GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Trichormus variabilis ATCC 29413

Found 150 low-confidence and 45 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 adh: acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase AVA_RS20055
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate actP: cation/acetate symporter ActP AVA_RS05970
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA AVA_RS03725 AVA_RS07575
arginine rocF: arginase
asparagine ans: asparaginase AVA_RS04880 AVA_RS03705
cellobiose SemiSWEET: Sugar transporter SemiSWEET AVA_RS02975
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AVA_RS03725 AVA_RS07575
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 AVA_RS03730
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 AVA_RS19700
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-alanine dadA: D-alanine dehydrogenase AVA_RS16300
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 AVA_RS13915 AVA_RS06945
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
deoxyinosine deoB: phosphopentomutase AVA_RS19095
deoxyinosine deoD: deoxyinosine phosphorylase AVA_RS08380
deoxyinosine nupC: deoxyinosine:H+ symporter NupC AVA_RS14285
deoxyribonate aacS: acetoacetyl-CoA synthetase AVA_RS20210
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AVA_RS01555 AVA_RS21960
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) AVA_RS17895 AVA_RS18330
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
fructose scrK: fructokinase AVA_RS14780 AVA_RS01255
fucose aldA: lactaldehyde dehydrogenase AVA_RS07875 AVA_RS14900
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
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase AVA_RS05305 AVA_RS09875
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose pgmA: alpha-phosphoglucomutase AVA_RS08810 AVA_RS19095
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
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) AVA_RS23500 AVA_RS17650
glucosamine nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX AVA_RS19040
glucose SemiSWEET: Sugar transporter SemiSWEET AVA_RS02975
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
glutamate gtrA: tripartite L-glutamate:Na+ symporter, small membrane component GtrA AVA_RS04480
glutamate gtrB: tripartite L-glutamate:Na+ symporter, large membrane component GtrB AVA_RS04475
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase AVA_RS20215
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine natB: L-histidine ABC transporter, substrate-binding component NatB AVA_RS24325
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AVA_RS00835
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AVA_RS19075 AVA_RS09415
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine prpB: 2-methylisocitrate lyase AVA_RS24140
isoleucine prpC: 2-methylcitrate synthase AVA_RS13735
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate Shew_2732: L-lactate:Na+ symporter, small component
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
lactose SemiSWEET: Sugar transporter SemiSWEET AVA_RS02975
leucine aacS: acetoacetyl-CoA synthetase AVA_RS20210
leucine atoB: acetyl-CoA C-acetyltransferase
leucine ilvE: L-leucine transaminase AVA_RS09755
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AVA_RS02615
leucine liuC: 3-methylglutaconyl-CoA hydratase AVA_RS00835
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) AVA_RS07875 AVA_RS14900
lysine hglS: D-2-hydroxyglutarate synthase
lysine hisP: L-lysine ABC transporter, ATPase component HisP AVA_RS03725 AVA_RS14480
lysine lysN: 2-aminoadipate transaminase AVA_RS10755 AVA_RS01075
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose SemiSWEET: Sugar transporter SemiSWEET AVA_RS02975
maltose susB: alpha-glucosidase (maltase) AVA_RS10190
mannitol mt2d: mannitol 2-dehydrogenase AVA_RS11870 AVA_RS16885
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase AVA_RS14780 AVA_RS01255
mannose man-isomerase: D-mannose isomerase
mannose scrK: fructokinase AVA_RS14780 AVA_RS01255
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 AVA_RS13955
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase AVA_RS12615
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase AVA_RS07875 AVA_RS14900
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) AVA_RS23500 AVA_RS17650
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
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 AVA_RS00835
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AVA_RS00835 AVA_RS16900
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase AVA_RS19075 AVA_RS28475
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase AVA_RS20210
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase AVA_RS20210
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase AVA_RS01450 AVA_RS25360
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase AVA_RS12710
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase AVA_RS14900
propionate prpB: 2-methylisocitrate lyase AVA_RS24140
propionate prpC: 2-methylcitrate synthase AVA_RS13735
propionate prpD: 2-methylcitrate dehydratase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase AVA_RS01075 AVA_RS18905
putrescine patA: putrescine aminotransferase (PatA/SpuC) AVA_RS01075 AVA_RS18905
putrescine patD: gamma-aminobutyraldehyde dehydrogenase AVA_RS07875 AVA_RS14900
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) AVA_RS11645
rhamnose LRA1: L-rhamnofuranose dehydrogenase AVA_RS09415 AVA_RS19075
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase AVA_RS19075 AVA_RS17510
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase AVA_RS10475
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase AVA_RS03415 AVA_RS13915
sorbitol scrK: fructokinase AVA_RS14780 AVA_RS01255
sorbitol sdh: sorbitol dehydrogenase AVA_RS00775 AVA_RS17510
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose scrK: fructokinase AVA_RS14780 AVA_RS01255
threonine adh: acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
thymidine adh: acetaldehyde dehydrogenase (not acylating) AVA_RS17895 AVA_RS18330
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase AVA_RS19095
thymidine nupC: thymidine permease NupC AVA_RS14285
trehalose SemiSWEET: Sugar transporter SemiSWEET AVA_RS02975
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase AVA_RS20210
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase AVA_RS01450 AVA_RS25360
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase AVA_RS00835
valine mmsA: methylmalonate-semialdehyde dehydrogenase AVA_RS07875 AVA_RS14900
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine prpB: 2-methylisocitrate lyase AVA_RS24140
valine prpC: 2-methylcitrate synthase AVA_RS13735
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase AVA_RS00775 AVA_RS11870
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylF: ABC transporter for xylose, substrate binding component xylF
xylose xylH: ABC transporter for xylose, permease component xylH AVA_RS10985

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