GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pontimonas salivibrio CL-TW6

Found 151 low-confidence and 83 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 C3B54_RS06245
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
alanine TRIC: TRIC-type L-alanine transporter C3B54_RS01290
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase C3B54_RS06590 C3B54_RS01280
arabinose xacC: L-arabinono-1,4-lactonase
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arabinose xacF: alpha-ketoglutarate semialdehyde dehydrogenase C3B54_RS06650 C3B54_RS06570
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase C3B54_RS01080 C3B54_RS06570
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine ans: asparaginase C3B54_RS06930
asparagine bgtA: aspartate ABC transporter, ATPase component BgtA C3B54_RS04180 C3B54_RS05880
asparagine natG: aspartate ABC transporter, permease component 1 (NatG)
asparagine natH: aspartate ABC transporter, permease component 2 (NatH) C3B54_RS04185 C3B54_RS05875
aspartate bgtA: aspartate ABC transporter, ATPase component BgtA C3B54_RS04180 C3B54_RS05880
aspartate natG: aspartate ABC transporter, permease component 1 (NatG)
aspartate natH: aspartate ABC transporter, permease component 2 (NatH) C3B54_RS04185 C3B54_RS05875
cellobiose glk: glucokinase C3B54_RS04510 C3B54_RS04755
cellobiose mglB: glucose ABC transporter, substrate-binding component C3B54_RS03355
cellobiose mglC: glucose ABC transporter, permease component (MglC) C3B54_RS07375 C3B54_RS06505
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component C3B54_RS04180 C3B54_RS05880
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 C3B54_RS04185
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase C3B54_RS01080 C3B54_RS06570
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase C3B54_RS05670 C3B54_RS07685
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 C3B54_RS02615
deoxyinosine deoB: phosphopentomutase C3B54_RS08145
deoxyinosine H281DRAFT_01112: deoxynucleoside transporter, permease component 2 C3B54_RS06180 C3B54_RS06505
deoxyinosine H281DRAFT_01115: deoxynucleoside transporter, permease component 1 C3B54_RS06175
deoxyribonate atoA: acetoacetyl-CoA transferase, A subunit C3B54_RS06550
deoxyribonate atoB: acetyl-CoA C-acetyltransferase C3B54_RS06540
deoxyribonate atoD: acetoacetyl-CoA transferase, B subunit C3B54_RS06545
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase C3B54_RS06685 C3B54_RS01280
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase C3B54_RS02810
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) C3B54_RS04105 C3B54_RS06210
fructose 1pfk: 1-phosphofructokinase C3B54_RS05660
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fdh: L-fucose 1-dehydrogenase C3B54_RS06675
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase C3B54_RS06685 C3B54_RS06590
fucose fuconolactonase: L-fucono-1,5-lactonase C3B54_RS06660
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming) C3B54_RS08440
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose pgmA: alpha-phosphoglucomutase C3B54_RS08145 C3B54_RS07915
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase C3B54_RS06650 C3B54_RS06570
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate garD: meso-galactarate dehydratase (L-threo-forming) GarD C3B54_RS06340 C3B54_RS06705
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase C3B54_RS06830
galacturonate udh: D-galacturonate dehydrogenase
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose glk: glucokinase C3B54_RS04510 C3B54_RS04755
glucose mglB: glucose ABC transporter, substrate-binding component C3B54_RS03355
glucose mglC: glucose ABC transporter, permease component (MglC) C3B54_RS07375 C3B54_RS06505
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase C3B54_RS06650 C3B54_RS06570
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase C3B54_RS06830
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) C3B54_RS07470
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine natB: L-histidine ABC transporter, substrate-binding component NatB C3B54_RS01770
histidine natC: L-histidine ABC transporter, permease component 1 (NatC)
histidine natD: L-histidine ABC transporter, permease component 2 (NatD) C3B54_RS01790
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C3B54_RS00880 C3B54_RS07325
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C3B54_RS06255
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase C3B54_RS06540
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C3B54_RS05130 C3B54_RS06285
isoleucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component C3B54_RS04565 C3B54_RS00740
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit C3B54_RS08130 C3B54_RS04740
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming) C3B54_RS08440
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase C3B54_RS04510 C3B54_RS04755
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) C3B54_RS02725
lactose pgmA: alpha-phosphoglucomutase C3B54_RS08145 C3B54_RS07915
leucine atoA: acetoacetyl-CoA transferase, A subunit C3B54_RS06550
leucine atoB: acetyl-CoA C-acetyltransferase C3B54_RS06540
leucine atoD: acetoacetyl-CoA transferase, B subunit C3B54_RS06545
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C3B54_RS00880 C3B54_RS07325
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit C3B54_RS08130 C3B54_RS04740
leucine liuC: 3-methylglutaconyl-CoA hydratase C3B54_RS06255
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit C3B54_RS08095
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component C3B54_RS04565 C3B54_RS00740
leucine natB: L-leucine ABC transporter, substrate-binding component NatB C3B54_RS01770
leucine natC: L-leucine ABC transporter, permease component 1 (NatC)
leucine natD: L-leucine ABC transporter, permease component 2 (NatD) C3B54_RS01790
lysine cadA: lysine decarboxylase
lysine davD: glutarate semialdehyde dehydrogenase C3B54_RS06570 C3B54_RS06115
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase C3B54_RS01095 C3B54_RS06925
maltose glk: glucokinase C3B54_RS04510 C3B54_RS04755
maltose mglB: glucose ABC transporter, substrate-binding component C3B54_RS03355
maltose mglC: glucose ABC transporter, permease component (MglC) C3B54_RS07375 C3B54_RS06505
mannitol mak: mannose kinase
mannitol mt1d: mannitol 1-dehydrogenase C3B54_RS04105
mannitol PLT5: polyol transporter PLT5
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
myoinositol mmsA: malonate-semialdehyde dehydrogenase C3B54_RS06115 C3B54_RS02765
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase C3B54_RS02375
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 C3B54_RS06255
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase C3B54_RS06685 C3B54_RS06560
phenylacetate paaK: phenylacetate-CoA ligase C3B54_RS03390
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 atoA: acetoacetyl-CoA transferase, A subunit C3B54_RS06550
phenylalanine atoB: acetyl-CoA C-acetyltransferase C3B54_RS06540
phenylalanine atoD: acetoacetyl-CoA transferase, B subunit C3B54_RS06545
phenylalanine fahA: fumarylacetoacetate hydrolase C3B54_RS02790
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline natB: proline ABC transporter, substrate-binding component NatB C3B54_RS01770
proline natC: proline ABC transporter, permease component 1 (NatC)
proline natD: proline ABC transporter, permease component 2 (NatD) C3B54_RS01790
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase C3B54_RS01080 C3B54_RS06570
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit C3B54_RS08130 C3B54_RS04740
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase C3B54_RS06925 C3B54_RS01095
putrescine patA: putrescine aminotransferase (PatA/SpuC) C3B54_RS01095 C3B54_RS06925
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase C3B54_RS07785 C3B54_RS06590
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase C3B54_RS05130 C3B54_RS06615
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) C3B54_RS01770
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C3B54_RS01790
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C3B54_RS01785
sorbitol mtlA: PTS system for polyols, EII-CBA components C3B54_RS05650
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase C3B54_RS01280 C3B54_RS06590
succinate sdc: succinate:Na+ symporter Sdc
sucrose 1pfk: 1-phosphofructokinase C3B54_RS05660
sucrose ams: sucrose hydrolase (invertase) C3B54_RS08620 C3B54_RS05100
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) C3B54_RS01770
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C3B54_RS01790
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C3B54_RS01785
threonine lpd: dihydrolipoyl dehydrogenase C3B54_RS04565 C3B54_RS00740
thymidine deoB: phosphopentomutase C3B54_RS08145
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase C3B54_RS04510 C3B54_RS04755
trehalose mglB: glucose ABC transporter, substrate-binding component C3B54_RS03355
trehalose mglC: glucose ABC transporter, permease component (MglC) C3B54_RS07375 C3B54_RS06505
trehalose treF: trehalase C3B54_RS08620 C3B54_RS05100
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoA: acetoacetyl-CoA transferase, A subunit C3B54_RS06550
tyrosine atoB: acetyl-CoA C-acetyltransferase C3B54_RS06540
tyrosine atoD: acetoacetyl-CoA transferase, B subunit C3B54_RS06545
tyrosine fahA: fumarylacetoacetate hydrolase C3B54_RS02790
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C3B54_RS00880 C3B54_RS07325
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C3B54_RS06255
valine epi: methylmalonyl-CoA epimerase
valine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component C3B54_RS04565 C3B54_RS00740
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase C3B54_RS03975 C3B54_RS06275
valine mmsB: 3-hydroxyisobutyrate dehydrogenase C3B54_RS06160
valine pccA: propionyl-CoA carboxylase, alpha subunit C3B54_RS08130 C3B54_RS04740
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase C3B54_RS05635 C3B54_RS06210
xylitol xylB: xylulokinase C3B54_RS06200 C3B54_RS02365
xylose dopDH: 2,5-dioxopentanonate dehydrogenase C3B54_RS06650 C3B54_RS06570
xylose xad: D-xylonate dehydratase C3B54_RS06640 C3B54_RS07715
xylose xdh: D-xylose dehydrogenase C3B54_RS02285 C3B54_RS05750
xylose xylC: xylonolactonase
xylose xylF: ABC transporter for xylose, substrate binding component xylF C3B54_RS03355 C3B54_RS05735
xylose xylH: ABC transporter for xylose, permease component xylH C3B54_RS07375 C3B54_RS03365

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