GapMind for catabolism of small carbon sources

 

Finding step potA for putrescine catabolism in Dyella japonica UNC79MFTsu3.2

5 candidates for potA: putrescine ABC transporter, ATPase component (PotA/PotG)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med N515DRAFT_1562 sulfate transport system ATP-binding protein PotG aka B0855, component of Putrescine porter (characterized) 41% 92% 242.3 CysA aka B2422, component of Sulfate/thiosulfate porter 55% 297.4
med N515DRAFT_4212 multiple sugar transport system ATP-binding protein PotG aka B0855, component of Putrescine porter (characterized) 42% 76% 210.7 ABC-type maltose transporter (EC 7.5.2.1) 54% 375.2
lo N515DRAFT_1085 D-methionine transport system ATP-binding protein spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 36% 62% 154.5 Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN 71% 458.8
lo N515DRAFT_1821 putative ABC transport system ATP-binding protein Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 39% 59% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 208.8
lo N515DRAFT_2307 molybdate/tungstate transport system ATP-binding protein PotG aka B0855, component of Putrescine porter (characterized) 33% 86% 140.2 Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter 39% 151.4

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 potA

Or cluster all characterized potA 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, the preprint on GapMind for carbon sources, 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