GapMind for catabolism of small carbon sources


Finding step frcA for sucrose catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for frcA: fructose ABC transporter, ATPase component FrcA

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Pf1N1B4_4286 Inositol transport system ATP-binding protein ABC-type sugar transport system, ATP-binding protein; EC (characterized, see rationale) 46% 94% 401.4 m-Inositol ABC transporter, ATPase component (itaA) 96% 976.5
med Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2) ABC-type sugar transport system, ATP-binding protein; EC (characterized, see rationale) 44% 89% 355.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 59% 572.0
lo Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1) ABC-type sugar transport system, ATP-binding protein; EC (characterized, see rationale) 38% 94% 314.3 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 42% 354.8
lo Pf1N1B4_1243 ABC transporter ATP-binding protein ABC-type sugar transport system, ATP-binding protein; EC (characterized, see rationale) 35% 94% 267.7 Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement 39% 344.0

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 frcA

Or cluster all characterized frcA 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