GapMind for catabolism of small carbon sources

 

Finding step PS417_11890 for myo-inositol catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for PS417_11890: myo-inositol ABC transporter, ATPase component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_4286 Inositol transport system ATP-binding protein m-Inositol ABC transporter, ATPase component (itaA) (characterized) 96% 100% 976.5 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 50% 473.0
med Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2) Inositol transport system ATP-binding protein (characterized) 42% 94% 394 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 59% 572.0
lo Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1) Inositol transport system ATP-binding protein (characterized) 39% 94% 347.8 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 m-Inositol ABC transporter, ATPase component (itaA) (characterized) 34% 93% 268.5 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 PS417_11890

Or cluster all characterized PS417_11890 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