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.

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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