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= 003149
         (844 letters)

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

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



>pdb|1E6Y|B Chain B, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
 pdb|1E6Y|E Chain E, Methyl-Coenzyme M Reductase From Methanosarcina Barkeri
          Length = 433

 Score = 34.3 bits (77), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 137 NHPVTQHVEGHSYAGRLTEQEANILVDLSRSNISPKEILQTLKQRDMHNVSTIKAIYNAR 196
           ++P T  + G    G L+  + N  +  S  NI    +   +  R+  N S + +IY   
Sbjct: 159 SYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMANHV-AAISNRNAMNASALSSIYEQS 217

Query: 197 HKYRVGEQVGQLHMHQLL 214
             + +G  VG    HQLL
Sbjct: 218 GIFEMGGAVGMFERHQLL 235


>pdb|1DAB|A Chain A, The Structure Of Bordetella Pertussis Virulence Factor
           P.69 Pertactin
          Length = 539

 Score = 32.7 bits (73), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 25/46 (54%)

Query: 642 SELQYVLSVQDSDSAPLRTSSATSMQLKGRQKEKVFRTKSHQPLCF 687
            E Q+ + +Q SD   +RT+S T++++ GRQ + +        L F
Sbjct: 11  GERQHGIHIQGSDPGGVRTASGTTIKVSGRQAQGILLENPAAELQF 56


>pdb|2IOU|G Chain G, Major Tropism Determinant P1 (Mtd-P1) Variant Complexed
           With Bordetella Brochiseptica Virulence Factor Pertactin
           Extracellular Domain (Prn-E).
 pdb|2IOU|H Chain H, Major Tropism Determinant P1 (Mtd-P1) Variant Complexed
           With Bordetella Brochiseptica Virulence Factor Pertactin
           Extracellular Domain (Prn-E)
          Length = 535

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 12/36 (33%), Positives = 24/36 (66%)

Query: 642 SELQYVLSVQDSDSAPLRTSSATSMQLKGRQKEKVF 677
            E Q+ + ++ SD A +RT++ T++++ GRQ + V 
Sbjct: 11  GERQHGIHIKQSDGAGVRTATGTTIKVSGRQAQGVL 46


>pdb|3MRS|A Chain A, Crystal Structure Of Shikimate Kinase Mutant (R57a) From
           Helicobacter Pylori
          Length = 168

 Score = 30.8 bits (68), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 704 DVIADGHCGFRVVAELMDIGEDNWAQVRRDLVDELQSHYDDYIQLYGDAEIARELLHSL 762
           D+I     G  V     ++GEDN+A   ++L+DEL++    ++   G   +  E L  L
Sbjct: 39  DMIISERVGLSVREIFEELGEDNFAMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGL 97


  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    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,388,116
Number of Sequences: 62578
Number of extensions: 984833
Number of successful extensions: 2086
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2081
Number of HSP's gapped (non-prelim): 6
length of query: 844
length of database: 14,973,337
effective HSP length: 107
effective length of query: 737
effective length of database: 8,277,491
effective search space: 6100510867
effective search space used: 6100510867
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: 56 (26.2 bits)