GapMind for catabolism of small carbon sources

 

Finding step pccA1 for L-isoleucine catabolism in Pseudomonas stutzeri RCH2

4 candidates for pccA1: propionyl-CoA carboxylase, biotin carboxyl carrier subunit

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Psest_4085 Biotin carboxylase acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 46% 93% 422.9 2-oxoglutarate carboxylase small subunit; 2-oxoglutarate carboxylase beta subunit; EC 6.4.1.7 53% 518.8
med Psest_1019 acetyl-CoA carboxylase, biotin carboxylase subunit acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 45% 88% 386 biotin carboxylase (EC 6.3.4.14) 86% 792.7
med Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 41% 97% 367.9 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) 77% 980.3
med Psest_2351 urea carboxylase acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) 40% 86% 333.6 urea carboxylase (EC 6.3.4.6) 56% 1302.3

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 pccA1

Or cluster all characterized pccA1 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, the preprint 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