), Positives = 51/65 (78%)

Query: 445 ERRQANNVRERIRIRDINEALKELGRMCMAHLKTDKPQTKLGILNMAVEVIMSLEQQVRE 504
           ++R  +N  ER R RDINEA +ELGRMC  HLK+DK QTKL IL  AV+VI+ LEQQVRE
Sbjct: 4   DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRE 63

Query: 505 RNLNP 509
           RNLNP
Sbjct: 64  RNLNP 68


>pdb|4ATI|A Chain A, Mitf:m-Box Complex
 pdb|4ATI|B Chain B, Mitf:m-Box Complex
 pdb|4ATK|A Chain A, Mitf:e-Box Complex
 pdb|4ATK|B Chain B, Mitf:e-Box Complex
          Length = 118

 Score = 32.7 bits (73), Expect = 0.51,   Method: Composition-based stats.
 Identities = 21/67 (31%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 442 REKERRQANNVRERIRIRDINEALKELGRMCMAHLKTDKPQTKLGILNMAVEVIMSLE-Q 500
           +E++++  +N+ ER R  +IN+ +KELG +       D    K  IL  +V+ I  L+ +
Sbjct: 23  KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQRE 82

Query: 501 QVRERNL 507
           Q R ++L
Sbjct: 83  QQRAKDL 89


>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 = 32.7 bits (73), Expect = 0.63,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 445 ERRQANNVRERIRIRDINEALKELGRMCMAHLKTDKPQTKLGILNMAVEVIMSLEQQVRE 504
           +RR+A  +RER R+  +NEA + L R   ++     P  K+ IL  A+  I  L+  +R+
Sbjct: 11  DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLP--KVEILRNAIRYIEGLQALLRD 68


>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 = 32.3 bits (72), Expect = 0.82,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 445 ERRQANNVRERIRIRDINEALKELGRMCMAHLKTDKPQTKLGILNMAVEVIMSLEQQVRE 504
           +RR+A  +RER R+  +NEA + L R   ++     P  K+ IL  A+  I  L+  +R+
Sbjct: 5   DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLP--KVEILRNAIRYIEGLQALLRD 62


>pdb|2IQC|A Chain A, Crystal Structure Of Human Fancf Protein That Functions In
           The Assembly Of A Dna Damage Signaling Complex
          Length = 210

 Score = 30.4 bits (67), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 3/43 (6%)

Query: 327 PGLSHPSPG--GSLLYHQHLGNSHAVSSTVGAIPAGYLAGLAS 367
           PG+ H SPG    +L H  LGNS   ++   A+PAG L  + S
Sbjct: 77  PGI-HKSPGEGSQVLVHWLLGNSEVFAAFCRALPAGLLTLVTS 118


  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
   0.311    0.128    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,530,051
Number of Sequences: 62578
Number of extensions: 638058
Number of successful extensions: 1099
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1094
Number of HSP's gapped (non-prelim): 10
length of query: 566
length of database: 14,973,337
effective HSP length: 104
effective length of query: 462
effective length of database: 8,465,225
effective search space: 3910933950
effective search space used: 3910933950
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)