GapMind for catabolism of small carbon sources

 

Finding step proV for L-proline catabolism in Bacteroides thetaiotaomicron VPI-5482

4 candidates for proV: proline ABC transporter, ATPase component ProV

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file) glycine betaine/l-proline transport atp-binding protein prov (characterized) 47% 99% 367.1 Glycine betaine/carnitine transport ATP-binding protein GbuA; EC 7.6.2.9 53% 417.5
lo BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file) Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 32% 74% 164.5 Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD 53% 366.3
lo BT1214 putative ABC transporter ATP-binding protein (NCBI ptt file) glycine betaine/l-proline transport atp-binding protein prov (characterized) 37% 58% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 234.2
lo BT3839 ABC transporter ATP-binding protein (NCBI ptt file) Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 31% 65% 135.6 Probable bifunctional ABC transport system, component of The cholesterol uptake porter (Mohn et al., 2008). Takes up cholesterol, 5-α-cholestanol, 5-α-cholestanone, β-sitosterol, etc. (It is not established that all of these proteins comprise the system or that other gene products are not involved.) 36% 170.2

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 proV

Or cluster all characterized proV 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