GapMind for catabolism of small carbon sources

 

Finding step hutV for L-proline catabolism in Pseudomonas putida KT2440

4 candidates for hutV: proline ABC transporter, ATPase component HutV

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PP_0294 choline / betaine / carnitine ABC transporter - ATP binding subunit HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 46% 99% 236.9 ABC transporter for Carnitine, ATPase component 87% 677.6
med PP_2774 glycine betaine ABC transporter, ATPase/permease fusion protein HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 50% 87% 235.7 ABC transporter for L-Histidine, ATPase component 52% 240.4
med PP_5137 ferric iron ABC transporter, ATP-binding protein HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 87% 174.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 44% 252.3
lo PP_0868 ABC transporter ATP-binding subunit HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 95% 177.2 ABC-type quaternary amine transporter (EC 7.6.2.9) 90% 694.1

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 hutV

Or cluster all characterized hutV 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