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= psy12031
         (128 letters)

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

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



>pdb|2P3D|A Chain A, Crystal Structure Of The Multi-Drug Resistant Mutant
          Subtype F Hiv Protease Complexed With Tl-3 Inhibitor
 pdb|2P3D|B Chain B, Crystal Structure Of The Multi-Drug Resistant Mutant
          Subtype F Hiv Protease Complexed With Tl-3 Inhibitor
          Length = 99

 Score = 29.6 bits (65), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 12/46 (26%), Positives = 23/46 (50%)

Query: 5  EKVEVKQKWASRLLGKLRKDITQECREDFVLSITGKKPAMCVLSNP 50
          E + +  KW  +++G +R  +  +  ED ++ I G +    VL  P
Sbjct: 34 EDINLSGKWKPKIIGGIRGFVKVKQYEDILIEICGHRAVGAVLVGP 79


>pdb|3MWS|A Chain A, Crystal Structure Of Group N Hiv-1 Protease
 pdb|3MWS|B Chain B, Crystal Structure Of Group N Hiv-1 Protease
          Length = 99

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 11/46 (23%), Positives = 24/46 (52%)

Query: 5  EKVEVKQKWASRLLGKLRKDITQECREDFVLSITGKKPAMCVLSNP 50
          E+++++ KW  +++G +   I     ++  + I G+K    VL  P
Sbjct: 34 EEIQLEGKWKPKMIGGIGGFIKVRQYDNVTIDIQGRKAVGTVLVGP 79


>pdb|3IXO|A Chain A, Crystal Structure Of Uncomplexed Hiv_1 Protease Subtype
          A
 pdb|3IXO|B Chain B, Crystal Structure Of Uncomplexed Hiv_1 Protease Subtype
          A
          Length = 99

 Score = 26.2 bits (56), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 12/46 (26%), Positives = 23/46 (50%)

Query: 5  EKVEVKQKWASRLLGKLRKDITQECREDFVLSITGKKPAMCVLSNP 50
          E++ +  KW  +++G +   I  +  +  ++ I GKK    VL  P
Sbjct: 34 EEINLPGKWKPKMIGGIGGFIKVKQYDQILIEICGKKAIGTVLVGP 79


>pdb|1PDU|A Chain A, Ligand-Binding Domain Of Drosophila Orphan Nuclear
           Receptor Dhr38
 pdb|1PDU|B Chain B, Ligand-Binding Domain Of Drosophila Orphan Nuclear
           Receptor Dhr38
          Length = 244

 Score = 26.2 bits (56), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 4   NEKVEVKQKWASRLLGK---LRKDITQECREDFVLSITGKKPAMCVLSN 49
           N + + KQ + SRLLGK   LR    Q  +  F L +    PA  ++ N
Sbjct: 188 NAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIEN 236


  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
   0.321    0.136    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,839,246
Number of Sequences: 62578
Number of extensions: 136316
Number of successful extensions: 205
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 201
Number of HSP's gapped (non-prelim): 6
length of query: 128
length of database: 14,973,337
effective HSP length: 87
effective length of query: 41
effective length of database: 9,529,051
effective search space: 390691091
effective search space used: 390691091
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)