GapMind for catabolism of small carbon sources

 

Finding step rocA for L-arginine catabolism in Caulobacter crescentus NA1000

4 candidates for rocA: 1-pyrroline-5-carboxylate dehydrogenase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized) 52% 97% 963
hi CCNA_00846 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88) (TIGR01238) 99% 606.4
lo CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 91% 261.9 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) 100% 940.6
lo CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 88% 251.9 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) 56% 555.8
lo CCNA_02480 NAD-dependent benzaldehyde dehydrogenase II 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized) 32% 88% 235 vanillin dehydrogenase (EC 1.2.1.67) 54% 499.2

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 rocA

Or cluster all characterized rocA 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