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= 0002.0015.p
         (104 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314071|ref|YP_003778163.1| amino acid ABC transporter peri...   135   7e-34
gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC t...   115   8e-28
gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC t...   111   1e-26
gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC t...    96   6e-22

>gi|300314071|ref|YP_003778163.1| amino acid ABC transporter
           periplasmic protein [Herbaspirillum seropedicae SmR1]
          Length = 402

 Score =  135 bits (340), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 74/109 (67%), Positives = 78/109 (71%), Gaps = 24/109 (22%)

Query: 2   AKVANEKKKVFI------------------------XVALAKGTGSAVVKQGGKSWFFLT 37
           AKVA EKKKV++                         VALAKGTGSAVVKQGGKSWFFLT
Sbjct: 114 AKVAAEKKKVYMQIGAGSARLTNEECSPYTVHYAYDTVALAKGTGSAVVKQGGKSWFFLT 173

Query: 38  ADYAFGHSLESDTSNVVKASGGTVVGSVKHPLGASDFSSFLLQVSERPA 86
           ADYAFGHSLESDT+NVVKASGGTVVG+VKHPLGASDFSSFLLQ     A
Sbjct: 174 ADYAFGHSLESDTANVVKASGGTVVGAVKHPLGASDFSSFLLQAQSSKA 222


>gi|300312339|ref|YP_003776431.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 404

 Score =  115 bits (288), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 63/104 (60%), Positives = 69/104 (66%), Gaps = 24/104 (23%)

Query: 1   MAKVANEKKKVFI------------------------XVALAKGTGSAVVKQGGKSWFFL 36
           M KV  EKK+V+I                         VALAKGT SAV+KQGGKSWFFL
Sbjct: 115 MNKVMAEKKRVYINIGAGTARLTNEECTPYTVHYEYDTVALAKGTASAVIKQGGKSWFFL 174

Query: 37  TADYAFGHSLESDTSNVVKASGGTVVGSVKHPLGASDFSSFLLQ 80
            ADYAFGHSL +DTS VVKASGGTVVGS+KHP  +SD SSFLLQ
Sbjct: 175 VADYAFGHSLANDTSAVVKASGGTVVGSIKHPPQSSDLSSFLLQ 218


>gi|300309490|ref|YP_003773582.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 404

 Score =  111 bits (277), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 60/110 (54%), Positives = 69/110 (62%), Gaps = 24/110 (21%)

Query: 1   MAKVANEKKKVFIXV------------------------ALAKGTGSAVVKQGGKSWFFL 36
           M KVA EKKKVFI V                        ALA+GTG+A+ +QGGKSW+FL
Sbjct: 115 MGKVAGEKKKVFISVGAGTTRQTNEECNAYTIQYAYDTTALARGTGAAITRQGGKSWYFL 174

Query: 37  TADYAFGHSLESDTSNVVKASGGTVVGSVKHPLGASDFSSFLLQVSERPA 86
           TADYAFG SLE DTS VVK++GG VVG+ + PL  SDFSSFLLQ     A
Sbjct: 175 TADYAFGTSLEKDTSEVVKSNGGNVVGATRVPLATSDFSSFLLQAQSSKA 224


>gi|300312372|ref|YP_003776464.1| branched-chain amino acid ABC
           transporter periplasmic protein [Herbaspirillum
           seropedicae SmR1]
          Length = 410

 Score = 95.9 bits (237), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 43/56 (76%), Positives = 49/56 (87%)

Query: 25  VVKQGGKSWFFLTADYAFGHSLESDTSNVVKASGGTVVGSVKHPLGASDFSSFLLQ 80
           + K G KSW+F+T DYAFGHSLE D S+VVKA+GGTVVGSV+HPL ASDFSSFLLQ
Sbjct: 167 LTKLGNKSWYFVTVDYAFGHSLEKDASDVVKANGGTVVGSVRHPLNASDFSSFLLQ 222


  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
   0.314    0.127    0.371 

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: 320,912
Number of extensions: 11342
Number of successful extensions: 63
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 61
Number of HSP's successfully gapped: 4
Length of query: 104
Length of database: 1,619,870
Length adjustment: 71
Effective length of query: 33
Effective length of database: 1,283,685
Effective search space: 42361605
Effective search space used: 42361605
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 (21.6 bits)
S2: 123 (52.0 bits)