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= 031276
         (162 letters)

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

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



>pdb|2WXU|A Chain A, Clostridium Perfringens Alpha-Toxin Strain Nctc8237 Mutant
           T74i
 pdb|2WY6|A Chain A, Clostridium Perfringens Alpha-Toxin Strain Nctc8237 Mutant
           T74i
 pdb|2WY6|B Chain B, Clostridium Perfringens Alpha-Toxin Strain Nctc8237 Mutant
           T74i
 pdb|2WY6|C Chain C, Clostridium Perfringens Alpha-Toxin Strain Nctc8237 Mutant
           T74i
          Length = 370

 Score = 30.8 bits (68), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 10/50 (20%)

Query: 73  FYETQIDN----------AYDFPIFGAGQARKYSAMLPLQWLRCSFCMGT 112
           F++  IDN          AY  P  G  Q RK+SA+   +W R ++   T
Sbjct: 69  FWDPDIDNNFSKDNSWYLAYSIPDTGESQIRKFSALARYEWQRGNYKQAT 118


>pdb|1QM6|A Chain A, R32 Form Of Clostridium Perfringens Alpha-Toxin Strain
 pdb|1QM6|B Chain B, R32 Form Of Clostridium Perfringens Alpha-Toxin Strain
 pdb|1QMD|A Chain A, Calcium Bound Closed Form Alpha-Toxin From Clostridium
           Perfringens
 pdb|1QMD|B Chain B, Calcium Bound Closed Form Alpha-Toxin From Clostridium
           Perfringens
 pdb|2WXT|A Chain A, Clostridium Perfringens Alpha-Toxin Strain Nctc8237
          Length = 370

 Score = 29.6 bits (65), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 81  AYDFPIFGAGQARKYSAMLPLQWLRCSFCMGT 112
           AY  P  G  Q RK+SA+   +W R ++   T
Sbjct: 87  AYSIPDTGESQIRKFSALARYEWQRGNYKQAT 118


>pdb|1GYG|A Chain A, R32 Closed Form Of Alpha-Toxin From Clostridium
           Perfringens Strain Cer89l43
 pdb|1GYG|B Chain B, R32 Closed Form Of Alpha-Toxin From Clostridium
           Perfringens Strain Cer89l43
 pdb|1CA1|A Chain A, Alpha-Toxin From Clostridium Perfringens
          Length = 370

 Score = 29.6 bits (65), Expect = 0.85,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 81  AYDFPIFGAGQARKYSAMLPLQWLRCSFCMGT 112
           AY  P  G  Q RK+SA+   +W R ++   T
Sbjct: 87  AYSIPDTGESQIRKFSALARYEWQRGNYKQAT 118


>pdb|2Q6T|A Chain A, Crystal Structure Of The Thermus Aquaticus Dnab Monomer
 pdb|2Q6T|B Chain B, Crystal Structure Of The Thermus Aquaticus Dnab Monomer
 pdb|2Q6T|C Chain C, Crystal Structure Of The Thermus Aquaticus Dnab Monomer
 pdb|2Q6T|D Chain D, Crystal Structure Of The Thermus Aquaticus Dnab Monomer
          Length = 444

 Score = 28.1 bits (61), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 24/48 (50%)

Query: 36  QRSSAPYPCIRAELDQNTVVAISVGLVSVAVGIGIPIFYETQIDNAYD 83
           Q  S P      E  Q  + AIS GL ++A  +GIPI   +Q+  A +
Sbjct: 320 QLMSGPGSGKSGENRQQEIAAISRGLKALARELGIPIIALSQLSRAVE 367


>pdb|3N6X|A Chain A, Crystal Structure Of A Putative Glutathionylspermidine
           Synth (Mfla_0391) From Methylobacillus Flagellatus Kt At
           2.35 A R
          Length = 474

 Score = 26.6 bits (57), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 139 TCTTCQGTGIQPRYLDRREF 158
           TC T   TGI PR++D R F
Sbjct: 413 TCPTLVETGIAPRHVDLRPF 432


  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    0.136    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,594,966
Number of Sequences: 62578
Number of extensions: 179170
Number of successful extensions: 302
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 8
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
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: 47 (22.7 bits)