GapMind for catabolism of small carbon sources

 

Finding step braF for L-arginine catabolism in Pandoraea thiooxydans ATSB16

4 candidates for braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PATSB16_RS05695 ABC transporter ATP-binding protein ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 93% 238.4 High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine 48% 246.1
med PATSB16_RS12750 ABC transporter ATP-binding protein ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 45% 91% 203 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 51% 244.6
med PATSB16_RS01005 ABC transporter ATP-binding protein ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 44% 90% 201.1 High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter 47% 228.0
med PATSB16_RS19085 branched-chain amino acid ABC transporter ATP-binding protein/permease ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 194.1 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 57% 666.8

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 braF

Or cluster all characterized braF 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