GapMind for catabolism of small carbon sources

 

Finding step PS417_11890 for myo-inositol catabolism in Pseudomonas simiae WCS417

5 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 PS417_11890 D-ribose transporter ATP-binding protein Inositol transport system ATP-binding protein (characterized) 100% 100% 1003.4 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 50% 474.6
hi PS417_12065 D-ribose transporter ATP-binding protein m-Inositol ABC transporter, ATPase component (itaA) (characterized) 45% 94% 402.9 ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 43% 356.7
med PS417_13635 D-ribose transporter ATP-binding protein Inositol transport system ATP-binding protein (characterized) 46% 95% 417.9 Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 46% 424.9
med PS417_17730 ribonucleotide-diphosphate reductase subunit alpha m-Inositol ABC transporter, ATPase component (itaA) (characterized) 43% 95% 405.6 Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 44% 409.5
med PS417_21330 L-arabinose transporter ATP-binding protein Inositol transport system ATP-binding protein (characterized) 42% 94% 397.5 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 61% 586.6

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 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