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= 027982
         (216 letters)

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

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



>pdb|4GVF|A Chain A, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (nagz) Bound To Glcnac
 pdb|4GVF|B Chain B, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (nagz) Bound To Glcnac
 pdb|4GVG|A Chain A, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (Nagz)
 pdb|4GVG|B Chain B, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (Nagz)
 pdb|4GVH|A Chain A, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (Nagz) Covalently Bound To
           5-Fluoro-Glcnac.
 pdb|4GVH|B Chain B, Crystal Structure Of Salmonella Typhimurium Family 3
           Glycoside Hydrolase (Nagz) Covalently Bound To
           5-Fluoro-Glcnac
          Length = 349

 Score = 30.4 bits (67), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 15  GKGLTCVCFKRKGTYERICINLTPQQAERLRRLKHR 50
           G  +  VC  RKG    +  NL+P +AER+ RL H+
Sbjct: 272 GCDMILVCNNRKGAVS-VLDNLSPIKAERVTRLYHK 306


>pdb|4GVI|A Chain A, Crystal Structure Of Mutant (D248n) Salmonella Typhimurium
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-1,6-Anhmurnac
 pdb|4GVI|B Chain B, Crystal Structure Of Mutant (D248n) Salmonella Typhimurium
           Family 3 Glycoside Hydrolase (Nagz) In Complex With
           Glcnac-1,6-Anhmurnac
          Length = 349

 Score = 30.4 bits (67), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 15  GKGLTCVCFKRKGTYERICINLTPQQAERLRRLKHR 50
           G  +  VC  RKG    +  NL+P +AER+ RL H+
Sbjct: 272 GCDMILVCNNRKGAVS-VLDNLSPIKAERVTRLYHK 306


>pdb|3ALF|A Chain A, Crystal Structure Of Class V Chitinase From Nicotiana
           Tobaccum
          Length = 353

 Score = 28.9 bits (63), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 117 KTFSTSFQRLLRKQG--GKRADWEYPFAVAGV-NITFMLMQMLDLEATKPRTFVRSVFL- 172
           K+F  S  RL R+ G  G   DWEYP + A + N+  +L +      T+ R   R+  L 
Sbjct: 93  KSFIDSSIRLARQLGFHGLDLDWEYPLSAADMTNLGTLLNEWRTAINTEARNSGRAALLL 152

Query: 173 -QMLSDNEWAFDLLYCVAFVVMDKQWLE 199
              +S++     L Y V  +  +  W+ 
Sbjct: 153 TAAVSNSPRVNGLNYPVESLARNLDWIN 180


  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
   0.327    0.138    0.449 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,708,899
Number of Sequences: 62578
Number of extensions: 257482
Number of successful extensions: 749
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 727
Number of HSP's gapped (non-prelim): 25
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)