GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Halioglobus japonicus S1-36

Found 123 low-confidence and 41 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) C0029_RS01440 C0029_RS01835
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase C0029_RS08550
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK C0029_RS03975
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase C0029_RS08545
acetate actP: cation/acetate symporter ActP C0029_RS02085
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine adiA: arginine decarboxylase (AdiA/SpeA)
arginine gabD: succinate semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
arginine patD: gamma-aminobutyraldehyde dehydrogenase C0029_RS01835 C0029_RS09070
arginine rocE: L-arginine permease
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter C0029_RS15135
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component C0029_RS05165 C0029_RS10470
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 C0029_RS11700
citrulline rocD: ornithine aminotransferase C0029_RS18740 C0029_RS13280
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 C0029_RS16810 C0029_RS12560
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) C0029_RS01440 C0029_RS01835
deoxyinosine deoB: phosphopentomutase C0029_RS11865
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase C0029_RS10405
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme C0029_RS04750
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) C0029_RS01440 C0029_RS01835
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) C0029_RS01440 C0029_RS01835
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) C0029_RS03565 C0029_RS09135
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase C0029_RS01835 C0029_RS01440
fucose fucA: L-fuculose-phosphate aldolase FucA C0029_RS02930
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component C0029_RS07195
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
galactose galE: UDP-glucose 4-epimerase C0029_RS17390 C0029_RS17395
galactose galP: galactose:H+ symporter GalP
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase C0029_RS12020 C0029_RS07055
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagP: N-acetylglucosamine transporter NagP
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase C0029_RS12020 C0029_RS07055
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) C0029_RS13165
glycerol glpF: glycerol facilitator glpF C0029_RS00215
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 Bap2: L-isoleucine permease Bap2
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit C0029_RS03860 C0029_RS16990
isoleucine pccB: propionyl-CoA carboxylase, beta subunit C0029_RS16980 C0029_RS11170
L-lactate lutC: L-lactate dehydrogenase, LutC subunit C0029_RS02445
L-lactate Shew_2731: L-lactate:Na+ symporter, large component C0029_RS02085
L-malate sdlC: L-malate:Na+ symporter SdlC C0029_RS15135
lactose galE: UDP-glucose 4-epimerase C0029_RS17390 C0029_RS17395
lactose lacP: lactose permease LacP
leucine leuT: L-leucine:Na+ symporter LeuT
lysine davA: 5-aminovaleramidase
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase C0029_RS18740 C0029_RS09770
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C0029_RS04910 C0029_RS05670
lysine lysP: L-lysine:H+ symporter LysP
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase C0029_RS14320
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase C0029_RS12065
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase C0029_RS01440 C0029_RS01630
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 C0029_RS01675 C0029_RS04910
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C0029_RS02370 C0029_RS04920
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase C0029_RS06075 C0029_RS18680
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase C0029_RS06075 C0029_RS18680
phenylacetate paaK: phenylacetate-CoA ligase C0029_RS07560
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase C0029_RS02370 C0029_RS01675
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine PAH: phenylalanine 4-monooxygenase C0029_RS03515
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit C0029_RS03860 C0029_RS16990
propionate pccB: propionyl-CoA carboxylase, beta subunit C0029_RS16980 C0029_RS11170
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
putrescine patD: gamma-aminobutyraldehyde dehydrogenase C0029_RS01835 C0029_RS09070
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) C0029_RS02080
rhamnose aldA: lactaldehyde dehydrogenase C0029_RS01835 C0029_RS01440
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase C0029_RS05205 C0029_RS04455
succinate sdc: succinate:Na+ symporter Sdc C0029_RS15135
sucrose ams: sucrose hydrolase (invertase)
sucrose MFS-glucose: glucose transporter, MFS superfamily
thymidine adh: acetaldehyde dehydrogenase (not acylating) C0029_RS01440 C0029_RS01835
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase C0029_RS11865
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine hmgA: homogentisate dioxygenase
valine acdH: isobutyryl-CoA dehydrogenase C0029_RS01670 C0029_RS16975
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase C0029_RS01680
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C0029_RS04910 C0029_RS05670
valine mmsA: methylmalonate-semialdehyde dehydrogenase C0029_RS01440 C0029_RS01835
valine mmsB: 3-hydroxyisobutyrate dehydrogenase C0029_RS01685 C0029_RS08845
valine pccA: propionyl-CoA carboxylase, alpha subunit C0029_RS03860 C0029_RS16990
valine pccB: propionyl-CoA carboxylase, beta subunit C0029_RS16980 C0029_RS11170
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase C0029_RS01485 C0029_RS03490
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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.

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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