GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Aquimarina macrocephali JAMB N27

Found 114 low-confidence and 32 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 Z054_RS0121885
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate praC: 2-hydroxymuconate tautomerase
4-hydroxybenzoate praD: 2-oxohex-3-enedioate decarboxylase Z054_RS0121885
acetate actP: cation/acetate symporter ActP Z054_RS0124480
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose Echvi_1880: L-arabinose:Na+ symporter Z054_RS0102200 Z054_RS0102230
arginine rocE: L-arginine permease
cellobiose glk: glucokinase
citrate SLC13A5: citrate:Na+ symporter Z054_RS0115240
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component Z054_RS0118835 Z054_RS0100810
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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 Z054_RS0122935 Z054_RS0120090
deoxyinosine deoB: phosphopentomutase Z054_RS0115890
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Z054_RS0106690 Z054_RS0106190
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 deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter Z054_RS0118270
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) Z054_RS0106690 Z054_RS0117925
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase Z054_RS0121915 Z054_RS0110935
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 Z054_RS0118270
fucose fucU: L-fucose mutarotase FucU
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
galacturonate udh: D-galacturonate dehydrogenase Z054_RS0113935
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 glk: glucokinase
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
glucuronate udh: D-glucuronate dehydrogenase Z054_RS0113935
glycerol glpF: glycerol facilitator glpF Z054_RS0105730 Z054_RS0120270
glycerol glpK: glycerol kinase
histidine hutG': N-formylglutamate amidohydrolase Z054_RS0105670
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Z054_RS0105825 Z054_RS0121170
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Z054_RS0121175 Z054_RS0117330
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB Z054_RS0102630
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Z054_RS0106690 Z054_RS0109740
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit Z054_RS0117505 Z054_RS0101825
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
lactose glk: glucokinase
lactose lacP: lactose permease LacP
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Z054_RS0105825 Z054_RS0121170
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Z054_RS0121175 Z054_RS0117330
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB Z054_RS0102630
leucine liuA: isovaleryl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Z054_RS0114230 Z054_RS0117505
leucine liuC: 3-methylglutaconyl-CoA hydratase Z054_RS0108580 Z054_RS0106865
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit Z054_RS0107360 Z054_RS0117500
lysine davD: glutarate semialdehyde dehydrogenase Z054_RS0121915 Z054_RS0121900
lysine davT: 5-aminovalerate aminotransferase Z054_RS0124165 Z054_RS0107025
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase Z054_RS0117465 Z054_RS0116790
lysine patD: 5-aminopentanal dehydrogenase Z054_RS0121900 Z054_RS0110935
maltose glk: glucokinase
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase Z054_RS0109375 Z054_RS0124565
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 Z054_RS0121915 Z054_RS0121900
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit Z054_RS0117505 Z054_RS0101825
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase Z054_RS0121900 Z054_RS0121915
putrescine gabT: gamma-aminobutyrate transaminase Z054_RS0124165 Z054_RS0107025
putrescine patA: putrescine aminotransferase (PatA/SpuC) Z054_RS0117465 Z054_RS0116790
putrescine patD: gamma-aminobutyraldehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component Z054_RS0114255
rhamnose aldA: lactaldehyde dehydrogenase Z054_RS0121915 Z054_RS0110935
rhamnose LRA1: L-rhamnofuranose dehydrogenase Z054_RS0106690 Z054_RS0109740
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase Z054_RS0121890
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase Z054_RS0106690 Z054_RS0125590
sucrose ams: sucrose hydrolase (invertase)
sucrose glk: glucokinase
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase Z054_RS0115890
thymidine nupC: thymidine permease NupC Z054_RS0113545
trehalose glk: glucokinase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase Z054_RS0109545
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
valine bch: 3-hydroxyisobutyryl-CoA hydrolase Z054_RS0108580
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Z054_RS0105825 Z054_RS0121170
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component Z054_RS0121175 Z054_RS0117330
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB Z054_RS0102630
valine mmsA: methylmalonate-semialdehyde dehydrogenase Z054_RS0121900 Z054_RS0110935
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit Z054_RS0117505 Z054_RS0101825
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose Echvi_1871: sodium/xylose cotransporter Z054_RS0102230 Z054_RS0102200
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.



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