GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Crocosphaera subtropica ATCC 51142

Found 163 low-confidence and 26 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 mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase CCE_RS01185
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate actP: cation/acetate symporter ActP
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocD: ornithine aminotransferase CCE_RS14630 CCE_RS00820
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine bgtA: aspartate ABC transporter, ATPase component BgtA CCE_RS04500 CCE_RS18105
aspartate bgtA: aspartate ABC transporter, ATPase component BgtA CCE_RS04500 CCE_RS18105
cellobiose SemiSWEET: Sugar transporter SemiSWEET CCE_RS12790
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component CCE_RS04500 CCE_RS01765
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 CCE_RS19480
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocD: ornithine aminotransferase CCE_RS14630 CCE_RS00820
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component CCE_RS10750
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 CCE_RS19480
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component CCE_RS04500 CCE_RS19420
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
deoxyinosine deoB: phosphopentomutase CCE_RS03375
deoxyinosine deoD: deoxyinosine phosphorylase CCE_RS05605
deoxyinosine nupC: deoxyinosine:H+ symporter NupC CCE_RS13115
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CCE_RS12275 CCE_RS01045
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CCE_RS07510 CCE_RS23020
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase CCE_RS15270 CCE_RS12090
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
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase CCE_RS13840
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase CCE_RS02835
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) CCE_RS06280 CCE_RS05990
glucose SemiSWEET: Sugar transporter SemiSWEET CCE_RS12790
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase CCE_RS15270 CCE_RS07540
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent CCE_RS04740
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) CCE_RS12360
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CCE_RS14550
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CCE_RS03960
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CCE_RS11410 CCE_RS01045
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase CCE_RS09005
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase CCE_RS13840
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CCE_RS15485
leucine liuC: 3-methylglutaconyl-CoA hydratase CCE_RS03960
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) CCE_RS15270 CCE_RS07540
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase CCE_RS14630
lysine lysN: 2-aminoadipate transaminase CCE_RS12755 CCE_RS14630
lysine lysP: L-lysine:H+ symporter LysP
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase CCE_RS10690
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 CCE_RS06405
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase CCE_RS15270 CCE_RS07540
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) CCE_RS06280 CCE_RS05990
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
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 CCE_RS03960
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CCE_RS03960
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CCE_RS11410 CCE_RS13000
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase CCE_RS13960
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase CCE_RS07540
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase CCE_RS09005
propionate prpD: 2-methylcitrate dehydratase
propionate putP: propionate transporter; proline:Na+ symporter CCE_RS14750
putrescine gabT: gamma-aminobutyrate transaminase CCE_RS14630 CCE_RS00820
putrescine patA: putrescine aminotransferase (PatA/SpuC) CCE_RS14630 CCE_RS00820
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CCE_RS15270 CCE_RS07540
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase CCE_RS15270 CCE_RS12090
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase CCE_RS12090
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase CCE_RS11410 CCE_RS01045
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) CCE_RS06885 CCE_RS06880
sucrose SemiSWEET: Sugar transporter SemiSWEET CCE_RS12790
threonine ltaE: L-threonine aldolase CCE_RS18650
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CCE_RS03375
thymidine nupC: thymidine permease NupC CCE_RS13115
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE CCE_RS14925
trehalose thuK: trehalose ABC transporter, ATPase component ThuK CCE_RS19270 CCE_RS01305
trehalose treF: trehalase CCE_RS06885 CCE_RS10150
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase CCE_RS13960
valine acdH: isobutyryl-CoA dehydrogenase CCE_RS14550
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase CCE_RS03960
valine mmsA: methylmalonate-semialdehyde dehydrogenase CCE_RS07540 CCE_RS15270
valine mmsB: 3-hydroxyisobutyrate dehydrogenase CCE_RS01955
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase CCE_RS09005
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
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