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= psy3606
         (96 letters)

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

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



>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
          Structure Of Human Clock-bmal1 Basic Helix-loop-helix
          Domains With E-box Dna
          Length = 71

 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/50 (58%), Positives = 37/50 (74%)

Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCL 84
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +  +   L
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWL 64


>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
          Transcriptional Activator Complex
          Length = 361

 Score = 59.3 bits (142), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 28/43 (65%), Positives = 35/43 (81%)

Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKH 61


>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 3/49 (6%)

Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGLY 81
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G +
Sbjct: 17 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGAW 65


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

 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGLYDCLIMIGYFTN 92
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G  +      Y   
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEANYKPT 80

Query: 93 F 93
          F
Sbjct: 81 F 81


>pdb|1KMC|A Chain A, Crystal Structure Of The Caspase-7  XIAP-Bir2 Complex
 pdb|1KMC|B Chain B, Crystal Structure Of The Caspase-7  XIAP-Bir2 Complex
          Length = 303

 Score = 25.4 bits (54), Expect = 7.5,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 42  QFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGLYDCLIMIGY 89
           Q+NM   +L   +  NN+  DK T +       K+   L+ C   +G+
Sbjct: 59  QYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGF 106


>pdb|3N9X|A Chain A, Crystal Structure Of Map Kinase From Plasmodium Berghei,
           Pb000659.00.0
 pdb|3N9X|B Chain B, Crystal Structure Of Map Kinase From Plasmodium Berghei,
           Pb000659.00.0
          Length = 432

 Score = 25.4 bits (54), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 11/35 (31%), Positives = 20/35 (57%)

Query: 34  LSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLK 68
           + EK  RDQ N++ N + T    + + ++K  V+K
Sbjct: 280 VHEKSNRDQLNIIFNIIGTPTEDDLKNINKPEVIK 314


  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
   0.325    0.134    0.390 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,786,360
Number of Sequences: 62578
Number of extensions: 42755
Number of successful extensions: 135
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 128
Number of HSP's gapped (non-prelim): 19
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)