GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Thermophagus xiamenensis HS1

Found 132 low-confidence and 36 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)
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
acetate actP: cation/acetate symporter ActP
arginine arcA: arginine deiminase GQW_RS0109710
arginine arcC: carbamate kinase GQW_RS0112540
arginine rocE: L-arginine permease
asparagine glt: aspartate:proton symporter Glt GQW_RS0112710
aspartate glt: aspartate:proton symporter Glt GQW_RS0112710
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component GQW_RS0104065 GQW_RS0116060
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 arcC: carbamate kinase GQW_RS0112540
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 GQW_RS0108825
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating)
deoxyinosine deoB: phosphopentomutase GQW_RS0100500
deoxyinosine nupC: deoxyinosine:H+ symporter NupC GQW_RS0101985
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase GQW_RS0114440 GQW_RS0109830
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase GQW_RS17140
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating)
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter GQW_RS0103410
ethanol adh: acetaldehyde dehydrogenase (not acylating)
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) GQW_RS0114435 GQW_RS0107725
fructose scrK: fructokinase GQW_RS0112765
fucose aldA: lactaldehyde dehydrogenase GQW_RS0109070
fucose fucA: L-fuculose-phosphate aldolase FucA GQW_RS0111715
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fumarate dctA: fumarate:H+ symporter DctA GQW_RS0112710
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagA: N-acetylglucosamine 6-phosphate deacetylase
glucosamine nagP: N-acetylglucosamine transporter NagP GQW_RS0103785
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX GQW_RS0102100
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component GQW_RS17010
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate uxuB: D-mannonate dehydrogenase GQW_RS0112770
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol dhaD: glycerol dehydrogenase GQW_RS0111630 GQW_RS0107020
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
glycerol glpF: glycerol facilitator glpF
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 GQW_RS0111130 GQW_RS0108020
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase GQW_RS0104270
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase GQW_RS0111140
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase GQW_RS0114440 GQW_RS0109830
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit GQW_RS0115970 GQW_RS0111915
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GQW_RS0114000
L-lactate L-LDH: L-lactate dehydrogenase GQW_RS0100745
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose lacP: lactose permease LacP
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT GQW_RS0115780
leucine liuA: isovaleryl-CoA dehydrogenase GQW_RS0111130 GQW_RS0108020
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit GQW_RS0115970 GQW_RS0111125
leucine liuC: 3-methylglutaconyl-CoA hydratase GQW_RS0111120 GQW_RS0104270
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit GQW_RS0111115 GQW_RS0102665
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GQW_RS0114000
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase GQW_RS0109860
lysine lysN: 2-aminoadipate transaminase GQW_RS0104695 GQW_RS0109860
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase GQW_RS0103050
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannose manA: mannose-6-phosphate isomerase GQW_RS0115690 GQW_RS0100715
mannose STP6: mannose:H+ symporter GQW_RS0115525
myoinositol iolG: myo-inositol 2-dehydrogenase GQW_RS0109950
myoinositol iolM: 2-inosose 4-dehydrogenase GQW_RS0103415
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter GQW_RS0115525
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase GQW_RS0112770
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagP: N-acetylglucosamine transporter NagP GQW_RS0103785
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 GQW_RS0104270
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase GQW_RS0104270
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase GQW_RS0107585 GQW_RS0114440
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase GQW_RS0106210 GQW_RS0110670
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
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 GQW_RS0105510
propionate pccA: propionyl-CoA carboxylase, alpha subunit GQW_RS0115970 GQW_RS0111915
propionate prpE: propionyl-CoA synthetase GQW_RS0106210
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase GQW_RS0106785 GQW_RS0113245
putrescine patA: putrescine aminotransferase (PatA/SpuC) GQW_RS0109860 GQW_RS0106785
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase GQW_RS0109070
rhamnose rhaD: rhamnulose 1-phosphate aldolase
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase GQW_RS0108825
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase GQW_RS0111760 GQW_RS0114440
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating)
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase GQW_RS0100500
thymidine nupC: thymidine permease NupC GQW_RS0101985
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 GQW_RS0111130 GQW_RS0108020
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase GQW_RS0104270
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit GQW_RS0115970 GQW_RS0111915
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GQW_RS0114000
xylitol PLT5: xylitol:H+ symporter PLT5 GQW_RS0115525
xylitol xdhA: xylitol dehydrogenase GQW_RS0107725 GQW_RS0114440

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