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= 039918
         (140 letters)

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

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



>pdb|3KYC|B Chain B, Human Sumo E1 Complex With A Sumo1-Amp Mimic
          Length = 660

 Score = 30.8 bits (68), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 2/51 (3%)

Query: 31  DLFQSNSGSSEGSTRAVYSDDERKKRRMISNRE--SARRSRWRKKKQLEDL 79
           D+   +S   + S  A  S++ER ++R +  +E  SA+RSR  +K++L+D+
Sbjct: 606 DVLIVDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDV 656


>pdb|1Y8Q|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
 pdb|1Y8Q|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
 pdb|1Y8R|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
 pdb|1Y8R|E Chain E, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
          Length = 640

 Score = 30.8 bits (68), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 32/51 (62%), Gaps = 2/51 (3%)

Query: 31  DLFQSNSGSSEGSTRAVYSDDERKKRRMISNRE--SARRSRWRKKKQLEDL 79
           D+   +S   + S  A  S++ER ++R +  +E  SA+RSR  +K++L+D+
Sbjct: 586 DVLIVDSDEEDSSNNADVSEEERSRKRKLDEKENLSAKRSRIEQKEELDDV 636


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

 Score = 27.7 bits (60), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 18/26 (69%), Gaps = 3/26 (11%)

Query: 61 NRESARRSRWRK---KKQLEDLTEEL 83
          N E+ARRSR RK    KQLED  EEL
Sbjct: 17 NTEAARRSRARKLQRMKQLEDKVEEL 42


>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 = 27.3 bits (59), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 18/26 (69%), Gaps = 3/26 (11%)

Query: 61 NRESARRSRWRK---KKQLEDLTEEL 83
          N E+ARRSR RK    KQLED  EEL
Sbjct: 16 NTEAARRSRARKLQRMKQLEDKVEEL 41


>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 = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 18/36 (50%), Positives = 25/36 (69%), Gaps = 4/36 (11%)

Query: 57 RMISNRESARRSRWRKKKQLEDLTEELNRSAV-ENQ 91
          R++ NRE+AR SR +KK+ ++ L    NR AV ENQ
Sbjct: 5  RLMKNREAARESRRKKKEYVKSLE---NRVAVLENQ 37


>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 = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 18/26 (69%), Gaps = 3/26 (11%)

Query: 61 NRESARRSRWRK---KKQLEDLTEEL 83
          N E+ARRSR RK    KQLED  EEL
Sbjct: 12 NTEAARRSRARKLQRMKQLEDKVEEL 37


>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 = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 17/26 (65%), Positives = 18/26 (69%), Gaps = 3/26 (11%)

Query: 61 NRESARRSRWRK---KKQLEDLTEEL 83
          N E+ARRSR RK    KQLED  EEL
Sbjct: 11 NTEAARRSRARKLQRMKQLEDKVEEL 36


>pdb|2Y09|A Chain A, The Cyanobacterial Pp2c-Like Phosphatase Tppha Requires
           Three Metals In The Catalytic Center For Efficient
           Catalysis
          Length = 240

 Score = 26.2 bits (56), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 34  QSNSGSSEGSTRAVYSDDERKKRRMISNRESARRSRWRKKKQLEDLTEE 82
           Q+++ +  G+T  V   DE+  R   ++  ++R  RWR K QL+ +T +
Sbjct: 89  QNSARADMGTTAVVILLDEKGDRAWCAHVGASRIYRWR-KDQLQQITSD 136


>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
          Length = 493

 Score = 25.4 bits (54), Expect = 9.8,   Method: Composition-based stats.
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 110 ENEQLTSEYVALRTRLSNLYRILGS 134
           E+E+L  EY  L  +++ L RILGS
Sbjct: 441 EHEKLLDEYKELLDQIAELLRILGS 465


  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
   0.313    0.127    0.350 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,720,975
Number of Sequences: 62578
Number of extensions: 127858
Number of successful extensions: 356
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 328
Number of HSP's gapped (non-prelim): 49
length of query: 140
length of database: 14,973,337
effective HSP length: 89
effective length of query: 51
effective length of database: 9,403,895
effective search space: 479598645
effective search space used: 479598645
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: 46 (22.3 bits)