GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Rhizobium etli CFN 42

Best path

aroP, HPD, hmgA, maiA, fahA, aacS, atoB

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) RHE_RS25845
HPD 4-hydroxyphenylpyruvate dioxygenase RHE_RS08930 RHE_RS23940
hmgA homogentisate dioxygenase RHE_RS08935
maiA maleylacetoacetate isomerase RHE_RS08945 RHE_RS12310
fahA fumarylacetoacetate hydrolase RHE_RS08940 RHE_RS00085
aacS acetoacetyl-CoA synthetase RHE_RS03640 RHE_RS04635
atoB acetyl-CoA C-acetyltransferase RHE_RS20545 RHE_RS23190
Alternative steps:
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 RHE_RS16995 RHE_RS25475
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 RHE_RS17000 RHE_RS25470
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 RHE_RS17005
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 RHE_RS17010
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component RHE_RS16985 RHE_RS15820
atoA acetoacetyl-CoA transferase, A subunit RHE_RS25065
atoD acetoacetyl-CoA transferase, B subunit RHE_RS25070
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 Apr 09 2024. 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:

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