GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Aquimarina longa SW024

Found 122 low-confidence and 40 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 praC: 2-hydroxymuconate tautomerase N456_RS09570
4-hydroxybenzoate praD: 2-oxohex-3-enedioate decarboxylase
acetate actP: cation/acetate symporter ActP N456_RS06000
alanine alsT: L-alanine symporter AlsT/DagA N456_RS00330 N456_RS01700
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose Echvi_1880: L-arabinose:Na+ symporter N456_RS22690
arginine rocE: L-arginine permease
arginine rocF: arginase N456_RS21540
asparagine glt: aspartate:proton symporter Glt N456_RS13010 N456_RS04135
aspartate glt: aspartate:proton symporter Glt N456_RS13010 N456_RS04135
cellobiose bgl: cellobiase N456_RS09290
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter N456_RS19010 N456_RS19890
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component N456_RS10120 N456_RS11950
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 lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase N456_RS19560 N456_RS00650
deoxyinosine deoB: phosphopentomutase N456_RS15205
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase N456_RS05650 N456_RS09560
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 deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter N456_RS18345
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) N456_RS05650 N456_RS09575
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase N456_RS01240 N456_RS08060
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose sglS: sodium/galactose cotransporter N456_RS22690
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 N456_RS09275
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 ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter N456_RS22685
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 N456_RS09275
glutamate gdhA: glutamate dehydrogenase, NAD-dependent N456_RS11775
glutamate gltP: L-glutamate:cation symporter GltP/GltT N456_RS13010 N456_RS04135
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF N456_RS15730 N456_RS17915
glycerol glpK: glycerol kinase
histidine hutG': N-formylglutamate amidohydrolase N456_RS15635
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase N456_RS22100 N456_RS15100
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N456_RS15790 N456_RS22000
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N456_RS21995 N456_RS12980
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB N456_RS02630
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase N456_RS05650 N456_RS09575
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit N456_RS12590 N456_RS03300
lactose galK: galactokinase (-1-phosphate forming)
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) N456_RS09290
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N456_RS15790 N456_RS22000
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N456_RS21995 N456_RS12980
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB N456_RS02630
leucine liuA: isovaleryl-CoA dehydrogenase N456_RS22100 N456_RS01710
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit N456_RS12590 N456_RS03300
leucine liuC: 3-methylglutaconyl-CoA hydratase N456_RS12090 N456_RS12755
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit N456_RS13035 N456_RS12585
lysine davD: glutarate semialdehyde dehydrogenase N456_RS01240
lysine davT: 5-aminovalerate aminotransferase N456_RS06040 N456_RS01140
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase N456_RS18100 N456_RS06530
lysine patD: 5-aminopentanal dehydrogenase N456_RS01240
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase N456_RS06280 N456_RS05925
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 N456_RS01240
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase N456_RS12755 N456_RS12090
phenylacetate paaK: phenylacetate-CoA ligase N456_RS13585
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 N456_RS12755 N456_RS12090
proline proY: proline:H+ symporter
propionate pccA: propionyl-CoA carboxylase, alpha subunit N456_RS12590 N456_RS03300
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase N456_RS01240 N456_RS08060
putrescine gabT: gamma-aminobutyrate transaminase N456_RS06530 N456_RS16190
putrescine patA: putrescine aminotransferase (PatA/SpuC) N456_RS18100 N456_RS06530
putrescine patD: gamma-aminobutyraldehyde dehydrogenase N456_RS01240 N456_RS01325
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctP: pyruvate TRAP transporter, substrate-binding component N456_RS17215
rhamnose aldA: lactaldehyde dehydrogenase N456_RS01240 N456_RS08060
rhamnose LRA1: L-rhamnofuranose dehydrogenase N456_RS09575 N456_RS05650
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 serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase N456_RS06835 N456_RS09560
sucrose 1pfk: 1-phosphofructokinase
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA N456_RS04195
thymidine deoB: phosphopentomutase N456_RS15205
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC N456_RS09660
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
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 N456_RS22100 N456_RS01710
valine bch: 3-hydroxyisobutyryl-CoA hydrolase N456_RS12090
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit N456_RS15790 N456_RS22000
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N456_RS21995 N456_RS12980
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB N456_RS02630
valine mmsA: methylmalonate-semialdehyde dehydrogenase N456_RS01240 N456_RS08060
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit N456_RS12590 N456_RS03300
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose Echvi_1871: sodium/xylose cotransporter N456_RS22690
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