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= 035924
         (138 letters)

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

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



>pdb|3T4E|A Chain A, 1.95 Angstrom Crystal Structure Of Shikimate
           5-Dehydrogenase (Aroe) From Salmonella Enterica Subsp.
           Enterica Serovar Typhimurium In Complex With Nad
 pdb|3T4E|B Chain B, 1.95 Angstrom Crystal Structure Of Shikimate
           5-Dehydrogenase (Aroe) From Salmonella Enterica Subsp.
           Enterica Serovar Typhimurium In Complex With Nad
          Length = 312

 Score = 26.6 bits (57), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 11/30 (36%), Positives = 19/30 (63%)

Query: 31  ITMLRPEALYSMFVEDPHVLERMDGAAAAG 60
           +++LRPE L +  V +PH+ + +  A  AG
Sbjct: 244 VSLLRPELLVTECVYNPHMTKLLQQAQQAG 273


>pdb|2UWF|A Chain A, Crystal Structure Of Family 10 Xylanase From Bacillus
           Halodurans
          Length = 356

 Score = 26.6 bits (57), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 9/22 (40%), Positives = 12/22 (54%)

Query: 80  NHLWLSPHARGFVGGIAIDVLF 101
           NH WL   AR +  G+ +D  F
Sbjct: 312 NHTWLDDRAREYNNGVGVDAPF 333


>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure
 pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure
 pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure
          Length = 537

 Score = 26.6 bits (57), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)

Query: 37 EALYSMFVEDPHVLER-----MDGAAAAGNNHFAMEMASLK 72
          E +Y +FV DPH +E        G++ AG N     + SLK
Sbjct: 31 EFMYPVFVIDPHYMESDPSAFSPGSSRAGVNRIRFLLESLK 71


  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
   0.324    0.135    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,159,263
Number of Sequences: 62578
Number of extensions: 152254
Number of successful extensions: 346
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 344
Number of HSP's gapped (non-prelim): 3
length of query: 138
length of database: 14,973,337
effective HSP length: 89
effective length of query: 49
effective length of database: 9,403,895
effective search space: 460790855
effective search space used: 460790855
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: 46 (22.3 bits)