GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Acidovorax sp. GW101-3H11

Found 70 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP Ac3H11_3022
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine TRIC: TRIC-type L-alanine transporter Ac3H11_3909
arginine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC Ac3H11_2396 Ac3H11_552
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) Ac3H11_1694 Ac3H11_1938
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) Ac3H11_4630 Ac3H11_1937
arginine braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) Ac3H11_1692 Ac3H11_1936
cellobiose bgl: cellobiase
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Ac3H11_4899 Ac3H11_2553
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 Ac3H11_3200 Ac3H11_3326
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 Ac3H11_2554 Ac3H11_3326
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component Ac3H11_2555
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
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
deoxyinosine deoB: phosphopentomutase Ac3H11_444
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Ac3H11_493 Ac3H11_2762
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme Ac3H11_1929
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
fucose aldA: lactaldehyde dehydrogenase Ac3H11_1496 Ac3H11_4393
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
galacturonate exuT: D-galacturonate transporter ExuT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) Ac3H11_3072
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF Ac3H11_2337 Ac3H11_3954
glutamate gdhA: glutamate dehydrogenase, NAD-dependent Ac3H11_3282 Ac3H11_315
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) Ac3H11_797
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase Ac3H11_1332 Ac3H11_4179
lysine patD: 5-aminopentanal dehydrogenase Ac3H11_1496 Ac3H11_1480
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase Ac3H11_2939 Ac3H11_3445
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE Ac3H11_2944
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) Ac3H11_2943
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) Ac3H11_2942 Ac3H11_794
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG Ac3H11_2941 Ac3H11_4785
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 Ac3H11_658
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Ac3H11_3072
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 paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Ac3H11_2719 Ac3H11_4989
phenylacetate paaK: phenylacetate-CoA ligase Ac3H11_4625 Ac3H11_964
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Ac3H11_3089
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase Ac3H11_1679
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase Ac3H11_4179 Ac3H11_4342
putrescine patA: putrescine aminotransferase (PatA/SpuC) Ac3H11_4342 Ac3H11_1332
putrescine patD: gamma-aminobutyraldehyde dehydrogenase Ac3H11_1496 Ac3H11_1486
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase Ac3H11_1496 Ac3H11_4393
rhamnose LRA1: L-rhamnofuranose dehydrogenase Ac3H11_2257 Ac3H11_2748
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase Ac3H11_3953 Ac3H11_600
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase Ac3H11_3372 Ac3H11_1482
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sucrose ams: sucrose hydrolase (invertase)
threonine adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
threonine snatA: L-threonine transporter snatA Ac3H11_2153 Ac3H11_817
thymidine adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
thymidine deoA: thymidine phosphorylase DeoA Ac3H11_2202 Ac3H11_2615
thymidine deoB: phosphopentomutase Ac3H11_444
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase
tryptophan adh: acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
tryptophan andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa Ac3H11_214 Ac3H11_2771
tryptophan andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb Ac3H11_215
tryptophan andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc Ac3H11_217
tryptophan andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd Ac3H11_216
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan mhpD: 2-hydroxypentadienoate hydratase Ac3H11_1483 Ac3H11_4809
tryptophan praD: 2-oxohex-3-enedioate decarboxylase Ac3H11_1483 Ac3H11_4809
tryptophan xylE: catechol 2,3-dioxygenase
tyrosine hmgA: homogentisate dioxygenase
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Ac3H11_2396 Ac3H11_4169
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) Ac3H11_1694 Ac3H11_4628
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase Ac3H11_2257 Ac3H11_1922
xylose xdh: D-xylose dehydrogenase Ac3H11_614 Ac3H11_2257
xylose xylC: xylonolactonase Ac3H11_615 Ac3H11_2081

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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