GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dechloromonas agitata is5

Found 126 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP K420_RS0110415
2-oxoglutarate dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
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
alanine TRIC: TRIC-type L-alanine transporter K420_RS0111465
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase K420_RS0109030
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
arginine rocF: arginase K420_RS0111690 K420_RS21080
asparagine ans: asparaginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase K420_RS0104195 K420_RS0107425
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component K420_RS0116480 K420_RS0113010
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 arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
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 K420_RS0104965
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
deoxyinosine deoB: phosphopentomutase K420_RS0100135
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase K420_RS0113955
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
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) K420_RS0109685 K420_RS0106575
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase K420_RS0109685 K420_RS0106575
fucose fucA: L-fuculose-phosphate aldolase FucA K420_RS0109030
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 K420_RS0106600 K420_RS0105875
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase K420_RS0106575 K420_RS0109685
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase K420_RS0109365
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) K420_RS0105870
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase K420_RS0106575 K420_RS0109685
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase K420_RS0109365
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent K420_RS0112630 K420_RS0101860
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
L-lactate Shew_2731: L-lactate:Na+ symporter, large component K420_RS0110285 K420_RS0102270
L-lactate Shew_2732: L-lactate:Na+ symporter, small component K420_RS0110280
lactose galE: UDP-glucose 4-epimerase K420_RS0106600 K420_RS0105875
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase K420_RS0104195 K420_RS0107425
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine davD: glutarate semialdehyde dehydrogenase K420_RS0106575 K420_RS0109685
lysine davT: 5-aminovalerate aminotransferase K420_RS0110205 K420_RS21080
lysine gcdG: succinyl-CoA:glutarate CoA-transferase K420_RS0117000 K420_RS0102905
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase K420_RS21080 K420_RS0110205
lysine patD: 5-aminopentanal dehydrogenase K420_RS0109685 K420_RS0106575
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase K420_RS0113760
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 K420_RS0101635
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase K420_RS0106575 K420_RS0109685
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) K420_RS0105870
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaZ1: oxepin-CoA hydrolase K420_RS0101385 K420_RS0103335
phenylacetate ppa: phenylacetate permease ppa K420_RS0103045 K420_RS0102270
phenylalanine iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit K420_RS0102205
phenylalanine paaZ1: oxepin-CoA hydrolase K420_RS0101385 K420_RS0103335
propionate mctC: propionate:H+ symporter K420_RS0103045 K420_RS0102270
putrescine gabT: gamma-aminobutyrate transaminase K420_RS21080 K420_RS0110205
putrescine patA: putrescine aminotransferase (PatA/SpuC) K420_RS21080 K420_RS0110205
putrescine patD: gamma-aminobutyraldehyde dehydrogenase K420_RS0109685 K420_RS0106575
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase K420_RS0109685 K420_RS0106575
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 rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase K420_RS0104965
sorbitol scrK: fructokinase K420_RS0104195
sorbitol sdh: sorbitol dehydrogenase K420_RS0113145 K420_RS0107705
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose scrK: fructokinase K420_RS0104195
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) K420_RS0102845
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) K420_RS0102840 K420_RS0101405
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) K420_RS0102835 K420_RS0101410
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) K420_RS0101415 K420_RS0102830
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) K420_RS0102825 K420_RS21120
threonine ltaE: L-threonine aldolase K420_RS0107485
thymidine adh: acetaldehyde dehydrogenase (not acylating) K420_RS0109685 K420_RS0106575
thymidine deoA: thymidine phosphorylase DeoA K420_RS0110225
thymidine deoB: phosphopentomutase K420_RS0100135
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase K420_RS0104195 K420_RS0107425
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine fahA: fumarylacetoacetate hydrolase K420_RS0108895
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase K420_RS0103335 K420_RS0101385
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) K420_RS0102840 K420_RS0101405
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) K420_RS0102845
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) K420_RS0102835 K420_RS0101410
valine mmsA: methylmalonate-semialdehyde dehydrogenase K420_RS0106575 K420_RS0109685
valine mmsB: 3-hydroxyisobutyrate dehydrogenase K420_RS0109015 K420_RS0109010
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
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