GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ady2 in Escherichia coli BW25113

Align Acetate permease A; Monocarboxylate transporter acpA (characterized)
to candidate 14155 b0010 conserved inner membrane protein associated with acetate transport (NCBI)

Query= SwissProt::Q5B2K4
         (298 letters)



>FitnessBrowser__Keio:14155
          Length = 188

 Score =  108 bits (270), Expect = 9e-29
 Identities = 67/197 (34%), Positives = 100/197 (50%), Gaps = 17/197 (8%)

Query: 81  KFANPAPLGLSAFALTTFVLSCINMGARDITHPNIVIALAFGYGGLVQLLAGMWEMAVGN 140
           K ANPAPLGL  F +TT +L+  N+G   +    I++A+   YGG+ Q+ AG+ E   GN
Sbjct: 5   KLANPAPLGLMGFGMTTILLNLHNVGYFALD--GIILAMGIFYGGIAQIFAGLLEYKKGN 62

Query: 141 TFGATALSSYGGFWIAFAIVLTPGGFNIQTALTAENGDEAMFYNSFGLFLMGWFIFTTIM 200
           TFG TA +SYG FW+    +L      +   L   +   A F    G++L  W +FT  M
Sbjct: 63  TFGLTAFTSYGSFWLTLVAIL------LMPKLGLTDAPNAQF---LGVYLGLWGVFTLFM 113

Query: 201 LFCTLRSTVAFFLLFLFLDLAFLLLGVGYIQRDDAGQPNPPVIKAGGFFGLLAAFAAWYN 260
            F TL+       +F  L + F LL +G I    AG  N  +I   G+ GL+   +A Y 
Sbjct: 114 FFGTLKGARVLQFVFFSLTVLFALLAIGNI----AG--NAAIIHFAGWIGLICGASAIYL 167

Query: 261 ALAGIADSSNSFFIIPV 277
           A+  + +      ++P+
Sbjct: 168 AMGEVLNEQFGRTVLPI 184


Lambda     K      H
   0.324    0.139    0.436 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 169
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 298
Length of database: 188
Length adjustment: 23
Effective length of query: 275
Effective length of database: 165
Effective search space:    45375
Effective search space used:    45375
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory