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= 023949
         (275 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 = 30.8 bits (68), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 9/49 (18%)

Query: 37  ASDDATCGTPTWIGKGLTCVCFKRKGTYERICINLTPQQAERLRRLKHR 85
           AS DA C         +  VC  RKG    +  NL+P +AER+ RL H+
Sbjct: 267 ASLDAGCD--------MILVCNNRKGAVS-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 = 30.8 bits (68), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 9/49 (18%)

Query: 37  ASDDATCGTPTWIGKGLTCVCFKRKGTYERICINLTPQQAERLRRLKHR 85
           AS DA C         +  VC  RKG    +  NL+P +AER+ RL H+
Sbjct: 267 ASLDAGCD--------MILVCNNRKGAVS-VLDNLSPIKAERVTRLYHK 306


>pdb|3FS3|A Chain A, Crystal Structure Of Malaria Parasite Nucleosome Assembly
           Protein (Nap)
          Length = 359

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 30  GSAPGPAASDDATCGTPTWIGKGLTCVCFKRKGTYERICINLTPQQAERLRRLKHRMKVY 89
           G+ P P   +         I  G T + ++    Y+    +LT +Q E L++LK   K Y
Sbjct: 6   GNQPIPPEEEKEISSLLESIKIGKTSLKYRCFYLYDDKMTDLTEEQKETLKKLKLYQKEY 65

Query: 90  FDASRPDHQEALRALWAATYPDQELHGLISDQWKE 124
           +D       E    L    Y D  L+G I D+ +E
Sbjct: 66  YDYESKFEYELF--LLRQKYHD--LYGPIYDKRRE 96


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

 Score = 27.7 bits (60), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 5/88 (5%)

Query: 152 KTFSTSFQRLLRKQG--GKRADWEYPFAVAGV-NITFMLMQMLDLEATKPRTFVRSVFL- 207
           K+F  S  RL R+ G  G   DWEYP + A + N+  +L +      T+ R   R+  L 
Sbjct: 93  KSFIDSSIRLARQLGFHGLDLDWEYPLSAADMTNLGTLLNEWRTAINTEARNSGRAALLL 152

Query: 208 -QMLSDNEWAFDLLYCVAFVVMDKQWLE 234
              +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
   0.323    0.135    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,418,878
Number of Sequences: 62578
Number of extensions: 334496
Number of successful extensions: 740
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 718
Number of HSP's gapped (non-prelim): 26
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)