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= 019282
         (343 letters)

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

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



>pdb|2JSD|A Chain A, Solution Structure Of Mmp20 Complexed With Nngh
          Length = 160

 Score = 29.3 bits (64), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 146 CPGELLVEEHHSNYGEPWAGGRDVFEFLAEASHITPNSHVLEIGCGTLRVGVHF--IRYL 203
            PGE L  + H +  E W  G + F     A+H     H L +   T    + +   +Y 
Sbjct: 82  APGEGLGGDTHFDNAEKWTMGTNGFNLFTVAAHEF--GHALGLAHSTDPSALMYPTYKYK 139

Query: 204 NPENFHCLERDELSLMAAF 222
           NP  FH  + D   + A +
Sbjct: 140 NPYGFHLPKDDVKGIQALY 158


>pdb|2YYZ|A Chain A, Crystal Structure Of Sugar Abc Transporter, Atp-Binding
           Protein
          Length = 359

 Score = 28.1 bits (61), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 27/57 (47%)

Query: 274 VGLERLASKLRPYDGRIFVSHNIKFCSRLGGEECTKRLTSLGLEYIGKKTHDSLLFN 330
           V L++   K++  DG  F   + +F + LG   C K  T L L  I K T   + F+
Sbjct: 7   VNLKKYFGKVKAVDGVSFEVKDGEFVALLGPSGCGKTTTLLMLAGIYKPTSGEIYFD 63


  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    0.138    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,270,845
Number of Sequences: 62578
Number of extensions: 369855
Number of successful extensions: 749
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 748
Number of HSP's gapped (non-prelim): 2
length of query: 343
length of database: 14,973,337
effective HSP length: 100
effective length of query: 243
effective length of database: 8,715,537
effective search space: 2117875491
effective search space used: 2117875491
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: 52 (24.6 bits)