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= 027682
         (220 letters)

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

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



>pdb|4A4A|A Chain A, Cpgh89 (E483q, E601q), From Clostridium Perfringens, In
           Complex With Its Substrate Glcnac-Alpha-1,4-Galactose
          Length = 914

 Score = 70.9 bits (172), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/116 (31%), Positives = 66/116 (56%), Gaps = 6/116 (5%)

Query: 100 GTPEIVISGVTGVEVLAGLHWYLRYWCGSHISWDKTGGVQVASMPKLGSFPRVQDAGVFV 159
           G  +++I G  GV + +G ++YL+ +C  ++S++   G  +  MP+  + P V +  V +
Sbjct: 233 GDGKVLIKGNNGVSLASGFNYYLKNYC--NVSYNPIMGSNL-KMPE--TMPSVGER-VVI 286

Query: 160 KRPIPLNYYQNAVTSSYTFAWWDWKRWEKEIDWMALQGINLPLAFTGQETIWQKVF 215
             P    Y  N  T SYT ++WDW ++E+ +DW A+ G+NL L   GQE + ++  
Sbjct: 287 DTPYEHRYALNFCTYSYTMSFWDWDQYEEFLDWCAMNGVNLVLDIIGQEEVLRRTL 342


>pdb|2VC9|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
           In Complex With 2-Acetamido-1,2-Dideoxynojirmycin
 pdb|2VCA|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
           In Complex With Beta-N-Acetyl-D-Glucosamine
 pdb|2VCB|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
           In Complex With Pugnac
 pdb|2VCC|A Chain A, Family 89 Glycoside Hydrolase From Clostridium Perfringens
          Length = 891

 Score = 70.9 bits (172), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/116 (31%), Positives = 66/116 (56%), Gaps = 6/116 (5%)

Query: 100 GTPEIVISGVTGVEVLAGLHWYLRYWCGSHISWDKTGGVQVASMPKLGSFPRVQDAGVFV 159
           G  +++I G  GV + +G ++YL+ +C  ++S++   G  +  MP+  + P V +  V +
Sbjct: 210 GDGKVLIKGNNGVSLASGFNYYLKNYC--NVSYNPIMGSNL-KMPE--TMPSVGER-VVI 263

Query: 160 KRPIPLNYYQNAVTSSYTFAWWDWKRWEKEIDWMALQGINLPLAFTGQETIWQKVF 215
             P    Y  N  T SYT ++WDW ++E+ +DW A+ G+NL L   GQE + ++  
Sbjct: 264 DTPYEHRYALNFCTYSYTMSFWDWDQYEEFLDWCAMNGVNLVLDIIGQEEVLRRTL 319


>pdb|1NIO|A Chain A, Crystal Structure Of Beta-Luffin, A Ribosome Inactivating
           Protein At 2.0a Resolution
          Length = 247

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 137 GVQVASMPKLGSFPRVQDAGVFVKRPIPLNY--YQNAVTS 174
           G  + ++P  G++ R+Q+A   V+  IPL +  + +A+TS
Sbjct: 99  GSTIVTLPYSGNYERLQNAAGKVREKIPLGFRAFDSAITS 138


>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 428

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 28  SSTIGVQYISRLLDIQDRERAPPSVQLA 55
           SST G+ Y+ R+L   DRE   PS+ +A
Sbjct: 111 SSTTGMSYVVRILSTLDRELLKPSMSVA 138


>pdb|1C8N|A Chain A, Tobacco Necrosis Virus
 pdb|1C8N|B Chain B, Tobacco Necrosis Virus
 pdb|1C8N|C Chain C, Tobacco Necrosis Virus
          Length = 276

 Score = 27.7 bits (60), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 18/34 (52%)

Query: 181 WDWKRWEKEIDWMALQGINLPLAFTGQETIWQKV 214
           W+ KRW  E  W A Q  N   A T  ++I +KV
Sbjct: 21  WNGKRWVTEASWRAGQAPNKERAATVTKSIARKV 54


  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    0.137    0.451 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,301,595
Number of Sequences: 62578
Number of extensions: 257487
Number of successful extensions: 707
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 701
Number of HSP's gapped (non-prelim): 5
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
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: 49 (23.5 bits)