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= 0001.2402.p
         (133 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310134|ref|YP_003774226.1| type III secretion HrpB protein...   141   2e-35

>gi|300310134|ref|YP_003774226.1| type III secretion HrpB protein
           [Herbaspirillum seropedicae SmR1]
          Length = 134

 Score =  141 bits (356), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 69/115 (60%), Positives = 91/115 (79%), Gaps = 1/115 (0%)

Query: 19  KNNNVTLDLQPANAADSGEFRAALERHLKNDPVHLKTDNASLGSVIVGRTTHLAAEIKQD 78
           ++  + +++QP   A++  F++  E++L  D + LK +  SLGS +  RT+ LAAE+KQD
Sbjct: 21  RDAGIHMEIQPG-GAEAEHFKSMFEQYLNKDALRLKPNTHSLGSALAQRTSSLAAEVKQD 79

Query: 79  QQYVSKLLEQATRTGDSMQLMKAMMALNDFQLRVQTVSKVVSKAVTSVDSLTKLQ 133
           Q YVS+LLEQATRTGDSMQLMKAMMAL+D+Q+RVQT+SK VSKA TSVDSLTKLQ
Sbjct: 80  QLYVSRLLEQATRTGDSMQLMKAMMALSDYQIRVQTISKCVSKASTSVDSLTKLQ 134


  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
   0.312    0.123    0.315 

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: 293,334
Number of extensions: 10160
Number of successful extensions: 24
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 24
Number of HSP's successfully gapped: 1
Length of query: 133
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 58
Effective length of database: 1,264,745
Effective search space: 73355210
Effective search space used: 73355210
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 (21.9 bits)
S2: 125 (52.8 bits)