GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Pseudomonas fluorescens FW300-N2C3

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-tyrosine transporter (AroP/FywP) AO356_18530 AO356_17670
HPD 4-hydroxyphenylpyruvate dioxygenase AO356_22845 AO356_15580
hmgA homogentisate dioxygenase AO356_16825
maiA maleylacetoacetate isomerase AO356_16835 AO356_11540
fahA fumarylacetoacetate hydrolase AO356_16830 AO356_29105
atoA acetoacetyl-CoA transferase, A subunit AO356_21650
atoD acetoacetyl-CoA transferase, B subunit AO356_21645
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
Alternative steps:
aacS acetoacetyl-CoA synthetase AO356_00425 AO356_01575
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 AO356_05340 AO356_08480
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 AO356_05335 AO356_08485
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 AO356_05330 AO356_08490
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 AO356_08495 AO356_05325
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component AO356_08500 AO356_05320
CAT L-tyrosine transporter CAT
MCT10 L-tyrosine transporter MCT10
TAT1 L-tyrosine permease TAT1
tyrP Tyrosine permease
tyt1 L-tyrosine:Na+ symporter Tyt1 AO356_07535

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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