GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Dinoroseobacter shibae DFL-12

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-tyrosine transporter (AroP/FywP)
HPD 4-hydroxyphenylpyruvate dioxygenase
hmgA homogentisate dioxygenase Dshi_3812
maiA maleylacetoacetate isomerase Dshi_3308
fahA fumarylacetoacetate hydrolase Dshi_3811
atoA acetoacetyl-CoA transferase, A subunit Dshi_1136
atoD acetoacetyl-CoA transferase, B subunit Dshi_1134
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
Alternative steps:
aacS acetoacetyl-CoA synthetase Dshi_3403 Dshi_0833
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Dshi_0381 Dshi_1520
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Dshi_0375 Dshi_1981
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 Dshi_1978
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 Dshi_2696 Dshi_0861
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component
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 (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