GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02161 H281DRAFT_04063
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 H281DRAFT_04062 H281DRAFT_06397
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 H281DRAFT_04061
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 H281DRAFT_04060 H281DRAFT_02383
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 H281DRAFT_04059 H281DRAFT_02384
HPD 4-hydroxyphenylpyruvate dioxygenase H281DRAFT_05849 H281DRAFT_03867
hmgA homogentisate dioxygenase H281DRAFT_04741
maiA maleylacetoacetate isomerase H281DRAFT_01970 H281DRAFT_05672
fahA fumarylacetoacetate hydrolase H281DRAFT_04742 H281DRAFT_02070
atoA acetoacetyl-CoA transferase, A subunit H281DRAFT_04495 H281DRAFT_01597
atoD acetoacetyl-CoA transferase, B subunit H281DRAFT_04496 H281DRAFT_01596
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
Alternative steps:
aacS acetoacetyl-CoA synthetase H281DRAFT_02398 H281DRAFT_06226
aroP L-tyrosine transporter (AroP/FywP) H281DRAFT_04042 H281DRAFT_01668
CAT L-tyrosine transporter CAT H281DRAFT_02180
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