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= 041521
         (524 letters)

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

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



>pdb|3RFZ|B Chain B, Crystal Structure Of The Fimd Usher Bound To Its Cognate
           Fimc:fimh Substrate
 pdb|3RFZ|E Chain E, Crystal Structure Of The Fimd Usher Bound To Its Cognate
           Fimc:fimh Substrate
          Length = 843

 Score = 30.8 bits (68), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 314 THIPIIAPKISVASYFNKRHTERNQKTSYSITVQ-GVVDTKGVFTD 358
           T+I ++  + S + YFN   T  ++   Y+I  Q GV+  K  FTD
Sbjct: 427 TNIQLVGYRYSTSGYFNFADTTYSRMNGYNIETQDGVIQVKPKFTD 472


>pdb|3OHN|A Chain A, Crystal Structure Of The Fimd Translocation Domain
 pdb|3OHN|B Chain B, Crystal Structure Of The Fimd Translocation Domain
          Length = 558

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 314 THIPIIAPKISVASYFNKRHTERNQKTSYSITVQ-GVVDTKGVFTD 358
           T+I ++  + S + YFN   T  ++   Y+I  Q GV+  K  FTD
Sbjct: 304 TNIQLVGYRYSTSGYFNFADTTYSRMNGYNIETQDGVIQVKPKFTD 349


>pdb|1SI9|A Chain A, Boiling Stable Protein Isolated From Populus Tremula
 pdb|1SI9|B Chain B, Boiling Stable Protein Isolated From Populus Tremula
 pdb|1SI9|C Chain C, Boiling Stable Protein Isolated From Populus Tremula
 pdb|1TR0|A Chain A, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|B Chain B, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|C Chain C, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|D Chain D, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|E Chain E, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|F Chain F, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|G Chain G, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|H Chain H, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|I Chain I, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|J Chain J, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|K Chain K, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|L Chain L, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|M Chain M, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|N Chain N, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|O Chain O, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|P Chain P, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|R Chain R, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|S Chain S, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|T Chain T, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|U Chain U, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|V Chain V, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|W Chain W, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|X Chain X, Crystal Structure Of A Boiling Stable Protein Sp1
 pdb|1TR0|Y Chain Y, Crystal Structure Of A Boiling Stable Protein Sp1
          Length = 108

 Score = 30.0 bits (66), Expect = 2.9,   Method: Composition-based stats.
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 2  EITRFPFLNQEEDYSHLLDLLPEMES 27
          EITR    N   DY++LLDL+P M+S
Sbjct: 20 EITREQIDNYINDYTNLLDLIPSMKS 45


  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
   0.321    0.135    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,597,503
Number of Sequences: 62578
Number of extensions: 561217
Number of successful extensions: 1109
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1104
Number of HSP's gapped (non-prelim): 7
length of query: 524
length of database: 14,973,337
effective HSP length: 103
effective length of query: 421
effective length of database: 8,527,803
effective search space: 3590205063
effective search space used: 3590205063
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: 54 (25.4 bits)