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= 005433
         (697 letters)

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

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



>pdb|2VQI|A Chain A, Structure Of The P Pilus Usher (Papc) Translocation Pore
 pdb|2VQI|B Chain B, Structure Of The P Pilus Usher (Papc) Translocation Pore
          Length = 515

 Score = 33.5 bits (75), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 243 FAGRSGLLRWSRKNENIEAQPTDASQLIPQHNYKLDVHALNSRHPGEFECRE 294
           F G+S  L +S++ +N +A  T A     + NY      LN+R+  ++  RE
Sbjct: 287 FQGKSWRLSYSKRFDNADADITFAGYRFSERNYXTXEQYLNARYRNDYSSRE 338


>pdb|3FIP|A Chain A, Crystal Structure Of Usher Papc Translocation Pore
 pdb|3FIP|B Chain B, Crystal Structure Of Usher Papc Translocation Pore
          Length = 493

 Score = 32.7 bits (73), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 27/52 (51%)

Query: 243 FAGRSGLLRWSRKNENIEAQPTDASQLIPQHNYKLDVHALNSRHPGEFECRE 294
           F G+S  L +S++ +N +A  T A     + NY      LN+R+  ++  RE
Sbjct: 273 FQGKSWRLSYSKRFDNADADITFAGYRFSERNYMTMEQYLNARYRNDYSSRE 324


  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
   0.319    0.135    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,115,149
Number of Sequences: 62578
Number of extensions: 950783
Number of successful extensions: 2271
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2269
Number of HSP's gapped (non-prelim): 3
length of query: 697
length of database: 14,973,337
effective HSP length: 106
effective length of query: 591
effective length of database: 8,340,069
effective search space: 4928980779
effective search space used: 4928980779
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)