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= psy3607
         (95 letters)

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

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



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

 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/46 (63%), Positives = 36/46 (78%)

Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGT 80
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +  T
Sbjct: 19 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET 64


>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 = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/43 (65%), Positives = 35/43 (81%)

Query: 35 SEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNY 77
          SEKKRRDQFN+LI EL +M+  N RKMDKSTVL+ +I FL+ +
Sbjct: 15 SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKH 57


>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 = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 3/49 (6%)

Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGTY 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 = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 3/48 (6%)

Query: 36 EKKRRDQFNMLINELCTMVSTNN---RKMDKSTVLKSTIAFLKNYNGT 80
          EK+RRD+ N  I+EL ++V T N   RK+DK TVL+  +  +K   G 
Sbjct: 21 EKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA 68


>pdb|3C7G|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 43
           Arabinoxylan Arabinofuranohydrolase From Bacillus
           Subtilis In Complex With Xylotetraose
          Length = 488

 Score = 26.2 bits (56), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 74  LKNYNGTYYFGCSLNF 89
           L  YNGTYY+   +NF
Sbjct: 230 LHKYNGTYYYSYCINF 245


>pdb|3C7E|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 43
           Arabinoxylan Arabinofuranohydrolase From Bacillus
           Subtilis.
 pdb|3C7F|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 43
           Arabinoxylan Arabinofuranohydrolase From Bacillus
           Subtilis In Complex With Xylotriose.
 pdb|3C7H|A Chain A, Crystal Structure Of Glycoside Hydrolase Family 43
           Arabinoxylan Arabinofuranohydrolase From Bacillus
           Subtilis In Complex With Axos-4- 0.5.
 pdb|3C7O|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 43
           Arabinoxylan Arabinofuranohydrolase From Bacillus
           Subtilis In Complex With Cellotetraose
          Length = 487

 Score = 26.2 bits (56), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 74  LKNYNGTYYFGCSLNF 89
           L  YNGTYY+   +NF
Sbjct: 229 LHKYNGTYYYSYCINF 244


  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
   0.322    0.130    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,775,136
Number of Sequences: 62578
Number of extensions: 43648
Number of successful extensions: 98
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 89
Number of HSP's gapped (non-prelim): 7
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)