GapMind for catabolism of small carbon sources

 

Finding step braF for L-arginine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_04060 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 47% 90% 213 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 50% 244.6
med H281DRAFT_02383 amino acid/amide ABC transporter membrane protein 2, HAAT family /amino acid/amide ABC transporter ATP-binding protein 1, HAAT family ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 42% 89% 184.5 Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 60% 686.0
lo H281DRAFT_01586 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 38% 89% 155.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 43% 188.0
lo H281DRAFT_05513 branched-chain amino acid transport system permease protein ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 37% 90% 154.8 ABC amino acid transporter, ATP-binding, component of Uptake transporter, CamABCD of cholate (steroid) metabolites, 1β(2'-propanoate)-3aα-H-4α(3"(R)-hydroxy-3"-propanoate)-7aβ-methylhexahydro-5-indanone and a desaturated analog 35% 309.7

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 braF

Or cluster all characterized braF 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