GapMind for catabolism of small carbon sources


Finding step PGA1_c12640 for D-lactate catabolism in Marivita geojedonensis DPG-138

3 candidates for PGA1_c12640: D-lactate ABC transporter, ATP-binding component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi MGEO_RS17175 ABC transporter ATP-binding protein D-lactate transporter, ATP-binding component (characterized) 80% 100% 408.7 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 38% 189.5
lo MGEO_RS10645 ABC transporter ATP-binding protein D-lactate transporter, ATP-binding component (characterized) 37% 99% 166.8 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 43% 168.3
lo MGEO_RS18510 urea ABC transporter ATP-binding protein UrtD D-lactate transporter, ATP-binding component (characterized) 35% 98% 163.3 UrtD, component of The high affinity urea/thiourea/hydroxyurea porter 43% 189.5

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.

Definition of step PGA1_c12640

Or cluster all characterized PGA1_c12640 proteins

This GapMind analysis is from Sep 24 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:

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