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= 034303
         (98 letters)

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

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



>pdb|1PRN|A Chain A, Refined Structure Of Porin From Rhodopseudomonas Blastica
           And Comparison With The Porin From Rhodobacter
           Capsulatus
          Length = 289

 Score = 25.4 bits (54), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|6PRN|A Chain A, E1m, K50a, R52a Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|1BH3|A Chain A, E1m, A116k Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|3PRN|A Chain A, E1m, A104w Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|7PRN|A Chain A, E1m, D97a, E99a Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|8PRN|A Chain A, E1m, K50a, R52a, D97a, E99a Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|5PRN|A Chain A, E1m, Y96w, S119w Mutant Of Rh. Blastica Porin
          Length = 289

 Score = 25.4 bits (54), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


>pdb|2PRN|A Chain A, Rhodopseudomonas Blastica Porin, Triple Mutant E1m, E99w,
           A116w
          Length = 289

 Score = 25.4 bits (54), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 15  VVQNKLRTVGSLWLSGIAGSIAYNWSQPGMKTS 47
           +V N +  VG+ +    AG++  NW   G+ T+
Sbjct: 188 IVDNDIAFVGAAYKFNDAGTVGLNWYDNGLSTA 220


  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
   0.314    0.129    0.394 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,626,171
Number of Sequences: 62578
Number of extensions: 64566
Number of successful extensions: 79
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 71
Number of HSP's gapped (non-prelim): 8
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)