GapMind for catabolism of small carbon sources

 

Definition of L-tyrosine catabolism

As rules and steps, or see full text

Rules

Overview: Tyrosine utilization in GapMind is based on MetaCyc pathway tyrosine degradation I, via homogentisate (link). This pathway requires oxygen. Another pathway via 4-hydroxyphenylacetate is known (link), but the 4-hydroxyphenylpyruvate oxidase has not been linked to sequence. The other MetaCyc pathways do not yield fixed carbon or are not reported in prokaryotes.

Steps

aroP: L-tyrosine transporter (AroP/FywP)

Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component

Ac3H11_1695: L-tyrosine ABC transporter, permease component 1

Ac3H11_1694: L-tyrosine ABC transporter, permease component 2

Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1

Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2

tyrP: Tyrosine permease

TAT1: L-tyrosine permease TAT1

MCT10: L-tyrosine transporter MCT10

CAT: L-tyrosine transporter CAT

tyt1: L-tyrosine:Na+ symporter Tyt1

atoA: acetoacetyl-CoA transferase, A subunit

atoD: acetoacetyl-CoA transferase, B subunit

aacS: acetoacetyl-CoA synthetase

atoB: acetyl-CoA C-acetyltransferase

HPD: 4-hydroxyphenylpyruvate dioxygenase

hmgA: homogentisate dioxygenase

maiA: maleylacetoacetate isomerase

fahA: fumarylacetoacetate hydrolase

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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