GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Erythrobacter gangjinensis K7-2

Found 114 low-confidence and 55 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP AAW01_RS02550
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) AAW01_RS11975 AAW01_RS00220
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
arginine astA: arginine N-succinyltransferase AAW01_RS05075
arginine astC: succinylornithine transaminase AAW01_RS09055
arginine astE: succinylglutamate desuccinylase
arginine rocE: L-arginine permease
aspartate glt: aspartate:proton symporter Glt AAW01_RS13020
cellobiose glk: glucokinase AAW01_RS12295
cellobiose MFS-glucose: glucose transporter, MFS superfamily AAW01_RS10155
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AAW01_RS09690 AAW01_RS11525
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 AAW01_RS09855
citrulline ocd: ornithine cyclodeaminase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase AAW01_RS00865 AAW01_RS11705
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase AAW01_RS06070 AAW01_RS03555
D-serine dsdX: D-serine transporter DsdX AAW01_RS06720
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) AAW01_RS11975 AAW01_RS00220
deoxyinosine deoB: phosphopentomutase AAW01_RS12560
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase AAW01_RS06200
deoxyinosine nupC: deoxyinosine:H+ symporter NupC AAW01_RS05185
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AAW01_RS06580 AAW01_RS03665
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) AAW01_RS11975 AAW01_RS00220
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase AAW01_RS08110
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) AAW01_RS11975 AAW01_RS00220
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase AAW01_RS04300 AAW01_RS09770
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 AAW01_RS10155
fucose fucU: L-fucose mutarotase FucU
galactose galE: UDP-glucose 4-epimerase AAW01_RS13100 AAW01_RS10190
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose HP1174: Na+-dependent galactose transporter AAW01_RS10155
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase AAW01_RS05290
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase AAW01_RS05315
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT AAW01_RS06720
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) AAW01_RS04965
glucose glk: glucokinase AAW01_RS12295
glucose MFS-glucose: glucose transporter, MFS superfamily AAW01_RS10155
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component AAW01_RS05305
glucuronate uxaC: D-glucuronate isomerase AAW01_RS05315
glutamate gdhA: glutamate dehydrogenase, NAD-dependent AAW01_RS07660 AAW01_RS13210
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) AAW01_RS13670
glycerol glpF: glycerol facilitator glpF AAW01_RS09185
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase AAW01_RS10540 AAW01_RS07145
isoleucine Bap2: L-isoleucine permease Bap2
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase AAW01_RS13100 AAW01_RS10190
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase AAW01_RS12295
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine leuT: L-leucine:Na+ symporter LeuT AAW01_RS01765
leucine liuC: 3-methylglutaconyl-CoA hydratase AAW01_RS13205 AAW01_RS11465
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit AAW01_RS07130 AAW01_RS04080
leucine liuE: hydroxymethylglutaryl-CoA lyase AAW01_RS11300
lysine davA: 5-aminovaleramidase AAW01_RS00785 AAW01_RS09855
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase AAW01_RS09770 AAW01_RS04300
lysine davT: 5-aminovalerate aminotransferase AAW01_RS09055 AAW01_RS12605
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AAW01_RS00825 AAW01_RS06205
lysine gcdG: succinyl-CoA:glutarate CoA-transferase AAW01_RS11415 AAW01_RS11420
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase AAW01_RS12295
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase AAW01_RS09890 AAW01_RS13200
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) AAW01_RS04965
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 AAW01_RS13205 AAW01_RS03435
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase AAW01_RS00825 AAW01_RS06205
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase AAW01_RS00830 AAW01_RS02970
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase AAW01_RS00830 AAW01_RS02970
phenylacetate paaK: phenylacetate-CoA ligase AAW01_RS11440 AAW01_RS00835
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase AAW01_RS13205
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter AAW01_RS00770
putrescine gabT: gamma-aminobutyrate transaminase AAW01_RS09055 AAW01_RS12605
putrescine patA: putrescine aminotransferase (PatA/SpuC) AAW01_RS09055 AAW01_RS12605
putrescine patD: gamma-aminobutyraldehyde dehydrogenase AAW01_RS09770 AAW01_RS04390
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) AAW01_RS03875
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) AAW01_RS03880
rhamnose aldA: lactaldehyde dehydrogenase AAW01_RS04300 AAW01_RS09770
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 AAW01_RS08110
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter AAW01_RS06870
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase AAW01_RS11455 AAW01_RS01220
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) AAW01_RS05140
sucrose glk: glucokinase AAW01_RS12295
sucrose MFS-glucose: glucose transporter, MFS superfamily AAW01_RS10155
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) AAW01_RS10165 AAW01_RS10170
threonine snatA: L-threonine transporter snatA AAW01_RS06870
thymidine adh: acetaldehyde dehydrogenase (not acylating) AAW01_RS11975 AAW01_RS00220
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase AAW01_RS12560
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase AAW01_RS12295
trehalose MFS-glucose: glucose transporter, MFS superfamily AAW01_RS10155
trehalose treF: trehalase AAW01_RS05140 AAW01_RS03580
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase AAW01_RS10540 AAW01_RS07145
valine Bap2: L-valine permease Bap2
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase AAW01_RS09765
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 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:

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