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= 042908
         (242 letters)

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

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



>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 = 37.4 bits (85), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 3/61 (4%)

Query: 127 AKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYK---TMGMAVMLDVIINYVRSLQN 183
           AK  Q  D+H+L ER RR  IN+R++ L  L+P             +L   ++Y+R LQ 
Sbjct: 22  AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQR 81

Query: 184 Q 184
           +
Sbjct: 82  E 82


>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
          Length = 82

 Score = 36.2 bits (82), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 32/55 (58%)

Query: 129 RGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQN 183
           RG+   +H+  E+  R  IN+++  L+DLV G    +  + +L   I+Y+R LQ+
Sbjct: 3   RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQH 57


>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
           Transcriptional Activator Complex
          Length = 387

 Score = 28.5 bits (62), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 132 ATDSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQ 182
           A ++HS  E+ RR+K+N  +  L  LVP C    + +    +L + + ++++L+
Sbjct: 13  AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66


>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
           Structure Of Human Clock-bmal1 Basic Helix-loop-helix
           Domains With E-box Dna
          Length = 73

 Score = 27.7 bits (60), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 132 ATDSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQ 182
           A ++HS  E+ RR+K+N  +  L  LVP C    + +    +L + + ++++L+
Sbjct: 9   AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62


>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
 pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
          Length = 87

 Score = 26.9 bits (58), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 136 HSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQIEFLSMKL 192
           H+  ER RR+ I +    L+D VP    +    A +LD    Y++ ++ ++  L   +
Sbjct: 8   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTLQQDI 65


  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    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,377,565
Number of Sequences: 62578
Number of extensions: 289294
Number of successful extensions: 665
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 661
Number of HSP's gapped (non-prelim): 7
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
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: 50 (23.9 bits)