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= 0001.2506.p
         (359 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasm...    56   4e-09

>gi|300310062|ref|YP_003774154.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 316

 Score = 56.2 bits (134), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 75/306 (24%), Positives = 125/306 (40%), Gaps = 41/306 (13%)

Query: 46  YFFVIEEAAVKRAVEAN-QGSFQATNASFDNTRQLEQWQSLMLSRPAALVSDPIDSQAIV 104
           +F  I + A   A + N        ++ +D   Q+ Q ++ + ++   +V +  DS+ + 
Sbjct: 43  FFVAIAKGAESGAHKINPDAKVTVVSSKYDLNTQVGQIENFIANKVDLIVLNAADSKGVG 102

Query: 105 SGLRRYNQQKIPVAIIDTPAESGNVAITVSFDNYLGGVMAAKEIINRLVKKHGSPKGKVL 164
             +++   QK  + ++     +    +TV  DN + G  + K +  +L       KG V+
Sbjct: 103 PAVKKA--QKAGIVVVAVDVAAAGADVTVMSDNTMAGAESCKFLAEKL-----QGKGNVV 155

Query: 165 NCYGALASVAWRQRKEGMDAEFAKYPGITYIA--RPTEGKLDQMLAVTLATLSEHPDLDA 222
              G   S A   R  G  AEF K PGI  ++  +   G  D  +      L+  P +DA
Sbjct: 156 IVNGPPVS-AVMDRVTGCKAEFKKSPGIKILSDNQNAGGSRDGGMTTMSNLLAAQPKIDA 214

Query: 223 VHAPSDSPARGIATALQQKNRWKKVDEKDHVIFVTIDGEPVALRWIQD--GYMDACVSQD 280
           V A +D  A G   A++Q  R       D      +DG P A R ++D      A  +QD
Sbjct: 215 VFAINDPTAIGAELAIRQAKR------SDIKWISGVDGAPDAERALKDSKSLFAASPAQD 268

Query: 281 PIAYGEVAVEMLVKYSIGGKEVPIGPYENKKYFWEKGQIVKGKTGPTLIIPPFVIDRSNA 340
           P  YG  A  + + Y++     P              Q VK       ++P  +I R N 
Sbjct: 269 P--YGMAAESVAIGYAVMNGRAP-------------QQKVK-------LLPVKLITRDNV 306

Query: 341 ADQRHW 346
           AD + W
Sbjct: 307 ADYQGW 312


  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
   0.318    0.133    0.399 

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: 1,149,545
Number of extensions: 46628
Number of successful extensions: 150
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 151
Number of HSP's successfully gapped: 4
Length of query: 359
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 273
Effective length of database: 1,212,660
Effective search space: 331056180
Effective search space used: 331056180
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 131 (55.1 bits)