GapMind for catabolism of small carbon sources

 

Finding step malK for D-maltose catabolism in Sphingomonas koreensis DSMZ 15582

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

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Ga0059261_3668 ABC transporter Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 52% 137.5 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
lo Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 57% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5
lo Ga0059261_0494 ABC-type antimicrobial peptide transport system, ATPase component Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 54% 114 Uncharacterized ABC transporter ATP-binding protein Rv0986 38% 132.1
lo Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 56% 112.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
lo Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 30% 59% 111.3 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) 54% 257.7

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

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 (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:

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. 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:

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 paper from 2022 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