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= 0001.2252.p
         (139 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR ...   238   1e-64
gi|300310024|ref|YP_003774116.1| biopolymer transport ExbD/TolR ...   128   2e-31
gi|300309939|ref|YP_003774031.1| biopolymer transport ExbD/TolR ...   103   6e-24

>gi|300312126|ref|YP_003776218.1| biopolymer transport ExbD/TolR
           protein [Herbaspirillum seropedicae SmR1]
          Length = 139

 Score =  238 bits (608), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 130/139 (93%), Positives = 136/139 (97%)

Query: 1   MSMMNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASK 60
           MSMMNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASK
Sbjct: 1   MSMMNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASK 60

Query: 61  DIDISIQADGTVLWNRVPANLDELRTRVAAAAAAAVPPAVNVYADEKVPYGSVARVLAGV 120
           DIDISIQADGTVLWNRVPANLDELR  V AAAAAAVPPAVNVYADE+VPYGSVA+VLAGV
Sbjct: 61  DIDISIQADGTVLWNRVPANLDELRAHVVAAAAAAVPPAVNVYADEQVPYGSVAKVLAGV 120

Query: 121 QSGGLTKINFVTEPVKDTQ 139
           Q+GGL++INFVTEPVK+TQ
Sbjct: 121 QAGGLSRINFVTEPVKETQ 139


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

 Score =  128 bits (322), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 65/136 (47%), Positives = 89/136 (65%), Gaps = 1/136 (0%)

Query: 1   MSMMNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASK 60
           M  ++D+  D    EIN TPL+DVMLVLLIIFI+T+P +N AVK+ LPKA++QP +   +
Sbjct: 3   MGSLSDSDDD-FNPEINTTPLVDVMLVLLIIFIITIPVMNHAVKIDLPKASSQPDQVKPE 61

Query: 61  DIDISIQADGTVLWNRVPANLDELRTRVAAAAAAAVPPAVNVYADEKVPYGSVARVLAGV 120
            I++SI A G V WN    +  EL  R+AAAA     P +++ A+    Y  VA+V++  
Sbjct: 62  SINLSIDASGNVFWNEEKIDSGELSVRIAAAAQKQPQPELHLRAERTTQYEKVAQVMSAA 121

Query: 121 QSGGLTKINFVTEPVK 136
           QSGGL KI FVT+P K
Sbjct: 122 QSGGLAKIGFVTDPDK 137


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

 Score =  103 bits (257), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 51/131 (38%), Positives = 76/131 (58%)

Query: 4   MNDAGGDGLATEINMTPLIDVMLVLLIIFIVTLPAINQAVKVTLPKATAQPTETASKDID 63
            ND        +IN+TP++DVMLVLL+IFI+T P    A+K+ LP A + P     + I 
Sbjct: 6   FNDNQNSAPMADINVTPMVDVMLVLLVIFIITAPMFTHALKLDLPTAQSAPAPEKPETIT 65

Query: 64  ISIQADGTVLWNRVPANLDELRTRVAAAAAAAVPPAVNVYADEKVPYGSVARVLAGVQSG 123
           + I A G + WN  P + +EL  R+ AAA     P + + AD+   Y ++A V++  Q  
Sbjct: 66  LGIDAAGKLYWNDQPVSSEELDARLTAAAGKQPQPELQLRADKSTRYQTIAEVMSAAQGA 125

Query: 124 GLTKINFVTEP 134
           GL+K+ FVT+P
Sbjct: 126 GLSKLGFVTDP 136


  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
   0.316    0.131    0.362 

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: 372,709
Number of extensions: 11280
Number of successful extensions: 64
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 63
Number of HSP's successfully gapped: 4
Length of query: 139
Length of database: 1,619,870
Length adjustment: 76
Effective length of query: 63
Effective length of database: 1,260,010
Effective search space: 79380630
Effective search space used: 79380630
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: 126 (53.1 bits)