GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Pseudomonas stutzeri RCH2

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) Psest_1697
HPD 4-hydroxyphenylpyruvate dioxygenase Psest_3514 Psest_4071
hmgA homogentisate dioxygenase Psest_3513
maiA maleylacetoacetate isomerase Psest_3511 Psest_3276
fahA fumarylacetoacetate hydrolase Psest_3512
atoA acetoacetyl-CoA transferase, A subunit Psest_1078
atoD acetoacetyl-CoA transferase, B subunit Psest_1077
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
Alternative steps:
aacS acetoacetyl-CoA synthetase Psest_1086 Psest_1334
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Psest_1308 Psest_3854
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Psest_1309 Psest_1089
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 Psest_1310 Psest_1093
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 Psest_1311 Psest_0566
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component Psest_1312
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