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= 038837
         (287 letters)

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

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



>pdb|3U0C|A Chain A, Crystal Structure Of N-Terminal Region Of Type Iii
           Secretion First Translocator Ipab (Residues 74-224)
 pdb|3U0C|B Chain B, Crystal Structure Of N-Terminal Region Of Type Iii
           Secretion First Translocator Ipab (Residues 74-224)
          Length = 201

 Score = 28.9 bits (63), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 67/154 (43%), Gaps = 18/154 (11%)

Query: 1   MAAAAHLTLL---LVILFWSFTLTS--------QNQQHSQQHLIAELQDAKLKIAGLETM 49
           + A++ LTLL   L+ +    +LT+        ++QQ ++Q    E  D   KI  L + 
Sbjct: 48  LNASSQLTLLIGNLIQILGEKSLTALTNKITAWKSQQQARQQKNLEFSD---KINTLLSE 104

Query: 50  LEESIRKVNGKSNYIEERDKLVDDMTNKIHHLQSLLSKIKDDSSXXXXXXXXXXXXXXXX 109
            E   R    + N ++  D  + D+ NKI+ +Q+ LS++  +S                 
Sbjct: 105 TEGLTRDYEKQINKLKNADSKIKDLENKINQIQTRLSELDPESPEKKKLSREEIQLTIKK 164

Query: 110 WAASRKNNFDIHNLESKALDAEDRLEEVSLQVEK 143
            AA +        +E K L    +L + S+Q+EK
Sbjct: 165 DAAVKDRTL----IEQKTLSIHSKLTDKSMQLEK 194


  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    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,867,601
Number of Sequences: 62578
Number of extensions: 222552
Number of successful extensions: 750
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 743
Number of HSP's gapped (non-prelim): 9
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)