Finding step malK for D-maltose catabolism in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Finding step malK for D-maltose catabolism in Pseudomonas stutzeri RCH2

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

Score	Gene	Description	Similar to	Id.	Cov.	Bits	Other hit	Other id.	Other bits
hi	Psest_0871	ABC-type sugar transport systems, ATPase components	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	100%	100%	738.4	ABC transporter for D-Sorbitol, ATPase component	58%	394.4
med	Psest_1899	ABC-type sugar transport systems, ATPase components	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	47%	96%	310.1	ABC transporter for D-Galactose and D-Glucose, ATPase component	78%	559.7
med	Psest_3658	spermidine/putrescine ABC transporter ATP-binding subunit	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	45%	77%	250	Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD	48%	319.7
med	Psest_4282	spermidine/putrescine ABC transporter ATP-binding subunit	Maltose-transporting ATPase (EC 3.6.3.19) (characterized)	41%	77%	227.3	PotG aka B0855, component of Putrescine porter	64%	437.6

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Also see fitness data for the candidates

Definition of step malK

Curated sequence P68187: ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1). maltose/maltodextrin import ATP-binding protein malK; EC 3.6.3.19. Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1. Maltose/maltodextrin import ATP-binding protein MalK aka B4035, component of Maltooligosaccharide porter. The 3-D structure has been reported by Oldham et al. (2007). An altering access mechanism has been suggested for the maltose transporter resulting from rigid-body rotations (Khare et al., 2009). Bordignon et al. (2010) and Schneider et al. (2012) have reviewed the extensive knowledge available on MalEFGK2, its mode of action and its regulatory interactions. maltose ABC transporter ATP binding subunit (EC 7.5.2.1). maltose ABC transporter ATP binding subunit (EC 7.5.2.1)
Curated sequence P19566: Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1
Curated sequence GFF857: Maltose-transporting ATPase (EC 3.6.3.19)

Or cluster all characterized malK proteins

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources