GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Pseudomonas simiae WCS417

Best path

aroP, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

Also see fitness data for the top candidates

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.

19 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-tyrosine transporter (AroP/FywP) PS417_22235 PS417_23700
HPD 4-hydroxyphenylpyruvate dioxygenase PS417_14005 PS417_24445
hmgA homogentisate dioxygenase PS417_05015
maiA maleylacetoacetate isomerase PS417_05025 PS417_17970
fahA fumarylacetoacetate hydrolase PS417_05020 PS417_18185
atoA acetoacetyl-CoA transferase, A subunit PS417_10525
atoD acetoacetyl-CoA transferase, B subunit PS417_10520
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
Alternative steps:
aacS acetoacetyl-CoA synthetase PS417_12145 PS417_17010
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 PS417_06595 PS417_02675
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 PS417_06600 PS417_02670
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 PS417_06605 PS417_02665
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 PS417_02660 PS417_06610
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component PS417_02655 PS417_06615
CAT L-tyrosine transporter CAT
MCT10 L-tyrosine transporter MCT10
TAT1 L-tyrosine permease TAT1
tyrP Tyrosine permease
tyt1 L-tyrosine:Na+ symporter Tyt1

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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