GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Cupriavidus basilensis 4G11

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 RR42_RS16980 RR42_RS20120
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 RR42_RS16975 RR42_RS14420
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 RR42_RS16970 RR42_RS14415
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 RR42_RS16965 RR42_RS34795
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 RR42_RS16960 RR42_RS14405
HPD 4-hydroxyphenylpyruvate dioxygenase RR42_RS33500 RR42_RS32440
hmgA homogentisate dioxygenase RR42_RS31275
maiA maleylacetoacetate isomerase RR42_RS01970 RR42_RS30510
fahA fumarylacetoacetate hydrolase RR42_RS31270 RR42_RS09905
atoA acetoacetyl-CoA transferase, A subunit RR42_RS06555 RR42_RS35925
atoD acetoacetyl-CoA transferase, B subunit RR42_RS06560 RR42_RS35920
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
Alternative steps:
aacS acetoacetyl-CoA synthetase RR42_RS26915 RR42_RS10085
aroP L-tyrosine transporter (AroP/FywP) RR42_RS33495 RR42_RS28305
CAT L-tyrosine transporter CAT RR42_RS01585
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.

Links

Downloads

Related tools

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