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= 0004.0015.p
         (142 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-relat...   269   6e-74
gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ...    71   3e-14
gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ...    60   7e-11

>gi|300310501|ref|YP_003774593.1| biopolymer transport ExbD-related
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 142

 Score =  269 bits (688), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 129/142 (90%), Positives = 138/142 (97%)

Query: 1   MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQVTLPTADAQKALEQPFE 60
           MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQ+TLPTADA KALEQPFE
Sbjct: 1   MNFRKGRPREDLEINLIPFIDVLLVIVIFLMVTTTYSKFTALQLTLPTADAPKALEQPFE 60

Query: 61  INIAIDANGRYAINNKRIAARDAQGLSEEMQAAVRSSGSKADPVIIINADALATHQTVVN 120
           +NIA+DANGRYA+NNKRI+ARDAQGLSEEMQA VR+S SK DPVIIINADALATHQTVVN
Sbjct: 61  LNIAVDANGRYALNNKRISARDAQGLSEEMQAVVRASASKLDPVIIINADALATHQTVVN 120

Query: 121 VMEAARMAGYPKLTFAAQSSSK 142
           V+EAARMAGYPK+TFAAQ+SSK
Sbjct: 121 VLEAARMAGYPKVTFAAQASSK 142


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

 Score = 71.2 bits (173), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/125 (35%), Positives = 73/125 (58%), Gaps = 11/125 (8%)

Query: 13  EINLIPFIDVLLVIVIFLMVTTTYSKFT-ALQVTLPTADAQKALEQPFEINIAIDANGRY 71
           +IN+ P +DV+LV+++  ++T     FT AL++ LPTA +  A E+P  I + IDA G+ 
Sbjct: 17  DINVTPMVDVMLVLLVIFIITAPM--FTHALKLDLPTAQSAPAPEKPETITLGIDAAGKL 74

Query: 72  AINNKRIAARDAQGLSEEMQAAVR-SSGSKADPVIIINADALATHQTVVNVMEAARMAGY 130
             N++ ++       SEE+ A +  ++G +  P + + AD    +QT+  VM AA+ AG 
Sbjct: 75  YWNDQPVS-------SEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGAGL 127

Query: 131 PKLTF 135
            KL F
Sbjct: 128 SKLGF 132


>gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 138

 Score = 60.1 bits (144), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 67/130 (51%), Gaps = 7/130 (5%)

Query: 13  EINLIPFIDVLLVIVIFLMVTTTYSKFTALQVTLPTADAQKALEQPFEINIAIDANGRYA 72
           EIN  P +DV+LV++I  ++T       A+++ LP A +Q    +P  IN++IDA+G   
Sbjct: 16  EINTTPLVDVMLVLLIIFIITIPVMNH-AVKIDLPKASSQPDQVKPESINLSIDASGNVF 74

Query: 73  INNKRIAARDAQGLSEEMQAAVRSSGSKADPVIIINADALATHQTVVNVMEAARMAGYPK 132
            N ++I   D+  LS  + AA +    +  P + + A+    ++ V  VM AA+  G  K
Sbjct: 75  WNEEKI---DSGELSVRIAAAAQ---KQPQPELHLRAERTTQYEKVAQVMSAAQSGGLAK 128

Query: 133 LTFAAQSSSK 142
           + F      K
Sbjct: 129 IGFVTDPDKK 138


  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
   0.319    0.131    0.351 

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: 364,227
Number of extensions: 12191
Number of successful extensions: 50
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 50
Number of HSP's successfully gapped: 4
Length of query: 142
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 66
Effective length of database: 1,260,010
Effective search space: 83160660
Effective search space used: 83160660
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)