GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhodanobacter denitrificans FW104-10B01

Found 104 low-confidence and 31 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP LRK54_RS08410 LRK54_RS17455
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 xylF: 2-hydroxymuconate semialdehyde hydrolase
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter LRK54_RS13005
arginine rocE: L-arginine permease LRK54_RS02890 LRK54_RS15610
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component LRK54_RS14735 LRK54_RS15720
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
citrulline citrullinase: putative citrullinase LRK54_RS00340
D-lactate D-LDH: D-lactate dehydrogenase LRK54_RS03180 LRK54_RS12175
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase LRK54_RS10210 LRK54_RS10300
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase LRK54_RS15975 LRK54_RS09760
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 deoP: deoxyribose transporter LRK54_RS05055
fucose aldA: lactaldehyde dehydrogenase LRK54_RS17180 LRK54_RS02575
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 LRK54_RS05055
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase LRK54_RS17395 LRK54_RS10095
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase LRK54_RS05060
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX LRK54_RS07690
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase LRK54_RS05060
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT LRK54_RS00700 LRK54_RS11525
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) LRK54_RS15405
glycerol glpF: glycerol facilitator glpF LRK54_RS17450
histidine hutH: histidine ammonia-lyase LRK54_RS01300
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase LRK54_RS02105 LRK54_RS15685
isoleucine Bap2: L-isoleucine permease Bap2 LRK54_RS15610
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase LRK54_RS17395 LRK54_RS10095
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) LRK54_RS08685 LRK54_RS07660
leucine leuT: L-leucine:Na+ symporter LeuT
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase LRK54_RS00725 LRK54_RS04500
lysine lysP: L-lysine:H+ symporter LysP LRK54_RS02890 LRK54_RS15610
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase LRK54_RS03180 LRK54_RS12175
maltose susB: alpha-glucosidase (maltase) LRK54_RS13085 LRK54_RS13060
mannitol mt2d: mannitol 2-dehydrogenase LRK54_RS00650 LRK54_RS14815
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter LRK54_RS05055 LRK54_RS07710
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 LRK54_RS13005
myoinositol mmsA: malonate-semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter LRK54_RS02890 LRK54_RS15610
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 LRK54_RS15165 LRK54_RS02275
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase LRK54_RS15165 LRK54_RS02275
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase LRK54_RS15165 LRK54_RS02275
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP LRK54_RS02890 LRK54_RS15610
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase LRK54_RS17900
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
putrescine gabT: gamma-aminobutyrate transaminase LRK54_RS04500 LRK54_RS04150
putrescine patA: putrescine aminotransferase (PatA/SpuC) LRK54_RS04500 LRK54_RS04150
putrescine patD: gamma-aminobutyraldehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase LRK54_RS17180 LRK54_RS02575
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP LRK54_RS15610 LRK54_RS02890
sorbitol sdh: sorbitol dehydrogenase LRK54_RS11100 LRK54_RS16105
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 LRK54_RS13005
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) LRK54_RS13085 LRK54_RS13070
threonine serP1: L-threonine uptake transporter SerP1 LRK54_RS15610 LRK54_RS02890
tryptophan aroP: tryptophan:H+ symporter AroP LRK54_RS02890 LRK54_RS15610
tryptophan kynB: kynurenine formamidase
tryptophan mhpD: 2-hydroxypentadienoate hydratase
tryptophan mhpE: 4-hydroxy-2-oxovalerate aldolase
tryptophan nbaE: 2-aminomuconate 6-semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
tryptophan nbaF: 2-aminomuconate deaminase LRK54_RS02585 LRK54_RS05525
tryptophan nbaG: 2-oxo-3-hexenedioate decarboxylase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) LRK54_RS02890 LRK54_RS15610
valine acdH: isobutyryl-CoA dehydrogenase LRK54_RS02105 LRK54_RS15685
valine Bap2: L-valine permease Bap2 LRK54_RS15610
valine bch: 3-hydroxyisobutyryl-CoA hydrolase LRK54_RS15165
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase LRK54_RS15165 LRK54_RS16925
valine mmsA: methylmalonate-semialdehyde dehydrogenase LRK54_RS02575 LRK54_RS08020
valine mmsB: 3-hydroxyisobutyrate dehydrogenase LRK54_RS14685
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase LRK54_RS00650
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter LRK54_RS13005

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