GapMind for catabolism of small carbon sources

 

Finding step HSERO_RS00895 for L-proline catabolism in Cupriavidus basilensis 4G11

4 candidates for HSERO_RS00895: proline ABC transporter, ATPase component 1

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi RR42_RS16965 ABC transporter ABC transporter ATP-binding protein (characterized, see rationale) 75% 98% 383.3 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 48% 237.3
hi RR42_RS34795 leucine/isoleucine/valine transporter ATP-binding subunit ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 46% 98% 233 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 41% 197.2
med RR42_RS14410 leucine/isoleucine/valine transporter ATP-binding subunit ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 245 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 63% 328.6
med RR42_RS20240 hypothetical protein ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 46% 99% 217.6 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 58% 672.5

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 HSERO_RS00895

Or cluster all characterized HSERO_RS00895 proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 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