GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sphingomonas koreensis DSMZ 15582

Found 77 low-confidence and 40 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
alanine snatA: L-alanine symporter SnatA Ga0059261_1304
arabinose araE: L-arabinose:H+ symporter Ga0059261_1891 Ga0059261_1777
arabinose xacC: L-arabinono-1,4-lactonase Ga0059261_1893
arabinose xacD: L-arabinonate dehydratase Ga0059261_2649 Ga0059261_4216
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine astC: succinylornithine transaminase Ga0059261_3205 Ga0059261_4131
arginine astE: succinylglutamate desuccinylase
arginine rocE: L-arginine permease
asparagine ans: asparaginase Ga0059261_1159 Ga0059261_3119
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Ga0059261_3653 Ga0059261_2293
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 Ga0059261_1979
citrulline rocD: ornithine aminotransferase Ga0059261_3205 Ga0059261_4131
D-alanine cycA: D-alanine:H+ symporter CycA Ga0059261_1053
D-alanine dadA: D-alanine dehydrogenase Ga0059261_3351
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 Ga0059261_3754 Ga0059261_3694
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) Ga0059261_4132 Ga0059261_1495
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase Ga0059261_1576
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Ga0059261_2655 Ga0059261_2637
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) Ga0059261_4132 Ga0059261_1495
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) Ga0059261_4132 Ga0059261_1495
fucose fucD: L-fuconate dehydratase Ga0059261_2974
fucose fuconolactonase: L-fucono-1,5-lactonase Ga0059261_2638
fucose fucP: L-fucose:H+ symporter FucP Ga0059261_0767 Ga0059261_2650
fucose fucU: L-fucose mutarotase FucU Ga0059261_2663
galactose dgoD: D-galactonate dehydratase Ga0059261_2649 Ga0059261_4216
galactose dgoK: 2-dehydro-3-deoxygalactonokinase Ga0059261_2965 Ga0059261_1624
galactose galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) Ga0059261_1893
galacturonate exuT: D-galacturonate transporter ExuT Ga0059261_2977 Ga0059261_1901
galacturonate kdgK: 2-keto-3-deoxygluconate kinase Ga0059261_2965 Ga0059261_1055
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase Ga0059261_2969
gluconate gntK: D-gluconate kinase
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX Ga0059261_1643
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT Ga0059261_1901 Ga0059261_2977
glucuronate kdgK: 2-keto-3-deoxygluconate kinase Ga0059261_2965 Ga0059261_1055
glucuronate uxaC: D-glucuronate isomerase Ga0059261_2969
glucuronate uxuB: D-mannonate dehydrogenase Ga0059261_2975
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) Ga0059261_3265
glycerol glpF: glycerol facilitator glpF Ga0059261_1307 Ga0059261_3272
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) Ga0059261_0551
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit Ga0059261_0548
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase Ga0059261_2908 Ga0059261_3685
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine davA: 5-aminovaleramidase Ga0059261_3603
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase Ga0059261_0516 Ga0059261_1680
lysine davT: 5-aminovalerate aminotransferase Ga0059261_4131 Ga0059261_3205
lysine lysP: L-lysine:H+ symporter LysP
mannitol mt2d: mannitol 2-dehydrogenase Ga0059261_2975 Ga0059261_1451
mannitol PLT5: polyol transporter PLT5 Ga0059261_1777
mannose gluP: mannose:Na+ symporter Ga0059261_0767 Ga0059261_2650
mannose man-isomerase: D-mannose isomerase
myoinositol iolG: myo-inositol 2-dehydrogenase Ga0059261_0656 Ga0059261_3126
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol kdgK: 2-keto-3-deoxygluconate kinase Ga0059261_2965 Ga0059261_1055
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase Ga0059261_2975
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 Ga0059261_3685 Ga0059261_2668
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Ga0059261_2888 Ga0059261_0982
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Ga0059261_0982 Ga0059261_2888
phenylacetate paaK: phenylacetate-CoA ligase Ga0059261_0835
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase Ga0059261_2858 Ga0059261_2803
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine QDPR: 6,7-dihydropteridine reductase Ga0059261_2819
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase Ga0059261_4131 Ga0059261_3205
putrescine patA: putrescine aminotransferase (PatA/SpuC) Ga0059261_4131 Ga0059261_3205
putrescine patD: gamma-aminobutyraldehyde dehydrogenase Ga0059261_3374 Ga0059261_1680
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter Ga0059261_0571
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter Ga0059261_1304
sorbitol sdh: sorbitol dehydrogenase Ga0059261_2655 Ga0059261_2966
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 Ga0059261_1777
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) Ga0059261_3258 Ga0059261_3259
threonine snatA: L-threonine transporter snatA Ga0059261_1304
thymidine adh: acetaldehyde dehydrogenase (not acylating) Ga0059261_4132 Ga0059261_1495
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase Ga0059261_3681 Ga0059261_3793
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase Ga0059261_3683 Ga0059261_2668
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase

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 preprint 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