BLASTP 2.2.18 [Mar-02-2008]


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= 0188.0080.p
         (167 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

STM0456 [R] COG4533 ABC-type uncharacterized transport system, p...    82   3e-16

>STM0456 [R] COG4533 ABC-type uncharacterized transport system, periplasmic
           component
          Length = 566

 Score = 82.0 bits (201), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 11/158 (6%), Positives = 25/158 (15%), Gaps = 6/158 (3%)

Query: 8   QAKQDAVDVVTGKLQNSVSTVVADYRGLNVSQVTELRKQLREA---GVDFQVLKNXXXXX 64
                   +       +    V++           LR  LR+A   G      ++     
Sbjct: 5   NRLNQYQRLWQPSAGETQHVTVSELAERCFCSERHLRTLLRQAQQAGWLRWEAQSGRGKR 64

Query: 65  XXXXXXXXXXXXXXXGPTAVAF-SETDAVVAAKILNDFAK--KNDALKLKGGVVEGRVID 121
                                   +   V+    L                   +   + 
Sbjct: 65  GRLQFLVTPESLRTAMMEQALEKGQQLNVLELAQLAPGELRAMLQPFMGGQWQNDTPTLR 124

Query: 122 ADQLKALAELPSREGLLSMLLSVLQAPMRNFALAVKAV 159
               + L  L            +            +  
Sbjct: 125 IPYYRPLDPLQPGFLPGRAEQHLAGQVFSGLTRFDRDS 162


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.314    0.128    0.329 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 8,592,464
Number of extensions: 285253
Number of successful extensions: 515
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 514
Number of HSP's successfully gapped: 1
Length of query: 167
Length of database: 38,378,431
Length adjustment: 99
Effective length of query: 68
Effective length of database: 26,960,365
Effective search space: 1833304820
Effective search space used: 1833304820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 112 (47.8 bits)