GapMind for catabolism of small carbon sources


Finding step patA for putrescine catabolism in Pseudomonas fluorescens FW300-N1B4

5 candidates for patA: putrescine aminotransferase (PatA/SpuC)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_2257 Omega-amino acid--pyruvate aminotransferase (EC putrescine-pyruvate transaminase (EC (characterized) 80% 82% 647.1
lo Pf1N1B4_1239 Omega-amino acid--pyruvate aminotransferase (EC putrescine-pyruvate transaminase (EC (characterized) 36% 97% 280.4 Omega-amino acid--pyruvate aminotransferase; Omega-APT; Beta-alanine--pyruvate aminotransferase; EC 94% 858.6
lo Pf1N1B4_2980 Acetylornithine aminotransferase (EC putrescine-2-oxoglutarate transaminase (EC (characterized) 37% 84% 235.7 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:] 44% 296.2
lo Pf1N1B4_2377 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC putrescine-pyruvate transaminase (EC (characterized) 32% 96% 234.6 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase; 7,8-diamino-pelargonic acid aminotransferase; DAPA AT; DAPA aminotransferase; 7,8-diaminononanoate synthase; DANS; Diaminopelargonic acid synthase; EC 54% 495.4
lo Pf1N1B4_3440 Succinylornithine transaminase (EC Putrescine aminotransferase; PAT; PATase; EC; Cadaverine transaminase; EC 2.6.1.-; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase (uncharacterized) 37% 81% 211.8 Succinylornithine transaminase (EC 100% 808.5

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 patA

Or cluster all characterized patA 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