As text, or see rules and steps
# GapMind describes D-alanine catabolism via D-alanine dehydrogenase, which forms pyruvate. # This reaction is part of the # MetaCyc pathway for L-alanine catabolism via D-alanine (metacyc:ALADEG-PWY). In # principle, D-alanine might also be catabolized via racemization to # L-alanine and transamination to pyruvate, but this is not described # here. Pf6N2E2_5402 ABC transporter for D-Alanine, substrate-binding component curated:reanno::pseudo6_N2E2:Pf6N2E2_5402 Pf6N2E2_5403 ABC transporter for D-Alanine, permease component 2 curated:reanno::pseudo6_N2E2:Pf6N2E2_5403 Pf6N2E2_5404 ABC transporter for D-Alanine, permease component 1 curated:reanno::pseudo6_N2E2:Pf6N2E2_5404 Pf6N2E2_5405 ABC transporter for D-Alanine, ATPase component curated:reanno::pseudo6_N2E2:Pf6N2E2_5405 # Transporters were identified using: # query: transporter:D-alanine:D-ala. D-alanine-transport: Pf6N2E2_5402 Pf6N2E2_5403 Pf6N2E2_5404 Pf6N2E2_5405 # Spore germination proteins and B. subtilis ygqE, which is not really characterized, were ignored. # An ABC transporter from Azospirillum brasilense, with 5 # components, was identified in the fitness data. (Just one component was in the reannotations.) # MctP was missed by the clustering tool, but is annotated as transporting D-alanine # (see PMC135354, Figure 4A, showing that D-alanine inhibits transport). # A related protein, BPHYT_RS22245 (uniprot:B2T7V3), is involved in D-alanine utilization. AZOBR_RS08235 D-alanine ABC transporter, permease component 1 curated:reanno::azobra:AZOBR_RS08235 AZOBR_RS08240 D-alanine ABC transporter, permease component 2 uniprot:G8ALI9 AZOBR_RS08245 D-alanine ABC transporter, ATPase component 1 uniprot:G8ALJ0 AZOBR_RS08250 D-alanine ABC transporter, ATPase component 2 uniprot:G8ALJ1 AZOBR_RS08260 D-alanine ABC transporter, substrate-binding component uniprot:G8ALJ3 D-alanine-transport: AZOBR_RS08235 AZOBR_RS08240 AZOBR_RS08245 AZOBR_RS08250 AZOBR_RS08260 cycA D-alanine:H+ symporter CycA curated:SwissProt::A0A0H2VDI7 curated:SwissProt::P0AAE0 curated:TCDB::F2HQ24 curated:TCDB::M1IW84 curated:reanno::WCS417:GFF1065 curated:reanno::pseudo3_N2E3:AO353_16120 curated:reanno::pseudo5_N2C3_1:AO356_17670 curated:SwissProt::A2RI86 D-alanine-transport: cycA mctP D-alanine transporter MctP curated:TCDB::Q8VM88 curated:SwissProt::Q1M7A2 uniprot:B2T7V3 D-alanine-transport: mctP dadA D-alanine dehydrogenase term:D-alanine%dehydrogenase all: D-alanine-transport dadA
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