GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Halostagnicola larsenii XH-48

Found 126 low-confidence and 80 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 mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase HALLA_RS17020 HALLA_RS18275
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase HALLA_RS19675
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate actP: cation/acetate symporter ActP HALLA_RS04280
alanine TRIC: TRIC-type L-alanine transporter HALLA_RS19710
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arginine gabT: gamma-aminobutyrate transaminase HALLA_RS19230 HALLA_RS14205
arginine patA: putrescine aminotransferase (PatA/SpuC) HALLA_RS19230 HALLA_RS14205
arginine patD: gamma-aminobutyraldehyde dehydrogenase HALLA_RS18050 HALLA_RS14430
arginine rocE: L-arginine permease
asparagine ans: asparaginase HALLA_RS17120 HALLA_RS02145
cellobiose bgl: cellobiase HALLA_RS07580 HALLA_RS17945
cellobiose glk: glucokinase HALLA_RS12035
cellobiose MFS-glucose: glucose transporter, MFS superfamily HALLA_RS13415
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HALLA_RS09445 HALLA_RS13735
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 HALLA_RS19230 HALLA_RS14205
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) HALLA_RS19230 HALLA_RS14205
citrulline patD: gamma-aminobutyraldehyde dehydrogenase HALLA_RS18050 HALLA_RS14430
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase HALLA_RS07515 HALLA_RS07995
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 HALLA_RS11190 HALLA_RS14105
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component HALLA_RS06250
deoxyinosine deoB: phosphopentomutase HALLA_RS09890 HALLA_RS08790
deoxyinosine deoD: deoxyinosine phosphorylase HALLA_RS03035 HALLA_RS02200
deoxyinosine nupA: deoxyinosine ABC transporter, ATPase component HALLA_RS06245
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 HALLA_RS06240
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 HALLA_RS06235
deoxyribonate aacS: acetoacetyl-CoA synthetase HALLA_RS14455 HALLA_RS17725
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HALLA_RS09780 HALLA_RS01605
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase HALLA_RS16360
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase HALLA_RS07850
deoxyribose deoP: deoxyribose transporter
fucose fdh: L-fucose 1-dehydrogenase HALLA_RS17485 HALLA_RS13835
fucose fucD: L-fuconate dehydratase HALLA_RS16045 HALLA_RS14680
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase HALLA_RS01605 HALLA_RS00675
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA HALLA_RS19395
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP HALLA_RS13415
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase HALLA_RS16045
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT HALLA_RS17270 HALLA_RS16225
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) HALLA_RS08695 HALLA_RS08335
glucose glk: glucokinase HALLA_RS12035
glucose MFS-glucose: glucose transporter, MFS superfamily HALLA_RS13415
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase HALLA_RS19090 HALLA_RS18665
glucuronate uxuB: D-mannonate dehydrogenase
glycerol dhaD: glycerol dehydrogenase HALLA_RS06060 HALLA_RS00675
glycerol dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M HALLA_RS15725
glycerol glpF: glycerol facilitator glpF
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 bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HALLA_RS12955 HALLA_RS18190
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALLA_RS18415 HALLA_RS12950
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HALLA_RS14450 HALLA_RS17640
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase HALLA_RS01550 HALLA_RS17665
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HALLA_RS16020 HALLA_RS07355
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) HALLA_RS14500 HALLA_RS00025
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) HALLA_RS00015
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit HALLA_RS05450 HALLA_RS19235
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase HALLA_RS12035
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase HALLA_RS14455 HALLA_RS17725
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HALLA_RS12955 HALLA_RS18190
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALLA_RS18415 HALLA_RS12950
leucine liuA: isovaleryl-CoA dehydrogenase HALLA_RS03870 HALLA_RS05220
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HALLA_RS05450 HALLA_RS19235
leucine liuC: 3-methylglutaconyl-CoA hydratase HALLA_RS09800 HALLA_RS14450
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit HALLA_RS03905 HALLA_RS05460
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) HALLA_RS14500 HALLA_RS00025
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) HALLA_RS00015
lysine davA: 5-aminovaleramidase HALLA_RS05235
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase HALLA_RS14430 HALLA_RS18080
lysine davT: 5-aminovalerate aminotransferase HALLA_RS19230 HALLA_RS14145
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase HALLA_RS14450 HALLA_RS09800
lysine gcdG: succinyl-CoA:glutarate CoA-transferase HALLA_RS19310 HALLA_RS14165
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase HALLA_RS12035
maltose MFS-glucose: glucose transporter, MFS superfamily HALLA_RS13415
maltose susB: alpha-glucosidase (maltase) HALLA_RS12545 HALLA_RS15110
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase HALLA_RS00130 HALLA_RS08790
mannose manP: mannose PTS system, EII-CBA components HALLA_RS08425
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase HALLA_RS17075 HALLA_RS18025
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter HALLA_RS13415
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase HALLA_RS19090 HALLA_RS18665
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) HALLA_RS08695 HALLA_RS08335
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 HALLA_RS14450 HALLA_RS17640
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase HALLA_RS01550 HALLA_RS17665
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase HALLA_RS01550 HALLA_RS17665
phenylacetate paaK: phenylacetate-CoA ligase HALLA_RS17725 HALLA_RS18130
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase HALLA_RS14480 HALLA_RS11740
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
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 HALLA_RS14450 HALLA_RS17640
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase HALLA_RS01550 HALLA_RS17665
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase HALLA_RS01550 HALLA_RS17665
phenylalanine paaK: phenylacetate-CoA ligase HALLA_RS17725 HALLA_RS18130
phenylalanine paaZ1: oxepin-CoA hydrolase HALLA_RS14480 HALLA_RS11740
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine PPDCalpha: phenylpyruvate decarboxylase, alpha subunit HALLA_RS12960 HALLA_RS18515
phenylalanine PPDCbeta: phenylpyruvate decarboxylase, beta subunit HALLA_RS12955 HALLA_RS18190
proline ectP: proline transporter EctP HALLA_RS19430 HALLA_RS14125
proline put1: proline dehydrogenase HALLA_RS02400
proline putA: L-glutamate 5-semialdeyde dehydrogenase HALLA_RS16180 HALLA_RS14710
propionate pccA: propionyl-CoA carboxylase, alpha subunit HALLA_RS05450 HALLA_RS19235
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase HALLA_RS19230 HALLA_RS14205
putrescine patA: putrescine aminotransferase (PatA/SpuC) HALLA_RS19230 HALLA_RS14205
putrescine patD: gamma-aminobutyraldehyde dehydrogenase HALLA_RS18050 HALLA_RS14430
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase HALLA_RS14710 HALLA_RS14430
rhamnose LRA1: L-rhamnofuranose dehydrogenase HALLA_RS00675 HALLA_RS07805
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase HALLA_RS16045 HALLA_RS18665
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase HALLA_RS18275 HALLA_RS17020
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase HALLA_RS07850
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol scrK: fructokinase HALLA_RS15950
sorbitol sdh: sorbitol dehydrogenase HALLA_RS07805 HALLA_RS01605
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 HALLA_RS13415
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) HALLA_RS15745
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) HALLA_RS10160 HALLA_RS10165
threonine ltaE: L-threonine aldolase HALLA_RS05870
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase HALLA_RS09890 HALLA_RS08790
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase HALLA_RS12035
trehalose MFS-glucose: glucose transporter, MFS superfamily HALLA_RS13415
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tyrosine aacS: acetoacetyl-CoA synthetase HALLA_RS14455 HALLA_RS17725
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase HALLA_RS14925 HALLA_RS08240
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HALLA_RS12955 HALLA_RS18190
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALLA_RS18415 HALLA_RS12950
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase HALLA_RS14450 HALLA_RS09800
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit HALLA_RS05450 HALLA_RS19235
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) HALLA_RS08425
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase HALLA_RS14685 HALLA_RS16990
xylose xylT: D-xylose transporter HALLA_RS13415

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