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= 0001.2378.p
         (137 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR ...   156   5e-40
gi|300311921|ref|YP_003776013.1| biopolymer transport ExbD/TolR ...    82   1e-17
gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ...    57   6e-10

>gi|300309635|ref|YP_003773727.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 135

 Score =  156 bits (395), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 77/136 (56%), Positives = 106/136 (77%), Gaps = 2/136 (1%)

Query: 1   MRSWGETEKRRARIEIIPMIDVMMFLLVFFVLLSLNVIPALGIKTSLPSSSSASDLQTQH 60
           MRSW E +KR+AR+EIIPMIDVMMFLLVFFVL+SLNVIPALG+KT LPSSS+A DL+ Q 
Sbjct: 1   MRSWDEPKKRKARVEIIPMIDVMMFLLVFFVLISLNVIPALGLKTQLPSSSTAQDLKPQT 60

Query: 61  IARIALGVDGELELEGKPIKLDALVPNLKQLQQKEPGKKLVLIVNADQKIEFQRVIDLMD 120
            A I +  D  ++++G+   LDAL   L +L+ +  G+KL LI+N+D+ +E QR++D+MD
Sbjct: 61  KAVITIAKDEVIQVDGENTTLDALTARLDKLRHE--GEKLNLIINSDRGVEVQRLVDVMD 118

Query: 121 TLKGNGFDALSFVSKR 136
           TLK  GFD++S  +++
Sbjct: 119 TLKKGGFDSISIATRK 134


>gi|300311921|ref|YP_003776013.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 132

 Score = 82.0 bits (201), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/124 (35%), Positives = 76/124 (61%), Gaps = 4/124 (3%)

Query: 13  RIEIIPMIDVMMFLLVFFVLLSLNVIPALGIKTSLPSSSSASDLQTQHIARIALGVDGEL 72
            IEIIPMID+MMFLL+FF++  L +I   G+K ++P ++SA+ L ++ +  I +   G +
Sbjct: 13  HIEIIPMIDIMMFLLIFFMVTMLKMIDVSGLKINVPQAASAATLPSKSLT-IVVDKTGAM 71

Query: 73  ELEGKPIKLDALVPNLKQLQQKEPGKKLVLIVNADQKIEFQRVIDLMDTLKGNGFDALSF 132
             EGKP++ DALV  LK+  Q     KL ++V  D+++  + ++ +MD  +  G + +  
Sbjct: 72  FFEGKPLEHDALVAQLKERAQT---AKLEVLVAGDKEVSLENLLHVMDVARAAGIEDIGI 128

Query: 133 VSKR 136
            +K 
Sbjct: 129 AAKH 132


>gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 148

 Score = 56.6 bits (135), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 41/128 (32%), Positives = 64/128 (50%), Gaps = 8/128 (6%)

Query: 12  ARIEIIPMIDVMMFLLVFFVLLSLNVIPALGIKTSLPSSSSASDLQTQHIARIALGVD-- 69
           A I + PM+DVM+ LLV F++ +     AL  K  LP++ SA   +      I LG+D  
Sbjct: 16  ADINVTPMVDVMLVLLVIFIITAPMFTHAL--KLDLPTAQSAPAPEKPET--ITLGIDAA 71

Query: 70  GELELEGKPIKLDALVPNLKQLQQKEPGKKLVLIVNADQKIEFQRVIDLMDTLKGNGFDA 129
           G+L    +P+  + L   L     K+P  +L L   AD+   +Q + ++M   +G G   
Sbjct: 72  GKLYWNDQPVSSEELDARLTAAAGKQPQPELQL--RADKSTRYQTIAEVMSAAQGAGLSK 129

Query: 130 LSFVSKRK 137
           L FV+  K
Sbjct: 130 LGFVTDPK 137


  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
   0.321    0.138    0.378 

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: 340,604
Number of extensions: 10853
Number of successful extensions: 41
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 38
Number of HSP's successfully gapped: 3
Length of query: 137
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 61
Effective length of database: 1,260,010
Effective search space: 76860610
Effective search space used: 76860610
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 (21.8 bits)
S2: 126 (53.1 bits)