As text, or see rules and steps
# After uptake, acetate can be converted to acetyl-CoA by acs or by # ackA and pta, see MetaCyc's superpathway of acetate # utilization and formation (metacyc:ACETATEUTIL-PWY). # Acetyl-CoA is a central metabolic intermediate, so further reactions # are not represented in GapMind. Acetyl-CoA may be catabolized by the TCA # cycle or, in strict anaerobes, by the Wood-Ljungdahl pathway. If the # TCA cycle is used, then intermediates need to be replenished # by anaplaerotic reactions such as the glyoxylate cycle or the # ethylmalonyl-CoA pathway. actP cation/acetate symporter ActP curated:SwissProt::P32705 curated:SwissProt::Q8NS49 curated:TCDB::D5APM1 curated:TCDB::D5AU53 # Transporters were identified using # query: transporter:acetate:acetic. acetate-transport: actP # Ignore the poorly characterized protein GPR1_YARLI (uniprot:P41943) from Yarrowia lipolytica ady2 acetate permease Ady2 curated:SwissProt::P25613 curated:SwissProt::Q5B2K4 ignore:SwissProt::P41943 acetate-transport: ady2 patA Acetate transporter PatA curated:SwissProt::A0A075TRL0 curated:SwissProt::A1CFK8 acetate-transport: patA # Added the singleton Deh4p (M1Q159) from Dehalococcoides mccartyi, which has the same domain deh acetate/haloacid transporter curated:TCDB::F8SVK1 curated:TCDB::Q7X4L6 curated:TCDB::M1Q159 acetate-transport: deh satP acetate/proton symporter satP curated:SwissProt::P0AC98 acetate-transport: satP SLC5A8 actetate:Na+ symporter SLC5A8 curated:SwissProt::Q8N695 acetate-transport: SLC5A8 # TC 1.A.14.2.2 reports that E. coli yhbL is an acetate transporter, and cites a personal communication # from M. Inouye. ybhL acetate uptake transporter YbhL curated:TCDB::P0AAC4 acetate-transport: ybhL # A mutant in P. chlororaphis is reported to be defective in acetate utilization, implying uptake. # Fitness data for various strains of P. fluorescens did not indicate this, but uptake could be redundant; # for the ortholog in P. aeruginosa (uniprot:Q9I4F5), acetate does not seem to have been considered as a potential substrate dctA organic acid/proton symporter DctA curated:TCDB::Q848I3 ignore:SwissProt::Q9I4F5 ignore:reanno::pseudo5_N2C3_1:AO356_18980 acetate-transport: dctA # Ignored efflux systems, acyl-CoA transporter (annotated as actetate non-utilizing), # non-specific chloride channel protein, and # citrate:acetate antiporter. import ethanol.steps:acs ackA pta all: acetate-transport acs all: acetate-transport ackA pta
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