GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Found 130 low-confidence and 56 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) NPUN_RS23375 NPUN_RS04265
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase NPUN_RS02205 NPUN_RS04705
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 NPUN_RS23290
arabinose araE: L-arabinose:H+ symporter NPUN_RS26935
arabinose xacB: L-arabinose 1-dehydrogenase NPUN_RS02940 NPUN_RS10555
arabinose xacC: L-arabinono-1,4-lactonase NPUN_RS17600
arabinose xacD: L-arabinonate dehydratase NPUN_RS19105
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine rocF: arginase NPUN_RS30535
asparagine glt: aspartate:proton symporter Glt NPUN_RS24605
aspartate glt: aspartate:proton symporter Glt NPUN_RS24605
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component NPUN_RS14635 NPUN_RS32120
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 NPUN_RS14640 NPUN_RS32115
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 NPUN_RS14640 NPUN_RS32115
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component NPUN_RS03525 NPUN_RS14640
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase NPUN_RS44200
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 NPUN_RS06390 NPUN_RS03995
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) NPUN_RS23375 NPUN_RS04265
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoD: deoxyinosine phosphorylase NPUN_RS33640 NPUN_RS33380
deoxyinosine nupC: deoxyinosine:H+ symporter NupC NPUN_RS12200
deoxyribonate aacS: acetoacetyl-CoA synthetase NPUN_RS10400 NPUN_RS32195
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase NPUN_RS03135 NPUN_RS11785
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 adh: acetaldehyde dehydrogenase (not acylating) NPUN_RS23375 NPUN_RS04265
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) NPUN_RS23375 NPUN_RS04265
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) NPUN_RS25690 NPUN_RS02925
fructose scrK: fructokinase NPUN_RS21410 NPUN_RS09950
fucose aldA: lactaldehyde dehydrogenase NPUN_RS06130 NPUN_RS26800
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 galP: galactose:H+ symporter GalP NPUN_RS26935
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase NPUN_RS01080
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase NPUN_RS13725
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase NPUN_RS09950
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase NPUN_RS26985
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) NPUN_RS06640 NPUN_RS26365
glucosamine nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX NPUN_RS14610
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase NPUN_RS13725
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase NPUN_RS09950
glucuronate uxaC: D-glucuronate isomerase NPUN_RS26985
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT NPUN_RS24605
glycerol dhaD: glycerol dehydrogenase NPUN_RS25755 NPUN_RS02940
glycerol dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M NPUN_RS05980
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase NPUN_RS10405
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase NPUN_RS17395
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase NPUN_RS20040 NPUN_RS16025
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase NPUN_RS11785 NPUN_RS09090
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase NPUN_RS28465
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase NPUN_RS01080
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase NPUN_RS10400 NPUN_RS32195
leucine atoB: acetyl-CoA C-acetyltransferase
leucine ilvE: L-leucine transaminase NPUN_RS03530 NPUN_RS33160
leucine liuA: isovaleryl-CoA dehydrogenase NPUN_RS17395
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit NPUN_RS30115
leucine liuC: 3-methylglutaconyl-CoA hydratase NPUN_RS20040 NPUN_RS16025
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) NPUN_RS06130 NPUN_RS26800
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase NPUN_RS00985 NPUN_RS09825
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
mannitol mt2d: mannitol 2-dehydrogenase NPUN_RS13675 NPUN_RS10555
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase NPUN_RS21410 NPUN_RS09950
mannose man-isomerase: D-mannose isomerase
mannose scrK: fructokinase NPUN_RS21410 NPUN_RS09950
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 NPUN_RS08810
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase NPUN_RS28250
myoinositol iolT: myo-inositol:H+ symporter NPUN_RS26935
myoinositol mmsA: malonate-semialdehyde dehydrogenase NPUN_RS06130 NPUN_RS26800
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) NPUN_RS06640 NPUN_RS26365
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 NPUN_RS20040
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase NPUN_RS20040
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase NPUN_RS17405 NPUN_RS11785
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase NPUN_RS32195 NPUN_RS10400
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa NPUN_RS23290
phenylalanine aacS: acetoacetyl-CoA synthetase NPUN_RS10400 NPUN_RS32195
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 NPUN_RS28965 NPUN_RS12540
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase NPUN_RS22990
phenylalanine QDPR: 6,7-dihydropteridine reductase NPUN_RS11125
proline put1: proline dehydrogenase NPUN_RS26800
propionate mctC: propionate:H+ symporter NPUN_RS23290
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase NPUN_RS28465
propionate prpD: 2-methylcitrate dehydratase
putrescine gabT: gamma-aminobutyrate transaminase NPUN_RS25070 NPUN_RS09825
putrescine patA: putrescine aminotransferase (PatA/SpuC) NPUN_RS25070 NPUN_RS09825
putrescine patD: gamma-aminobutyraldehyde dehydrogenase NPUN_RS06130 NPUN_RS23375
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) NPUN_RS30400
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) NPUN_RS30395
rhamnose LRA1: L-rhamnofuranose dehydrogenase NPUN_RS11785 NPUN_RS11105
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase NPUN_RS11785 NPUN_RS10555
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase NPUN_RS28115
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase NPUN_RS03995 NPUN_RS06390
sorbitol scrK: fructokinase NPUN_RS21410 NPUN_RS09950
sorbitol sdh: sorbitol dehydrogenase NPUN_RS08770 NPUN_RS11785
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dauA: succinate:H+ symporter DauA NPUN_RS13810
threonine adh: acetaldehyde dehydrogenase (not acylating) NPUN_RS23375 NPUN_RS04265
thymidine adh: acetaldehyde dehydrogenase (not acylating) NPUN_RS23375 NPUN_RS04265
thymidine deoA: thymidine phosphorylase DeoA NPUN_RS33380
thymidine deoB: phosphopentomutase
thymidine nupC: thymidine permease NupC NPUN_RS12200
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase NPUN_RS28975
tyrosine aacS: acetoacetyl-CoA synthetase NPUN_RS10400 NPUN_RS32195
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase NPUN_RS28965 NPUN_RS12540
tyrosine tyrP: Tyrosine permease NPUN_RS30375
valine acdH: isobutyryl-CoA dehydrogenase NPUN_RS17395 NPUN_RS10485
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase NPUN_RS20040 NPUN_RS16025
valine mmsA: methylmalonate-semialdehyde dehydrogenase NPUN_RS06130 NPUN_RS26800
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase NPUN_RS28465
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase NPUN_RS08770 NPUN_RS15725
xylose xdhA: xylitol dehydrogenase NPUN_RS08770 NPUN_RS02940
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter NPUN_RS26935

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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