GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sphaerochaeta globosa Buddy

Found 128 low-confidence and 76 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components SPIBUDDY_RS08215 SPIBUDDY_RS09570
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component SPIBUDDY_RS08205 SPIBUDDY_RS09575
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase SPIBUDDY_RS03625 SPIBUDDY_RS01715
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
alanine cycA: L-alanine symporter CycA
arginine arcA: arginine deiminase
arginine arcC: carbamate kinase SPIBUDDY_RS08385
arginine putA: L-glutamate 5-semialdeyde dehydrogenase
arginine rocD: ornithine aminotransferase SPIBUDDY_RS08005 SPIBUDDY_RS00625
arginine rocE: L-arginine permease
asparagine peb1C: aspartate ABC transporter, ATPase component Peb1C SPIBUDDY_RS03030 SPIBUDDY_RS06000
asparagine peb1D: aspartate ABC transporter, permease component 2 (Peb1D) SPIBUDDY_RS03015 SPIBUDDY_RS04730
aspartate peb1C: aspartate ABC transporter, ATPase component Peb1C SPIBUDDY_RS03030 SPIBUDDY_RS06000
aspartate peb1D: aspartate ABC transporter, permease component 2 (Peb1D) SPIBUDDY_RS03015 SPIBUDDY_RS04730
cellobiose glk: glucokinase SPIBUDDY_RS04920
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SPIBUDDY_RS13835 SPIBUDDY_RS04725
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 SPIBUDDY_RS06005 SPIBUDDY_RS04730
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 SPIBUDDY_RS06005 SPIBUDDY_RS03020
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase SPIBUDDY_RS08385
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase
citrulline rocD: ornithine aminotransferase SPIBUDDY_RS08005 SPIBUDDY_RS00625
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
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
deoxyinosine deoB: phosphopentomutase SPIBUDDY_RS10130
deoxyinosine H281DRAFT_01112: deoxynucleoside transporter, permease component 2 SPIBUDDY_RS12235 SPIBUDDY_RS00345
deoxyinosine H281DRAFT_01113: deoxynucleoside transporter, ATPase component SPIBUDDY_RS12240 SPIBUDDY_RS01670
deoxyinosine H281DRAFT_01114: deoxynucleoside transporter, substrate-binding component SPIBUDDY_RS12245
deoxyinosine H281DRAFT_01115: deoxynucleoside transporter, permease component 1 SPIBUDDY_RS12230
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase SPIBUDDY_RS04555
deoxyribose deoP: deoxyribose transporter
fructose fruE: fructose ABC transporter, substrate-binding component FruE SPIBUDDY_RS12350
fructose fruF: fructose ABC transporter, permease component 1 (FruF) SPIBUDDY_RS12360 SPIBUDDY_RS01675
fructose fruG: fructose ABC transporter, permease component 2 (FruG) SPIBUDDY_RS12365 SPIBUDDY_RS12650
fructose fruK: fructose ABC transporter, ATPase component FruK SPIBUDDY_RS12355 SPIBUDDY_RS12645
fructose scrK: fructokinase SPIBUDDY_RS09745 SPIBUDDY_RS08730
fucose aldA: lactaldehyde dehydrogenase
fucose fucA: L-fuculose-phosphate aldolase FucA SPIBUDDY_RS14935
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component SPIBUDDY_RS12655
fumarate dauA: fumarate transporter DauA SPIBUDDY_RS02510
galactose galK: galactokinase (-1-phosphate forming) SPIBUDDY_RS14115 SPIBUDDY_RS01915
galacturonate exuT: D-galacturonate transporter ExuT
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine glc-kinase: glucosamine kinase SPIBUDDY_RS08730
glucosamine SM_b21216: ABC transporter for D-Glucosamine, ATPase component SPIBUDDY_RS04280 SPIBUDDY_RS01600
glucose glk: glucokinase SPIBUDDY_RS04920
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctP: D-glucuronate TRAP transporter, solute receptor component SPIBUDDY_RS06180 SPIBUDDY_RS00970
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glutamate gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C) SPIBUDDY_RS06000 SPIBUDDY_RS03030
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
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 PA5503: L-histidine ABC transporter, ATPase component SPIBUDDY_RS14530 SPIBUDDY_RS06000
histidine PA5504: L-histidine ABC transporter, permease component SPIBUDDY_RS14525
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SPIBUDDY_RS03310
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SPIBUDDY_RS03310 SPIBUDDY_RS11300
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component SPIBUDDY_RS12525 SPIBUDDY_RS11310
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase SPIBUDDY_RS12250
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase SPIBUDDY_RS13160
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase SPIBUDDY_RS06555 SPIBUDDY_RS02345
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SPIBUDDY_RS10695 SPIBUDDY_RS03065
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit SPIBUDDY_RS02365
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming) SPIBUDDY_RS14115 SPIBUDDY_RS01915
lactose glk: glucokinase SPIBUDDY_RS04920
lactose lacE: lactose ABC transporter, substrate-binding component SPIBUDDY_RS05035
lactose lacK: lactose ABC transporter, ATPase component SPIBUDDY_RS04280 SPIBUDDY_RS08265
leucine aacS: acetoacetyl-CoA synthetase
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SPIBUDDY_RS03310
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SPIBUDDY_RS03310 SPIBUDDY_RS11300
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component SPIBUDDY_RS12525 SPIBUDDY_RS11310
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SPIBUDDY_RS02365
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SPIBUDDY_RS10695 SPIBUDDY_RS03065
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase SPIBUDDY_RS00625 SPIBUDDY_RS08005
lysine lysN: 2-aminoadipate transaminase SPIBUDDY_RS10295 SPIBUDDY_RS00625
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase SPIBUDDY_RS02460
maltose glk: glucokinase SPIBUDDY_RS04920
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase SPIBUDDY_RS05145
myoinositol iolM: 2-inosose 4-dehydrogenase SPIBUDDY_RS02650 SPIBUDDY_RS11255
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase SPIBUDDY_RS15030 SPIBUDDY_RS15860
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase SPIBUDDY_RS14090
NAG nagK: N-acetylglucosamine kinase SPIBUDDY_RS01210
NAG SMc02869: N-acetylglucosamine ABC transporter, ATPase component SPIBUDDY_RS04280 SPIBUDDY_RS02620
NAG SMc02872: N-acetylglucosamine ABC transporter, permease component 1 SPIBUDDY_RS01225 SPIBUDDY_RS02590
NAG SMc02873: N-acetylglucosamine ABC transporter, substrate-binding component SPIBUDDY_RS01230
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
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase SPIBUDDY_RS11090 SPIBUDDY_RS02345
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine fahA: fumarylacetoacetate hydrolase SPIBUDDY_RS00685
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) SPIBUDDY_RS10680 SPIBUDDY_RS03080
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) SPIBUDDY_RS10690 SPIBUDDY_RS03070
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) SPIBUDDY_RS10685 SPIBUDDY_RS03075
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate epi: methylmalonyl-CoA epimerase SPIBUDDY_RS12250
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit SPIBUDDY_RS02365
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter SPIBUDDY_RS08805
putrescine gabD: succinate semialdehyde dehydrogenase SPIBUDDY_RS04860 SPIBUDDY_RS00900
putrescine gabT: gamma-aminobutyrate transaminase SPIBUDDY_RS08005 SPIBUDDY_RS00625
putrescine patA: putrescine aminotransferase (PatA/SpuC) SPIBUDDY_RS00625 SPIBUDDY_RS08005
putrescine patD: gamma-aminobutyraldehyde dehydrogenase SPIBUDDY_RS06305
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) SPIBUDDY_RS08790 SPIBUDDY_RS15310
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) SPIBUDDY_RS08795
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) SPIBUDDY_RS03220 SPIBUDDY_RS08800
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose rhaB: L-rhamnulokinase SPIBUDDY_RS11280
rhamnose rhaD: rhamnulose 1-phosphate aldolase
ribose rbsA: D-ribose ABC transporter, ATPase component RbsA SPIBUDDY_RS11335 SPIBUDDY_RS01670
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB SPIBUDDY_RS01665 SPIBUDDY_RS11340
ribose rbsC: D-ribose ABC transporter, permease component RbsC SPIBUDDY_RS01675 SPIBUDDY_RS00345
ribose rbsK: ribokinase SPIBUDDY_RS04555
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase SPIBUDDY_RS11290 SPIBUDDY_RS02345
succinate dauA: succinate:H+ symporter DauA SPIBUDDY_RS02510
sucrose ams: sucrose hydrolase (invertase) SPIBUDDY_RS05940
sucrose fruE: fructose ABC transporter, substrate-binding component FruE SPIBUDDY_RS12350
sucrose fruF: fructose ABC transporter, permease component 1 (FruF) SPIBUDDY_RS12360 SPIBUDDY_RS01675
sucrose fruG: fructose ABC transporter, permease component 2 (FruG) SPIBUDDY_RS12365 SPIBUDDY_RS12650
sucrose fruK: fructose ABC transporter, ATPase component FruK SPIBUDDY_RS12355 SPIBUDDY_RS12645
sucrose scrK: fructokinase SPIBUDDY_RS09745 SPIBUDDY_RS08730
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) SPIBUDDY_RS10635 SPIBUDDY_RS10640
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase SPIBUDDY_RS10130
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase SPIBUDDY_RS04920
trehalose treF: trehalase SPIBUDDY_RS05940
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase SPIBUDDY_RS00685
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SPIBUDDY_RS03310
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SPIBUDDY_RS03310 SPIBUDDY_RS11300
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component SPIBUDDY_RS12525 SPIBUDDY_RS11310
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine epi: methylmalonyl-CoA epimerase SPIBUDDY_RS12250
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SPIBUDDY_RS10695 SPIBUDDY_RS03065
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase SPIBUDDY_RS02570 SPIBUDDY_RS00900
valine pccA: propionyl-CoA carboxylase, alpha subunit SPIBUDDY_RS02365
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol PLT5: xylitol:H+ symporter PLT5

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