GapMind for catabolism of small carbon sources

 

L-tyrosine catabolism in Pseudomonas fluorescens FW300-N1B4

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) Pf1N1B4_3559 Pf1N1B4_801
HPD 4-hydroxyphenylpyruvate dioxygenase Pf1N1B4_5003 Pf1N1B4_2747
hmgA homogentisate dioxygenase Pf1N1B4_1025
maiA maleylacetoacetate isomerase Pf1N1B4_1023 Pf1N1B4_1955
fahA fumarylacetoacetate hydrolase Pf1N1B4_1024
atoA acetoacetyl-CoA transferase, A subunit Pf1N1B4_5833
atoD acetoacetyl-CoA transferase, B subunit Pf1N1B4_5834
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf1N1B4_5634 Pf1N1B4_3988
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Pf1N1B4_3214 Pf1N1B4_1378
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Pf1N1B4_3215 Pf1N1B4_1379
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 Pf1N1B4_3216 Pf1N1B4_1380
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 Pf1N1B4_1381 Pf1N1B4_3217
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component Pf1N1B4_3218 Pf1N1B4_1382
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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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