As text, or see rules and steps
# In most bacteria, gluconate degradation proceeds via D-gluconate 6-phosphate # and either the Entner-Doudoroff pathway or the oxidative pentose phosphate pathway (metacyc:GLUCONSUPER-PWY). # Alternatively, gluconate can be oxidized in the periplasm to # 2-ketogluconate before uptake (metacyc:DHGLUCONATE-PYR-CAT-PWY). # A TRAP type transporter for gluconate is described in Sinorhizobium meliloti (PMID:19060150). # SMa0249 (gntA, Q930R3) is the small permease component. # SMa0250 (gntB, Q930R2) is the large permease component. # SMa0252 (gntC, Q930R1) is the periplasmic solute-binding component. # Fitness data identified related systems in Azospirillum brasilense Sp245, Pseudomona stutzeri RCH2, Acidovorax sp. GW101-3H11. # AZOBR_RS15925 = AZOBR_p130075 = G8AR26 is the small permease component; it was originally # annotated as a pseudogene. # AZOBR_RS15920 is the large permease component. # AZOBR_RS15915 = G8AR24 is the solute receptor (DctP-like) . # In psRCH2, these are Psest_2123, Psest_2124, Psest_2125 (GFF2080:GFF2082); the small permease component # is fused to gluconokinase. # In Acidovorax, these are Ac3H11_3228 (A0A165IVI0), Ac3H11_3227 (A0A165IWV9), Ac3H11_3226 (A0A165IVH1). gntA gluconate TRAP transporter, small permease component uniprot:Q930R3 uniprot:G8AR26 curated:reanno::psRCH2:GFF2080 uniprot:A0A165IVI0 gntB gluconate TRAP transporter, large permease component uniprot:Q930R2 curated:reanno::azobra:AZOBR_RS15920 curated:reanno::psRCH2:GFF2081 uniprot:A0A165IWV9 gntC gluconate TRAP transporter, periplasmic solute-binding component uniprot:Q930R1 uniprot:G8AR24 curated:reanno::psRCH2:GFF2082 uniprot:A0A165IVH1 # Transporters and PTS systems were identified using # query: transporter:gluconate:D-gluconate gluconate-transport: gntA gntB gntC # Ignore TC 4.A.6.1.14 / Q8DR76 which transports disaccharides of glucuronate gntEIIA gluconate PTS system, IIA component curated:TCDB::Q82ZC8 gntEIIB gluconate PTS system, IIB component curated:TCDB::Q82ZC7 gntEIIC gluconate PTS system, IIC component curated:TCDB::Q82ZC5 gntEIID gluconate PTS system, IID component curated:TCDB::Q82ZC6 # PTS systems (forming 6-phosphogluconate) gluconate-PTS: gntEIIA gntEIIB gntEIIC gntEIID gntT gluconate:H+ symporter GntT curated:SwissProt::P39344 curated:SwissProt::P39835 curated:TCDB::P0AC94 curated:TCDB::P0AC96 curated:TCDB::P12012 curated:reanno::BFirm:BPHYT_RS16725 curated:reanno::Cup4G11:RR42_RS28835 gluconate-transport: gntT ght3 gluconate transporter Ght3 curated:CharProtDB::CH_091200 gluconate-transport: ght3 # Ignore CharProtDB::CH_122791 (PTH1), not actually characterized # Ignore Gluconate transport inducer 1 (O14367) # Ignore the non-specific transporter ClC-5 # Psest_2123 (GFF2080) is a fusion of the TRAP component and gluconate kinase (but was not given the EC number) # CH_125646 is annotated as gluconokinase but was not given the EC number gntK D-gluconate kinase EC:2.7.1.12 curated:reanno::psRCH2:GFF2080 ignore:BRENDA::Q61036 ignore:BRENDA::Q29502 curated:CharProtDB::CH_125646 # Cytoplasmic gluconate 6-phosphate can be formed by PTS systems or by the kinase gntK. to-gluconate-6-phosphate: gluconate-PTS to-gluconate-6-phosphate: gluconate-transport gntK # This forms ribulose-5-phosphate, which is an intermediate in the pentose phosphate pathway gnd 6-phosphogluconate dehydrogenase, decarboxylating EC:1.1.1.44 EC:1.1.1.343 import glucose.steps:edd eda gadh1 gadh2 gadh3 kguT kguK kguD # Gluconate 6-phosphate can be consumed by the Entner-Doudoroff pathway (edd and eda) or by # oxidative decarboxylation (by gnd) to ribulose 5-phosphate, an intermediate in the pentose phosphate # pathway. Alternatively, if gluconate is oxidized to 2-ketogluconate in the periplasm (by gadh123), it # can be taken up by kguT, phosphorylated, reduced to gluconate 6-phosphate, and consumed # by the Entner-Doudoroff pathway. all: to-gluconate-6-phosphate edd eda all: to-gluconate-6-phosphate gnd all: gadh1 gadh2 gadh3 kguT kguK kguD edd eda
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