GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Halococcus hamelinensis 100A6

Found 116 low-confidence and 83 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) C447_RS14150 C447_RS12725
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase C447_RS11295 C447_RS11285
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 C447_RS03850 C447_RS17195
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) C447_RS09460
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C447_RS09440
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C447_RS09445 C447_RS08145
arabinose xacC: L-arabinono-1,4-lactonase C447_RS09600
arabinose xacD: L-arabinonate dehydratase C447_RS02110 C447_RS13870
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine gabT: gamma-aminobutyrate transaminase C447_RS12035 C447_RS02065
arginine patA: putrescine aminotransferase (PatA/SpuC) C447_RS12035 C447_RS02065
arginine patD: gamma-aminobutyraldehyde dehydrogenase C447_RS14150 C447_RS12725
arginine rocE: L-arginine permease
asparagine ans: asparaginase C447_RS12975 C447_RS14305
cellobiose bgl: cellobiase C447_RS17345 C447_RS17350
cellobiose glk: glucokinase C447_RS07910
cellobiose MFS-glucose: glucose transporter, MFS superfamily C447_RS08630
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component C447_RS05920 C447_RS15655
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
citrulline gabT: gamma-aminobutyrate transaminase C447_RS12035 C447_RS02065
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) C447_RS12035 C447_RS02065
citrulline patD: gamma-aminobutyraldehyde dehydrogenase C447_RS14150 C447_RS12725
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase C447_RS06525 C447_RS09330
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase C447_RS04825 C447_RS15055
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) C447_RS14150 C447_RS12725
deoxyinosine deoB: phosphopentomutase C447_RS10955 C447_RS04600
deoxyinosine deoD: deoxyinosine phosphorylase C447_RS14700 C447_RS15095
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase C447_RS03510 C447_RS08130
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase C447_RS02885 C447_RS09975
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme C447_RS05595
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) C447_RS14150 C447_RS12725
deoxyribose deoK: deoxyribokinase C447_RS02450
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) C447_RS14150 C447_RS12725
fucose aldA: lactaldehyde dehydrogenase C447_RS14150 C447_RS12725
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 sdcL: fumarate:Na+ symporter SdcL C447_RS07255
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP C447_RS08630
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT C447_RS12060 C447_RS10255
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) C447_RS15235
glucose glk: glucokinase C447_RS07910
glucose MFS-glucose: glucose transporter, MFS superfamily C447_RS08630
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuA: D-mannonate dehydratase C447_RS02325 C447_RS01785
glucuronate uxuB: D-mannonate dehydrogenase
glycerol dhaD: glycerol dehydrogenase C447_RS15205 C447_RS02270
glycerol dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M C447_RS13130
glycerol glpF: glycerol facilitator glpF
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase C447_RS08590 C447_RS15870
isoleucine bcaP: L-isoleucine uptake transporter BcaP/CitA C447_RS14635
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C447_RS04265 C447_RS01450
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C447_RS08105 C447_RS11805
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C447_RS02885 C447_RS17005
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit C447_RS08245 C447_RS12030
L-malate sdlC: L-malate:Na+ symporter SdlC C447_RS07255
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase C447_RS07910
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) C447_RS11165 C447_RS17345
leucine aacS: acetoacetyl-CoA synthetase C447_RS03510 C447_RS08130
leucine bcaP: L-leucine uptake transporter BcaP C447_RS14635
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C447_RS04265 C447_RS01450
leucine liuA: isovaleryl-CoA dehydrogenase C447_RS08590 C447_RS15870
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit C447_RS08245 C447_RS12030
leucine liuC: 3-methylglutaconyl-CoA hydratase C447_RS08105 C447_RS15595
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit C447_RS06685 C447_RS08260
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine davA: 5-aminovaleramidase C447_RS11190
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase C447_RS12725 C447_RS14150
lysine davT: 5-aminovalerate aminotransferase C447_RS12035 C447_RS11500
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C447_RS08105 C447_RS15595
lysine gcdG: succinyl-CoA:glutarate CoA-transferase C447_RS07395 C447_RS12490
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase C447_RS07910
maltose MFS-glucose: glucose transporter, MFS superfamily C447_RS08630
maltose susB: alpha-glucosidase (maltase) C447_RS13145
mannitol mt2d: mannitol 2-dehydrogenase C447_RS02885 C447_RS07170
mannitol PLT5: polyol transporter PLT5 C447_RS08630
mannitol scrK: fructokinase C447_RS14185 C447_RS14190
mannose manA: mannose-6-phosphate isomerase C447_RS04600 C447_RS02840
mannose manP: mannose PTS system, EII-CBA components C447_RS02455
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase C447_RS14190
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
myoinositol iolT: myo-inositol:H+ symporter C447_RS08630
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) C447_RS15235
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 C447_RS08105 C447_RS11805
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C447_RS08125 C447_RS15595
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase C447_RS02785
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase C447_RS02785
phenylacetate paaK: phenylacetate-CoA ligase C447_RS08130
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase C447_RS08125 C447_RS02665
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylalanine paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase C447_RS08105 C447_RS11805
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C447_RS08125 C447_RS15595
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase C447_RS02785
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase C447_RS02785
phenylalanine paaZ1: oxepin-CoA hydrolase C447_RS08125 C447_RS02665
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase C447_RS01765 C447_RS14150
propionate lctP: propionate permease C447_RS01800
propionate pccA: propionyl-CoA carboxylase, alpha subunit C447_RS08245 C447_RS12030
propionate prpE: propionyl-CoA synthetase C447_RS05490 C447_RS05510
putrescine gabT: gamma-aminobutyrate transaminase C447_RS12035 C447_RS02065
putrescine patA: putrescine aminotransferase (PatA/SpuC) C447_RS12035 C447_RS02065
putrescine patD: gamma-aminobutyraldehyde dehydrogenase C447_RS14150 C447_RS12725
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) C447_RS05475
rhamnose aldA: lactaldehyde dehydrogenase C447_RS14150 C447_RS12725
rhamnose LRA1: L-rhamnofuranose dehydrogenase C447_RS05270 C447_RS01770
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase C447_RS02110 C447_RS01785
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase C447_RS11360 C447_RS02120
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase C447_RS02450
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) C447_RS09460
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C447_RS09440
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C447_RS09445 C447_RS08145
sorbitol scrK: fructokinase C447_RS14185 C447_RS14190
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 C447_RS08630
sucrose ams: sucrose hydrolase (invertase)
threonine adh: acetaldehyde dehydrogenase (not acylating) C447_RS14150 C447_RS12725
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) C447_RS09460
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) C447_RS09440
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) C447_RS09445 C447_RS08145
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) C447_RS06595 C447_RS06600
thymidine adh: acetaldehyde dehydrogenase (not acylating) C447_RS14150 C447_RS12725
thymidine deoB: phosphopentomutase C447_RS10955 C447_RS04600
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase C447_RS07910
trehalose MFS-glucose: glucose transporter, MFS superfamily C447_RS08630
trehalose treF: trehalase C447_RS10270 C447_RS05535
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase C447_RS03510 C447_RS08130
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase C447_RS02350 C447_RS12770
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase C447_RS08590 C447_RS15870
valine bcaP: L-valine uptake transporter BcaP/CitA C447_RS14635
valine bch: 3-hydroxyisobutyryl-CoA hydrolase C447_RS11805 C447_RS08105
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component C447_RS04265 C447_RS01450
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase C447_RS08105 C447_RS15595
valine mmsB: 3-hydroxyisobutyrate dehydrogenase C447_RS11635
valine pccA: propionyl-CoA carboxylase, alpha subunit C447_RS08245 C447_RS12030
xylitol PLT5: xylitol:H+ symporter PLT5 C447_RS08630
xylitol xdhA: xylitol dehydrogenase C447_RS10170 C447_RS05270
xylitol xylB: xylulokinase C447_RS11625
xylose xad: D-xylonate dehydratase C447_RS02110 C447_RS13870
xylose xylT: D-xylose transporter C447_RS08630

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