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= psy1130
         (135 letters)

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

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



>pdb|2ZBK|A Chain A, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|C Chain C, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|E Chain E, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
 pdb|2ZBK|G Chain G, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
           Insights Into Dna Transfer Mechanisms
          Length = 389

 Score = 28.5 bits (62), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 6/86 (6%)

Query: 41  FIDCNFPKAFIQFVLIMVHAFQLLFIDCNFPKAFVWWIGSHAVMFFFLFRNFYKEQYVKP 100
           F+D N  K F+Q VL+    +  L  D       +++ G H+     L ++    + V  
Sbjct: 70  FLDLNEAKRFMQTVLMASIIYDALVSDEYPTIRDLYYRGKHS----LLLKSIEGNKIVSE 125

Query: 101 VKTAKACTQKVPDSVPGKVEVFSTLC 126
             T     QK  DSV   +EVF++L 
Sbjct: 126 ENTWD--EQKESDSVIVDIEVFTSLL 149


>pdb|2WSC|2 Chain 2, Improved Model Of Plant Photosystem I
 pdb|2WSE|2 Chain 2, Improved Model Of Plant Photosystem I
 pdb|2WSF|2 Chain 2, Improved Model Of Plant Photosystem I
          Length = 269

 Score = 28.1 bits (61), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 1   MSGWLTGDYSFKCQPLDLGNHPRTMRIQFVLIMVHA 36
           + G L GD+ F   PL LG+ P ++R      +VH+
Sbjct: 77  LDGSLPGDFGF--DPLGLGSDPESLRWNVQAELVHS 110


  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
   0.335    0.145    0.493 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,961,199
Number of Sequences: 62578
Number of extensions: 135789
Number of successful extensions: 248
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 247
Number of HSP's gapped (non-prelim): 5
length of query: 135
length of database: 14,973,337
effective HSP length: 88
effective length of query: 47
effective length of database: 9,466,473
effective search space: 444924231
effective search space used: 444924231
T: 11
A: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 46 (22.3 bits)