As text, or see rules and steps
# Tyrosine utilization in GapMind is based on MetaCyc pathway # tyrosine degradation I, via homogentisate (metacyc:TYRFUMCAT-PWY). # This pathway requires oxygen. # Another pathway via 4-hydroxyphenylacetate is known (metacyc:PWY-5151), # 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. aroP L-tyrosine transporter (AroP/FywP) curated:TCDB::F2HN33 curated:TCDB::P15993 curated:TCDB::Q46065 curated:reanno::pseudo5_N2C3_1:AO356_18530 curated:SwissProt::A2RMP5 # Transporters were identified using # query: transporter:tyrosine:L-tyrosine:tyr. # The ABC transporter livFGHM (with substrate-binding component livK or livJ) may be able to # transport tyrosine, but it did not suffice to enable growth of a tyrosine auxotroph # (PMC305776), so it is not included. tyrosine-transport: aroP # A 5-part ABC transporter for tyrosine and other amino acids was identified in Acidovorax sp. GW101-3H11. # It is related to branched-amino-acid transporters. # The substrate-binding component (Ac3H11_2396) is not nearby but is cofit. Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component uniprot:A0A165KTD4 Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 uniprot:A0A165KC95 Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 uniprot:A0A165KER0 Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 uniprot:A0A165KC86 Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 uniprot:A0A165KC78 tyrosine-transport: Ac3H11_2396 Ac3H11_1695 Ac3H11_1694 Ac3H11_1693 Ac3H11_1692 tyrP Tyrosine permease curated:TCDB::P0AAD4 tyrosine-transport: tyrP TAT1 L-tyrosine permease TAT1 curated:CharProtDB::CH_091631 tyrosine-transport: TAT1 MCT10 L-tyrosine transporter MCT10 curated:SwissProt::Q91Y77 tyrosine-transport: MCT10 CAT L-tyrosine transporter CAT curated:TCDB::ALD51314.1 tyrosine-transport: CAT tyt1 L-tyrosine:Na+ symporter Tyt1 curated:TCDB::Q8RHM5 tyrosine-transport: tyt1 # Porins such as opdT are not included # The amino acid exchanger protein SteT (O34739) is not included # because it is not expected to support growth on tyrosine. Related # metazoan proteins are also not included. Similarly, 4F2_HUMAN / # P08195 and P_HUMAN / Q04671 are not included. # Amino acid exporters such as E. coli yddG are not included. # Steps for acetoacetate utilization import leucine.steps:acetoacetate-degradation # Q8EKK9 and Q9RSJ4 are misannotated in BRENDA HPD 4-hydroxyphenylpyruvate dioxygenase EC:1.13.11.27 ignore:BRENDA::Q8EKK9 ignore:BRENDA::Q9RSJ4 hmgA homogentisate dioxygenase EC:1.13.11.5 maiA maleylacetoacetate isomerase EC:5.2.1.2 fahA fumarylacetoacetate hydrolase EC:3.7.1.2 # In pathway I, an aminotransferase (not represented) forms 3-(4-hydroxyphenyl)pyruvate, # dioxygenase HPD forms homogentisate, another oxygenase forms 4-maleyl-acetoacetate, an # isomerase forms 4-fumaryl-acetoacetate, and a hydrolase yields acetoacetate # and fumarate. (Fumarate is part of the TCA cycle so its catabolism is # not described.) tyrosine-degradation: HPD hmgA maiA fahA acetoacetate-degradation all: tyrosine-transport tyrosine-degradation
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:
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