GapMind for catabolism of small carbon sources

 

Finding step gabT for L-arginine catabolism in Shewanella loihica PV-4

5 candidates for gabT: gamma-aminobutyrate transaminase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Shew_3172 4-aminobutyrate aminotransferase (RefSeq) 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 55% 99% 464.2 5-aminovalerate transaminase (EC 2.6.1.48) 55% 469.5
med Shew_3172 4-aminobutyrate aminotransferase (RefSeq) gabT: 4-aminobutyrate transaminase (EC 2.6.1.19) (TIGR00700) 98% 579.9 5-aminovalerate transaminase (EC 2.6.1.48) 55% 469.5
lo Shew_0966 beta alanine--pyruvate transaminase (RefSeq) Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized) 39% 94% 300.8 beta-alanine-pyruvate transaminase (EC 2.6.1.18) 61% 545.4
lo Shew_0578 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq) 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 37% 91% 228.4 Succinylornithine transaminase (EC 2.6.1.81) 66% 547.4
lo Shew_1718 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq) Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized) 30% 97% 189.5 adenosylmethionine-8-amino-7-oxononanoate transaminase (EC 2.6.1.62) 61% 507.7
lo Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq) 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized) 31% 85% 171.4 Glutamate-1-semialdehyde 2,1-aminomutase; GSA; Glutamate-1-semialdehyde aminotransferase; GSA-AT; EC 5.4.3.8 71% 643.3

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 gabT

Or cluster all characterized gabT proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 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