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= 026806
         (233 letters)

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

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



>pdb|2DGC|A Chain A, Gcn4 Basic Domain, Leucine Zipper Complexed With AtfCREB
           Site Dna
          Length = 63

 Score = 32.3 bits (72), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 113 AKRRQSNRESARRSRMRKQEEFKKLQKAVEELKAESAVLKDELLSLSAKYG 163
           A +R  N E+ARRSR RK +  K+L+  VEEL +++  L++E+  L    G
Sbjct: 11  ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG 61


>pdb|1DGC|A Chain A, The X-Ray Structure Of The Gcn4-Bzip Bound To AtfCREB SITE
           Dna Shows The Complex Depends On Dna Flexibility
          Length = 62

 Score = 32.0 bits (71), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 113 AKRRQSNRESARRSRMRKQEEFKKLQKAVEELKAESAVLKDELLSLSAKYG 163
           A +R  N E+ARRSR RK +  K+L+  VEEL +++  L++E+  L    G
Sbjct: 10  ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG 60


>pdb|3VQT|A Chain A, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|B Chain B, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|C Chain C, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VQT|D Chain D, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|A Chain A, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|B Chain B, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|C Chain C, Crystal Structure Analysis Of The Translation Factor Rf3
 pdb|3VR1|D Chain D, Crystal Structure Analysis Of The Translation Factor Rf3
          Length = 548

 Score = 32.0 bits (71), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 62  KNVTVCHSNTTNLASRDSAESMIKTTQNSGIVINESGT---GARITKDGEELKLAKRRQS 118
           K+VTV ++       R   E          I I   GT   G   T+  E LK       
Sbjct: 355 KDVTVANATIFMAQDRTGVEEAFP---GDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNF 411

Query: 119 NRESARRSRMRKQEEFKKLQKAVEELKAESAV 150
             E  RR R++   + K+LQK +E+L  E AV
Sbjct: 412 APEHFRRVRLKNPLKAKQLQKGLEQLAEEGAV 443


>pdb|1LD4|E Chain E, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|F Chain F, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|G Chain G, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|H Chain H, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|I Chain I, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|J Chain J, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|K Chain K, Placement Of The Structural Proteins In Sindbis Virus
 pdb|1LD4|L Chain L, Placement Of The Structural Proteins In Sindbis Virus
          Length = 57

 Score = 31.6 bits (70), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 113 AKRRQSNRESARRSRMRKQEEFKKLQKAVEELKAESAVLKDELLSLSAKYG 163
           A +R  N E+ARRSR RK +  K+L+  VEEL +++  L++E+  L    G
Sbjct: 5   ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG 55


>pdb|1YSA|C Chain C, The Gcn4 Basic Region Leucine Zipper Binds Dna As A Dimer
           Of Uninterrupted Alpha Helices: Crystal Structure Of The
           Protein-Dna Complex
 pdb|1YSA|D Chain D, The Gcn4 Basic Region Leucine Zipper Binds Dna As A Dimer
           Of Uninterrupted Alpha Helices: Crystal Structure Of The
           Protein-Dna Complex
          Length = 58

 Score = 31.6 bits (70), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 113 AKRRQSNRESARRSRMRKQEEFKKLQKAVEELKAESAVLKDELLSLSAKYG 163
           A +R  N E+ARRSR RK +  K+L+  VEEL +++  L++E+  L    G
Sbjct: 6   ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLVG 56


>pdb|3A6M|A Chain A, Crystal Structure Of Grpe From Thermus Thermophilus Hb8
 pdb|3A6M|B Chain B, Crystal Structure Of Grpe From Thermus Thermophilus Hb8
          Length = 177

 Score = 27.7 bits (60), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 7/59 (11%)

Query: 135 KKLQKAVEELKAESAVLKDELLSLSAKYGKLKDENEAIVEELKLRHRADAISYLEALMP 193
           ++L+ A EELK     LKD+ L L A +   +   E   EELK R R   +  L AL+P
Sbjct: 26  ERLKAAEEELKG----LKDKYLRLLADFDNYRKRME---EELKAREREGVLKALRALLP 77


>pdb|3A5T|A Chain A, Crystal Structure Of Mafg-Dna Complex
 pdb|3A5T|B Chain B, Crystal Structure Of Mafg-Dna Complex
          Length = 107

 Score = 27.3 bits (59), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 7/66 (10%)

Query: 109 ELKLAKRRQSNR---ESARRSRMRKQEEFKK----LQKAVEELKAESAVLKDELLSLSAK 161
           +LK  +R   NR    S R  R+ ++EE +K    LQ+ VE+L +E+A  K EL +L +K
Sbjct: 35  QLKQRRRTLKNRGYAASCRVKRVTQKEELEKQKAELQQEVEKLASENASXKLELDALRSK 94

Query: 162 YGKLKD 167
           Y  L++
Sbjct: 95  YEALQN 100


>pdb|1DH3|A Chain A, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
           Basis For Creb Faimly Selective Dimerization And Dna
           Binding
 pdb|1DH3|C Chain C, Crystal Structure Of A Creb Bzip-Cre Complex Reveals The
           Basis For Creb Faimly Selective Dimerization And Dna
           Binding
          Length = 55

 Score = 27.3 bits (59), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 28/49 (57%)

Query: 115 RRQSNRESARRSRMRKQEEFKKLQKAVEELKAESAVLKDELLSLSAKYG 163
           R   NRE+AR SR +K+E  K L+  V  L+ ++  L +EL +L   Y 
Sbjct: 5   RLMKNREAARESRRKKKEYVKSLENRVAVLENQNKTLIEELKALKDLYS 53


  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
   0.312    0.126    0.329 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,650,972
Number of Sequences: 62578
Number of extensions: 156996
Number of successful extensions: 650
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 60
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)