As text, or see rules and steps
# Asparagine catabolism in GapMind is based on asparaginase, which forms ammonia and aspartate. # The asparaginase may be secreted or cytoplasmic. # Asparatate can be transaminated to oxaloacetate, which is an intermediate in central metabolism. # ABC transporters # AatJMPQ from Pseudomonas or BztBACD from Rhodobacter capsulatus import aspartate.steps:bztA bztB bztC bztD aatJ aatQ aatM aatP # Transporters were identified using # query: transporter:asparagine:L-asparagine asparagine-transport: aatJ aatQ aatM aatP asparagine-transport: bztA bztB bztC bztD # glnQP from Lactococcus lactis, TC 3.A.1.3.25 glnQ L-asparagine ABC transporter, ATPase component GlnQ curated:TCDB::Q9CES4 glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP curated:TCDB::Q9CES5 asparagine-transport: glnQ glnP # AapJQMP from Rhizobium leguminosarum is described in glutamate.steps import glutamate.steps:aapJ aapQ aapM aapP asparagine-transport: aapJ aapQ aapM aapP # Other transporters ansP L-asparagine permease AnsP curated:SwissProt::P77610 curated:TCDB::P40812 asparagine-transport: ansP AGP1 L-asparagine permease AGP1 curated:CharProtDB::CH_091105 asparagine-transport: AGP1 yhiT probable L-asparagine transporter YhiT curated:TCDB::Q8ZLD2 asparagine-transport: yhiT agcS Probable asparagine:Na+ symporter AgcS curated:TCDB::W0WFC6 asparagine-transport: agcS # Ignored the export protein EamA # Ignored SLC38A3, which is a sodium/amino acid antiporter # Ignored gerBB (P39570), which is part of a receptor complex; it is not clear if it is # actually an amino acid transporter (see PMID:24488313) # Ignored the non-specific human permease SLC7A8 (TC 2.A.3.8.20) # Because many of the asparaginases are periplasmic, allow uptake of aspartate as well # (Also, some aspartate transporters probably transport asparagine as well.) import aspartate.steps:aspartate-transport # Isoaspartyl peptidases such as E. coli iaaA have this activity and are labeled heteromeric, # because the proenzyme is cleaved into two subunits; this need not be represented here. # TIGR00519 is not used because it hits GatD, a subunit of glutamyl-tRNA(Gln) amidotransferase ans asparaginase EC:3.5.1.1 EC:3.5.1.38 ignore_hmm:TIGR00519 all: ans aspartate-transport all: asparagine-transport ans
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