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= 0164.0003.p
         (148 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312085|ref|YP_003776177.1| transporter DNA uptake transmem...   108   2e-25

>gi|300312085|ref|YP_003776177.1| transporter DNA uptake
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 829

 Score =  108 bits (269), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 51/91 (56%), Positives = 65/91 (71%), Gaps = 5/91 (5%)

Query: 45  AVPEVRPGERWQFTVRLKRPHGNANPHGFDYEVWLLEQNLRATGSVRSDQQSAYK----- 99
           A+P++RPGERW+  VRLKRPHGNANP GFDYE+WLL+ ++RATG V     +        
Sbjct: 153 ALPDMRPGERWRLKVRLKRPHGNANPGGFDYELWLLQDDVRATGYVVGAPAAPGAPATAI 212

Query: 100 NHRLQEFIRTPSNAIERGRSWLRDRIMSALP 130
           N RL+ F+ TPS+AI+  R WLRD I +ALP
Sbjct: 213 NRRLEAFVWTPSHAIDYARGWLRDGIYAALP 243


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.323    0.134    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 460,643
Number of extensions: 16625
Number of successful extensions: 60
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 59
Number of HSP's successfully gapped: 1
Length of query: 148
Length of database: 1,619,870
Length adjustment: 77
Effective length of query: 71
Effective length of database: 1,255,275
Effective search space: 89124525
Effective search space used: 89124525
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 126 (53.1 bits)