GapMind for catabolism of small carbon sources


Finding step malK for D-maltose catabolism in Phaeobacter inhibens BS107

5 candidates for malK: maltose ABC transporter, ATPase component MalK

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PGA1_c16680 sugar ABC transporter, ATP-binding protein Maltose/maltodextrin import ATP-binding protein MalK; EC (characterized) 54% 98% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 52% 365.5
med PGA1_c07440 ABC transporter, ATP binding protein Maltose/maltodextrin import ATP-binding protein MalK; EC (characterized) 53% 99% 344.4 ABC transporter for Lactose, ATPase component 56% 373.6
med PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK ABC-type maltose transporter (subunit 3/3) (EC (characterized) 50% 96% 333.6 ABC transporter for D-Maltose and D-Trehalose, ATPase component 65% 447.2
med PGA1_78p00190 sn-glycerol-3-phosphate import ATP-binding protein UgbC Maltose-transporting ATPase (EC (characterized) 48% 96% 311.2 ABC transporter for D-Cellobiose and D-Salicin, ATPase component 63% 439.1
lo PGA1_c27970 ATP-binding transport protein SmoK ABC-type maltose transporter (subunit 3/3) (EC (characterized) 64% 66% 313.9 N-Acetyl-D-glucosamine ABC transport system, ATPase component 100% 651.0

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 malK

Or cluster all characterized malK 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