GapMind for catabolism of small carbon sources


Finding step braF for L-alanine catabolism in Escherichia coli BW25113

4 candidates for braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med b3455 leucine/isoleucine/valine transporter subunit (NCBI) High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 71% 100% 371.7 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 100% 506.5
lo b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI) NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 35% 97% 151 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 100% 471.9
lo b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI) High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 98% 124.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 100% 749.2
lo b3454 ATP-binding component of leucine transport (VIMSS) NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 119.4 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF 100% 465.7

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step braF

Or cluster all characterized braF proteins

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



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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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