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= psy2163
         (188 letters)

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

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



>pdb|2EHH|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
           Aquifex Aeolicus
 pdb|2EHH|C Chain C, Crystal Structure Of Dihydrodipicolinate Synthase From
           Aquifex Aeolicus
 pdb|2EHH|D Chain D, Crystal Structure Of Dihydrodipicolinate Synthase From
           Aquifex Aeolicus
 pdb|2EHH|E Chain E, Crystal Structure Of Dihydrodipicolinate Synthase From
           Aquifex Aeolicus
          Length = 294

 Score = 35.0 bits (79), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 6/99 (6%)

Query: 6   YKLVWRELVVYLVIYYIINFTYRFALIESHQRLFERLQKYCAKKTEVIPMSFVLGFYVSL 65
           +K V +E+ + ++IY I + T     +++  +L    +   A K     M       +S 
Sbjct: 118 FKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMD-----RISE 172

Query: 66  VVKRWWEQYRLLPWPDTLAL-FVSAAIPGVVSVVFLIFP 103
           +VKR  E + +L   D+L L  ++    GV+SV   + P
Sbjct: 173 IVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMP 211


>pdb|3UMC|A Chain A, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
 pdb|3UMC|B Chain B, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
 pdb|3UMC|C Chain C, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
 pdb|3UMC|D Chain D, Crystal Structure Of The L-2-Haloacid Dehalogenase Pa0810
          Length = 254

 Score = 27.3 bits (59), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 42/94 (44%), Gaps = 12/94 (12%)

Query: 1   WRGSV---YKLVWREL-----VVYLVIYYIINFTYRFALIESHQRLFERLQKYCAKKTEV 52
           WR S+   ++ + REL      V L   +   +      + + Q  ++ L +   +  E 
Sbjct: 36  WRSSLIEQFQALERELGGTLPCVELTDRWRQQYKPAXDRVRNGQAPWQHLDQLHRQSLEA 95

Query: 53  IPMSFVLGFYVSLV--VKRWWEQYRLLPWPDTLA 84
           +   F L    +L+  +  +W  +RL PWPDTLA
Sbjct: 96  LAGEFGLALDEALLQRITGFW--HRLRPWPDTLA 127


  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
   0.331    0.144    0.473 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,340,982
Number of Sequences: 62578
Number of extensions: 204462
Number of successful extensions: 381
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 378
Number of HSP's gapped (non-prelim): 5
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 bits)