GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Nafulsella turpanensis ZLM-10

Found 102 low-confidence and 43 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
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter F752_RS0122200 F752_RS0104840
arginine rocE: L-arginine permease
arginine rocF: arginase F752_RS0110890 F752_RS0100840
cellobiose glk: glucokinase F752_RS0110680
cellobiose MFS-glucose: glucose transporter, MFS superfamily F752_RS0122200 F752_RS0104840
citrate SLC13A5: citrate:Na+ symporter F752_RS0121580
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component F752_RS0106200 F752_RS0112795
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 F752_RS0116650 F752_RS0110570
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 F752_RS0103745 F752_RS0103525
deoxyinosine deoB: phosphopentomutase F752_RS0120770
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase F752_RS0114160 F752_RS0122285
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) F752_RS0116570 F752_RS0114210
fructose scrK: fructokinase F752_RS0104800
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase F752_RS0114210
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 F752_RS0122200 F752_RS0104840
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gluconate gntK: D-gluconate kinase F752_RS0117690
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) F752_RS0118615
glucose glk: glucokinase F752_RS0110680
glucose MFS-glucose: glucose transporter, MFS superfamily F752_RS0122200 F752_RS0104840
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT F752_RS0121210
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase F752_RS0118655 F752_RS0101760
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit F752_RS0108360 F752_RS0103345
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component F752_RS0110830 F752_RS0118755
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase F752_RS0112575 F752_RS0114160
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit F752_RS0101295 F752_RS0116595
L-lactate L-LDH: L-lactate dehydrogenase F752_RS0115105
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 F752_RS0110680
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) F752_RS0102810
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit F752_RS0108360 F752_RS0103345
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component F752_RS0110830 F752_RS0118755
leucine liuA: isovaleryl-CoA dehydrogenase F752_RS0101760 F752_RS0118655
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit F752_RS0101295 F752_RS0103845
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit F752_RS0112535 F752_RS0107940
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase F752_RS0110225
lysine lysN: 2-aminoadipate transaminase F752_RS0116115 F752_RS0110225
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase F752_RS0104975
maltose glk: glucokinase F752_RS0110680
maltose MFS-glucose: glucose transporter, MFS superfamily F752_RS0122200 F752_RS0104840
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase F752_RS0103050 F752_RS0103485
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase F752_RS0114695
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter F752_RS0122200 F752_RS0104840
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) F752_RS0118615
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C F752_RS0110050
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E F752_RS0110070 F752_RS0106290
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase F752_RS0119545 F752_RS0112240
phenylacetate paaK: phenylacetate-CoA ligase F752_RS0105800
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase F752_RS0119545 F752_RS0118960
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit F752_RS0101295 F752_RS0116595
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase F752_RS0110225 F752_RS0110815
putrescine patA: putrescine aminotransferase (PatA/SpuC) F752_RS0110225 F752_RS0107785
putrescine patD: gamma-aminobutyraldehyde dehydrogenase F752_RS0109595 F752_RS0122315
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter F752_RS0101065
rhamnose fucO: L-lactaldehyde reductase F752_RS0114210
rhamnose LRA1: L-rhamnofuranose dehydrogenase F752_RS0114160 F752_RS0118300
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase F752_RS0104150
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 F752_RS0111000
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase F752_RS0114160 F752_RS0110200
sucrose scrK: fructokinase F752_RS0104800
threonine snatA: L-threonine transporter snatA F752_RS0111000
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase F752_RS0120770
trehalose glk: glucokinase F752_RS0110680
trehalose MFS-glucose: glucose transporter, MFS superfamily F752_RS0122200 F752_RS0104840
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 F752_RS0118655 F752_RS0101760
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase F752_RS0112240 F752_RS0118960
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit F752_RS0108360 F752_RS0103345
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component F752_RS0110830 F752_RS0118755
valine mmsA: methylmalonate-semialdehyde dehydrogenase F752_RS0109595 F752_RS0117775
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit F752_RS0101295 F752_RS0116595
xylitol PLT5: xylitol:H+ symporter PLT5 F752_RS0122200 F752_RS0104840
xylitol xdhA: xylitol dehydrogenase F752_RS0114160 F752_RS0110200

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