GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Coprobacter fastidiosus NSB1

Found 158 low-confidence and 32 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) NSB1T_RS16830 NSB1T_RS21705
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
alanine TRIC: TRIC-type L-alanine transporter NSB1T_RS26895
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter NSB1T_RS27520 NSB1T_RS21520
arginine gabD: succinate semialdehyde dehydrogenase
arginine gabT: gamma-aminobutyrate transaminase NSB1T_RS26820 NSB1T_RS22540
arginine patA: putrescine aminotransferase (PatA/SpuC) NSB1T_RS26820 NSB1T_RS22540
arginine patD: gamma-aminobutyraldehyde dehydrogenase
arginine rocE: L-arginine permease
asparagine dauA: dicarboxylic acid transporter DauA NSB1T_RS18145
aspartate dauA: dicarboxylic acid transporter DauA NSB1T_RS18145
cellobiose bgl: cellobiase NSB1T_RS25470 NSB1T_RS28620
cellobiose MFS-glucose: glucose transporter, MFS superfamily NSB1T_RS21520 NSB1T_RS24425
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component NSB1T_RS18630 NSB1T_RS18380
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase NSB1T_RS15480
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase NSB1T_RS22540 NSB1T_RS26820
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase NSB1T_RS25900
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) NSB1T_RS16830 NSB1T_RS21705
deoxyinosine deoB: phosphopentomutase NSB1T_RS23180
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) NSB1T_RS16830 NSB1T_RS21705
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter NSB1T_RS20885
ethanol adh: acetaldehyde dehydrogenase (not acylating) NSB1T_RS16830 NSB1T_RS21705
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) NSB1T_RS16825 NSB1T_RS19010
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP NSB1T_RS20885
fucose fucU: L-fucose mutarotase FucU
fumarate dauA: fumarate transporter DauA NSB1T_RS18145
galactose galP: galactose:H+ symporter GalP NSB1T_RS27520 NSB1T_RS21520
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose MFS-glucose: glucose transporter, MFS superfamily NSB1T_RS21520 NSB1T_RS24425
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase NSB1T_RS15660
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase NSB1T_RS24770
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase NSB1T_RS15785 NSB1T_RS19540
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NSB1T_RS24210
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit NSB1T_RS24075
isoleucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA NSB1T_RS21620 with NSB1T_RS21615
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-lactate lldG: L-lactate dehydrogenase, LldG subunit NSB1T_RS25070
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT NSB1T_RS19720
leucine liuA: isovaleryl-CoA dehydrogenase NSB1T_RS15660
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit NSB1T_RS24075
leucine liuC: 3-methylglutaconyl-CoA hydratase NSB1T_RS24770
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit NSB1T_RS20175 NSB1T_RS23465
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA NSB1T_RS21620 with NSB1T_RS21615
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase NSB1T_RS22540
lysine lysN: 2-aminoadipate transaminase NSB1T_RS20455 NSB1T_RS22540
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
mannitol mt2d: mannitol 2-dehydrogenase NSB1T_RS19540 NSB1T_RS15785
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase NSB1T_RS26875 NSB1T_RS17275
mannose STP6: mannose:H+ symporter NSB1T_RS21520
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter NSB1T_RS21520 NSB1T_RS27520
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagP: N-acetylglucosamine transporter NagP
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase NSB1T_RS24770
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase NSB1T_RS24770
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase NSB1T_RS15785
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase NSB1T_RS24770
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NSB1T_RS24210
propionate pccA: propionyl-CoA carboxylase, alpha subunit NSB1T_RS24075
propionate prpE: propionyl-CoA synthetase NSB1T_RS22760
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase NSB1T_RS26820 NSB1T_RS22540
putrescine patA: putrescine aminotransferase (PatA/SpuC) NSB1T_RS26820 NSB1T_RS22540
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose LRA1: L-rhamnofuranose dehydrogenase NSB1T_RS15785 NSB1T_RS19540
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase NSB1T_RS19540 NSB1T_RS15785
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dauA: succinate:H+ symporter DauA NSB1T_RS18145
sucrose ams: sucrose hydrolase (invertase)
threonine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NSB1T_RS24210
threonine pccA: propionyl-CoA carboxylase, alpha subunit NSB1T_RS24075
threonine tdcB: L-threonine dehydratase NSB1T_RS25900
threonine tdcC: L-threonine:H+ symporter TdcC
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) NSB1T_RS16830 NSB1T_RS21705
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase NSB1T_RS23180
trehalose MFS-glucose: glucose transporter, MFS superfamily NSB1T_RS21520 NSB1T_RS24425
trehalose treF: trehalase NSB1T_RS24725
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase NSB1T_RS15660
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase NSB1T_RS24770
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase NSB1T_RS24770
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NSB1T_RS24210
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit NSB1T_RS24075
valine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA NSB1T_RS21620 with NSB1T_RS21615
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase NSB1T_RS15785

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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