GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Malonomonas rubra DSM 5091

Found 146 low-confidence and 71 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components BUB13_RS05730 BUB13_RS04630
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component BUB13_RS05735
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) BUB13_RS11870 BUB13_RS10015
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase BUB13_RS17380
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 BUB13_RS16955 BUB13_RS05475
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUB13_RS01980 BUB13_RS10000
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUB13_RS01970 BUB13_RS11895
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUB13_RS01965 BUB13_RS09985
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine put1: proline dehydrogenase BUB13_RS10010
arginine rocD: ornithine aminotransferase BUB13_RS15120 BUB13_RS11855
arginine rocE: L-arginine permease
asparagine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BUB13_RS11690 BUB13_RS17605
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB13_RS11695 BUB13_RS17610
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB13_RS11685
asparagine ans: asparaginase
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BUB13_RS11690 BUB13_RS17605
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB13_RS11695 BUB13_RS17610
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB13_RS11685
cellobiose bgl: cellobiase
cellobiose MFS-glucose: glucose transporter, MFS superfamily
citrate SLC13A5: citrate:Na+ symporter BUB13_RS01075
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BUB13_RS11695 BUB13_RS17610
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BUB13_RS12685 BUB13_RS17605
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BUB13_RS12685
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase BUB13_RS15350
citrulline put1: proline dehydrogenase BUB13_RS10010
citrulline rocD: ornithine aminotransferase BUB13_RS15120 BUB13_RS11855
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component BUB13_RS11680
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 BUB13_RS11685
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component BUB13_RS11695 BUB13_RS17610
D-lactate D-LDH: D-lactate dehydrogenase BUB13_RS07355 BUB13_RS06205
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 BUB13_RS11205 BUB13_RS02575
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BUB13_RS11870 BUB13_RS10015
deoxyinosine nupC: deoxyinosine:H+ symporter NupC BUB13_RS14580
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BUB13_RS03185
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) BUB13_RS11870 BUB13_RS10015
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) BUB13_RS11870 BUB13_RS10015
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BUB13_RS11045 BUB13_RS11870
fucose aldA: lactaldehyde dehydrogenase BUB13_RS10015
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 galE: UDP-glucose 4-epimerase BUB13_RS14475 BUB13_RS01530
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BUB13_RS11630
galactose pgmA: alpha-phosphoglucomutase BUB13_RS13075 BUB13_RS00970
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BUB13_RS15165
galacturonate udh: D-galacturonate dehydrogenase
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)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BUB13_RS09600
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BUB13_RS15165
glucuronate udh: D-glucuronate dehydrogenase
glutamate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BUB13_RS11690 BUB13_RS17605
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB13_RS11695 BUB13_RS17610
glutamate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB13_RS11685
glutamate gdhA: glutamate dehydrogenase, NAD-dependent BUB13_RS00065 BUB13_RS06685
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) BUB13_RS11690 BUB13_RS17605
histidine aapP: L-histidine ABC transporter, ATPase component AapP BUB13_RS11695 BUB13_RS17610
histidine aapQ: L-histidine ABC transporter, permease component 1 (AapQ) BUB13_RS11685 BUB13_RS12685
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
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BUB13_RS00930 BUB13_RS05985
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BUB13_RS03185
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BUB13_RS14815 BUB13_RS03690
L-lactate DVU3032: L-lactate dehydrogenase, LutC-like component BUB13_RS06180
L-lactate Shew_2731: L-lactate:Na+ symporter, large component BUB13_RS05645 BUB13_RS16955
lactose galE: UDP-glucose 4-epimerase BUB13_RS14475 BUB13_RS01530
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BUB13_RS11630
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase BUB13_RS13075 BUB13_RS00970
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BUB13_RS03690 BUB13_RS14815
leucine liuC: 3-methylglutaconyl-CoA hydratase BUB13_RS00930 BUB13_RS05985
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BUB13_RS07135
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine davA: 5-aminovaleramidase BUB13_RS08695 BUB13_RS04170
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase
lysine davT: 5-aminovalerate aminotransferase BUB13_RS15120 BUB13_RS08945
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lysP: L-lysine:H+ symporter LysP
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase BUB13_RS13080 BUB13_RS05520
mannose manP: mannose PTS system, EII-CBA components BUB13_RS10825
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 BUB13_RS04920
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BUB13_RS09600
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 BUB13_RS00930
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BUB13_RS00930 BUB13_RS05985
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase BUB13_RS03185
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) BUB13_RS01965 BUB13_RS09985
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) BUB13_RS01980 BUB13_RS10000
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK BUB13_RS01985 BUB13_RS10005
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proW: proline ABC transporter, permease component ProW BUB13_RS11055
proline proX: proline ABC transporter, substrate-binding component ProX BUB13_RS11060
proline put1: proline dehydrogenase BUB13_RS10010
propionate pccA: propionyl-CoA carboxylase, alpha subunit BUB13_RS14815 BUB13_RS03690
propionate prpE: propionyl-CoA synthetase BUB13_RS14945 BUB13_RS06560
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BUB13_RS15120 BUB13_RS11855
putrescine patA: putrescine aminotransferase (PatA/SpuC) BUB13_RS15120 BUB13_RS11855
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component BUB13_RS07845
rhamnose aldA: lactaldehyde dehydrogenase BUB13_RS10015
rhamnose LRA1: L-rhamnofuranose dehydrogenase BUB13_RS03185
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 braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUB13_RS01980 BUB13_RS10000
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUB13_RS01970 BUB13_RS11895
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUB13_RS01965 BUB13_RS09985
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BUB13_RS03185
sucrose ams: sucrose hydrolase (invertase)
threonine adh: acetaldehyde dehydrogenase (not acylating) BUB13_RS11870 BUB13_RS10015
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUB13_RS01980 BUB13_RS10000
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUB13_RS01970 BUB13_RS11895
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUB13_RS01965 BUB13_RS09985
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BUB13_RS00630 BUB13_RS00635
thymidine adh: acetaldehyde dehydrogenase (not acylating) BUB13_RS11870 BUB13_RS10015
thymidine deoA: thymidine phosphorylase DeoA BUB13_RS12860
thymidine nupG: thymidine permease NupG/XapB
trehalose MFS-glucose: glucose transporter, MFS superfamily
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 BUB13_RS01965 BUB13_RS09985
tyrosine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 BUB13_RS01970 BUB13_RS09990
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 BUB13_RS01975 BUB13_RS09995
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 BUB13_RS01980 BUB13_RS10000
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component BUB13_RS10005
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BUB13_RS00930
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BUB13_RS03800
valine pccA: propionyl-CoA carboxylase, alpha subunit BUB13_RS14815 BUB13_RS03690
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) BUB13_RS10825
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 Apr 09 2024. 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