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= 020455
         (326 letters)

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

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



>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 = 34.7 bits (78), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 33/54 (61%)

Query: 187 RGQATDSHSLAERVRREKISERMKILQKLVPGCDKVTGKAFMLDEIINYVQFLQ 240
           RG+   +H+  E+  R  I++++  L+ LV G +    K+ +L + I+Y++FLQ
Sbjct: 3   RGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQ 56


>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 = 34.3 bits (77), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 176 PPKDYIHVRARRGQATDSHSLAERVRREKISERMKILQKLVPGC---DKVTGKAFMLDEI 232
           P +      A+  Q  D+H+L ER RR  I++R+K L  L+P     D    K  +L   
Sbjct: 13  PTESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKAS 72

Query: 233 INYVQFLQNQ 242
           ++Y++ LQ +
Sbjct: 73  VDYIRKLQRE 82


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

 Score = 28.5 bits (62), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 179 DYIHVRARRGQATDSHSLAERVRREKISERMKILQKLVPGCDKVTGKAFMLDEIINYVQF 238
           +Y   + R   A ++HS  E+ RR+K++  +  L  LVP C+ ++ K   LD++      
Sbjct: 2   EYAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRK---LDKL----TV 54

Query: 239 LQNQVEFLSMKLASVNP 255
           L+  V+ +     + NP
Sbjct: 55  LRMAVQHMKTLRGATNP 71


>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 = 27.7 bits (60), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 194 HSLAERVRREKISERMKILQKLVPGCD-KVTGKAFMLDEIINYVQFLQNQVEFL 246
           H+  ER RR+ I +    L+  VP    +   +A +LD+   Y+Q+++ +V  L
Sbjct: 8   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTL 61


  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
   0.315    0.130    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,765,834
Number of Sequences: 62578
Number of extensions: 202756
Number of successful extensions: 462
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 451
Number of HSP's gapped (non-prelim): 22
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
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: 51 (24.3 bits)