GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Gillisia marina CBA3202

Found 157 low-confidence and 25 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 acs: acetyl-CoA synthetase, AMP-forming
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 acs: acetyl-CoA synthetase, AMP-forming
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 ON07_RS11360
arginine rocE: L-arginine permease
arginine rocF: arginase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter ON07_RS10105
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component ON07_RS02945 ON07_RS13600
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
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase ON07_RS00510 ON07_RS11025
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 ON07_RS11110
deoxyinosine acs: acetyl-CoA synthetase, AMP-forming
deoxyinosine deoB: phosphopentomutase ON07_RS02425
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase ON07_RS06995
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 acs: acetyl-CoA synthetase, AMP-forming
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol acs: acetyl-CoA synthetase, AMP-forming
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) ON07_RS03925 ON07_RS07800
fructose glcP: fructose:H+ symporter GlcP ON07_RS11360
fructose scrK: fructokinase
fucose aldA: lactaldehyde dehydrogenase ON07_RS04340 ON07_RS00880
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 ON07_RS03230
fucose fucU: L-fucose mutarotase FucU
fucose tpi: triose-phosphate isomerase ON07_RS03390
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP ON07_RS11360
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
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 gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase ON07_RS00880 ON07_RS04340
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 ON07_RS10445
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
glycerol tpi: triose-phosphate isomerase ON07_RS03390
histidine hutG: N-formiminoglutamate formiminohydrolase ON07_RS07810
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase ON07_RS12885 ON07_RS07325
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB ON07_RS01105
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase ON07_RS00995 ON07_RS02480
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ON07_RS06995 ON07_RS01530
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit ON07_RS04395 ON07_RS09970
L-lactate L-LDH: L-lactate dehydrogenase ON07_RS04850
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB ON07_RS01105
leucine liuA: isovaleryl-CoA dehydrogenase ON07_RS12885 ON07_RS07325
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ON07_RS04395 ON07_RS09970
leucine liuC: 3-methylglutaconyl-CoA hydratase ON07_RS00995
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit ON07_RS07875 ON07_RS04400
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase ON07_RS06450 ON07_RS10785
lysine lysN: 2-aminoadipate transaminase ON07_RS09615 ON07_RS10785
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase ON07_RS04180
maltose glk: glucokinase
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase ON07_RS07210 ON07_RS11175
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
myoinositol iolT: myo-inositol:H+ symporter ON07_RS11360
myoinositol mmsA: malonate-semialdehyde dehydrogenase
myoinositol tpi: triose-phosphate isomerase ON07_RS03390
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagK: N-acetylglucosamine kinase
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 ON07_RS11395
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase ON07_RS00995
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase ON07_RS00995
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase ON07_RS02490 ON07_RS01635
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase ON07_RS02490 ON07_RS01635
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 aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase ON07_RS11085
phenylalanine QDPR: 6,7-dihydropteridine reductase ON07_RS05115
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit ON07_RS04395 ON07_RS09970
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase ON07_RS10785 ON07_RS06450
putrescine patA: putrescine aminotransferase (PatA/SpuC) ON07_RS10785 ON07_RS06450
putrescine patD: gamma-aminobutyraldehyde dehydrogenase ON07_RS04340 ON07_RS09675
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase ON07_RS04340 ON07_RS00880
rhamnose LRA1: L-rhamnofuranose dehydrogenase ON07_RS06995 ON07_RS10040
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 snatA: L-serine transporter ON07_RS13735
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase ON07_RS06995 ON07_RS12520
sucrose ams: sucrose hydrolase (invertase)
sucrose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
threonine acs: acetyl-CoA synthetase, AMP-forming
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase)
threonine lpd: dihydrolipoyl dehydrogenase ON07_RS10590 ON07_RS08210
threonine snatA: L-threonine transporter snatA ON07_RS13735
thymidine acs: acetyl-CoA synthetase, AMP-forming
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase ON07_RS02425
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase ON07_RS12885 ON07_RS07325
valine bch: 3-hydroxyisobutyryl-CoA hydrolase ON07_RS00995
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB ON07_RS01105
valine mmsA: methylmalonate-semialdehyde dehydrogenase ON07_RS00880
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit ON07_RS04395 ON07_RS09970
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

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