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= 0013.0004.p
         (107 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312451|ref|YP_003776543.1| D-galactonate transporter prote...   149   4e-38
gi|300309918|ref|YP_003774010.1| major facilitator superfamily p...    61   2e-11
gi|300313658|ref|YP_003777750.1| transport transmembrane protein...    59   1e-10
gi|300309906|ref|YP_003773998.1| major facilitator superfamily p...    55   2e-09
gi|300313744|ref|YP_003777836.1| D-glucarate permease [Herbaspir...    54   3e-09

>gi|300312451|ref|YP_003776543.1| D-galactonate transporter
          protein [Herbaspirillum seropedicae SmR1]
          Length = 439

 Score =  149 bits (377), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 70/80 (87%), Positives = 75/80 (93%)

Query: 14 AKENIKPSHVRYLILFMLFIVTTVNYADRATLSIAGTSMKAELGLDPVMMGYIFSAFSWA 73
          A E  KP+HVRYLILF+LF+VTTVNYADRATLSIAG++MK EL LDPVMMGYIFSAFSWA
Sbjct: 2  AGEVAKPTHVRYLILFLLFVVTTVNYADRATLSIAGSAMKTELSLDPVMMGYIFSAFSWA 61

Query: 74 YVLAQLPGGWLLDRFGSKKI 93
          YVLAQLPGGWLLDRFGSKKI
Sbjct: 62 YVLAQLPGGWLLDRFGSKKI 81


>gi|300309918|ref|YP_003774010.1| major facilitator superfamily
          protein [Herbaspirillum seropedicae SmR1]
          Length = 428

 Score = 60.8 bits (146), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/69 (46%), Positives = 44/69 (63%)

Query: 23 VRYLILFMLFIVTTVNYADRATLSIAGTSMKAELGLDPVMMGYIFSAFSWAYVLAQLPGG 82
          ++ + L  L +   VNY DR+TLSIA  S+  EL L    MG + SAFS AY  +QLP G
Sbjct: 14 IQVVALSFLMLAGIVNYLDRSTLSIANHSVSQELNLSASQMGLLLSAFSLAYAFSQLPIG 73

Query: 83 WLLDRFGSK 91
           +LD+FG++
Sbjct: 74 AMLDKFGAR 82


>gi|300313658|ref|YP_003777750.1| transport transmembrane protein
          [Herbaspirillum seropedicae SmR1]
          Length = 404

 Score = 58.5 bits (140), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/57 (45%), Positives = 37/57 (64%)

Query: 37 VNYADRATLSIAGTSMKAELGLDPVMMGYIFSAFSWAYVLAQLPGGWLLDRFGSKKI 93
          V+Y DRA ++ A T + +E  L P  +G + S+F   Y L QLPGGWL DR+GS+ +
Sbjct: 24 VSYIDRAAITFAATQIASEFHLKPSDLGILLSSFFLGYSLLQLPGGWLADRYGSRPV 80


>gi|300309906|ref|YP_003773998.1| major facilitator superfamily
          permease [Herbaspirillum seropedicae SmR1]
          Length = 414

 Score = 54.7 bits (130), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/63 (44%), Positives = 36/63 (57%)

Query: 31 LFIVTTVNYADRATLSIAGTSMKAELGLDPVMMGYIFSAFSWAYVLAQLPGGWLLDRFGS 90
          LF+   V YADR  +S A   +  E  LD    G + SAF  +Y L QL GGWL DR+GS
Sbjct: 17 LFLAWAVGYADRIVMSTAIIPISKEFALDAQQAGMVLSAFYVSYALMQLMGGWLSDRYGS 76

Query: 91 KKI 93
          + +
Sbjct: 77 RIV 79


>gi|300313744|ref|YP_003777836.1| D-glucarate permease
          [Herbaspirillum seropedicae SmR1]
          Length = 441

 Score = 53.5 bits (127), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 47/83 (56%)

Query: 11 SASAKENIKPSHVRYLILFMLFIVTTVNYADRATLSIAGTSMKAELGLDPVMMGYIFSAF 70
          +A+ +   K +H R+++  ++FIV TV  ADRA L +A   ++ E  +     G + S F
Sbjct: 3  AAAIQHTKKKTHFRWVVGALIFIVYTVAAADRANLGVALPFLRKEFVMSNTEAGALASIF 62

Query: 71 SWAYVLAQLPGGWLLDRFGSKKI 93
           +AY LAQLP G    RFG  ++
Sbjct: 63 LFAYSLAQLPSGLAYTRFGIPRV 85


  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
   0.326    0.137    0.415 

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: 295,783
Number of extensions: 10001
Number of successful extensions: 99
Number of sequences better than 1.0e-08: 6
Number of HSP's gapped: 99
Number of HSP's successfully gapped: 6
Length of query: 107
Length of database: 1,619,870
Length adjustment: 72
Effective length of query: 35
Effective length of database: 1,278,950
Effective search space: 44763250
Effective search space used: 44763250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 124 (52.4 bits)