GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Burkholderia phytofirmans PsJN

Best path

Ac3H11_2396, Ac3H11_1695, Ac3H11_1694, Ac3H11_1693, Ac3H11_1692, 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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component BPHYT_RS01885 BPHYT_RS15610
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 BPHYT_RS15605 BPHYT_RS31740
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 BPHYT_RS15600 BPHYT_RS31745
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 BPHYT_RS15595 BPHYT_RS31750
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 BPHYT_RS15590 BPHYT_RS31755
HPD 4-hydroxyphenylpyruvate dioxygenase BPHYT_RS18295 BPHYT_RS33445
hmgA homogentisate dioxygenase BPHYT_RS03800
maiA maleylacetoacetate isomerase BPHYT_RS02805 BPHYT_RS17615
fahA fumarylacetoacetate hydrolase BPHYT_RS03805 BPHYT_RS11790
atoA acetoacetyl-CoA transferase, A subunit BPHYT_RS13675 BPHYT_RS21415
atoD acetoacetyl-CoA transferase, B subunit BPHYT_RS13670 BPHYT_RS21420
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
Alternative steps:
aacS acetoacetyl-CoA synthetase BPHYT_RS19375 BPHYT_RS23420
aroP L-tyrosine transporter (AroP/FywP) BPHYT_RS15500 BPHYT_RS21680
CAT L-tyrosine transporter CAT BPHYT_RS33230 BPHYT_RS01785
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