GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Hippea jasoniae Mar08-272r

Found 160 low-confidence and 58 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 EK17_RS07690 EK17_RS06455
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component EK17_RS07695 EK17_RS06450
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) EK17_RS08750 EK17_RS06045
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase EK17_RS01845
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 snatA: L-alanine symporter SnatA EK17_RS02595
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine put1: proline dehydrogenase EK17_RS03485
arginine rocD: ornithine aminotransferase EK17_RS05995 EK17_RS07835
arginine rocE: L-arginine permease
arginine rocF: arginase EK17_RS08100
asparagine ans: asparaginase
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component EK17_RS07620 EK17_RS04610
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 EK17_RS07615
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 put1: proline dehydrogenase EK17_RS03485
citrulline rocD: ornithine aminotransferase EK17_RS05995 EK17_RS07835
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase EK17_RS06325 EK17_RS02610
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 EK17_RS06155
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) EK17_RS08750 EK17_RS06045
deoxyinosine deoB: phosphopentomutase EK17_RS02620
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase EK17_RS00290
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase EK17_RS08300
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) EK17_RS08750 EK17_RS06045
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) EK17_RS08750 EK17_RS06045
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) EK17_RS08755 EK17_RS05625
fructose scrK: fructokinase
fructose Slc2a5: fructose:H+ symporter
fucose fucA: L-fuculose-phosphate aldolase FucA EK17_RS05195
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 dctQ: fumarate TRAP transporter, small permease component DctQ EK17_RS08660 EK17_RS02850
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase EK17_RS04970
galactose pgmA: alpha-phosphoglucomutase EK17_RS05875 EK17_RS02620
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) EK17_RS01610
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase EK17_RS06045 EK17_RS08750
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent EK17_RS07975
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase EK17_RS01265 EK17_RS08100
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase EK17_RS08525 EK17_RS08775
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase EK17_RS00745 EK17_RS05695
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase EK17_RS00290
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) EK17_RS01270 EK17_RS03230
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) EK17_RS03220 EK17_RS04040
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit EK17_RS05865 EK17_RS01750
L-lactate L-LDH: L-lactate dehydrogenase EK17_RS02830
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate dctQ: L-malate TRAP tranpsorter, small permease component DctQ EK17_RS08660 EK17_RS02850
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase EK17_RS04970
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase EK17_RS05875 EK17_RS02620
leucine liuA: isovaleryl-CoA dehydrogenase EK17_RS08525 EK17_RS08775
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit EK17_RS05865 EK17_RS02835
leucine liuC: 3-methylglutaconyl-CoA hydratase EK17_RS00745 EK17_RS05695
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit EK17_RS05870
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) EK17_RS01270 EK17_RS03230
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) EK17_RS03220 EK17_RS04040
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) EK17_RS06045
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase EK17_RS07835
lysine lysN: 2-aminoadipate transaminase EK17_RS03975 EK17_RS07835
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
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
myoinositol mmsA: malonate-semialdehyde dehydrogenase EK17_RS06045
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) EK17_RS01610
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 EK17_RS00745 EK17_RS01785
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase EK17_RS00745 EK17_RS01785
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase EK17_RS08780 EK17_RS00755
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase EK17_RS08780 EK17_RS00755
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase EK17_RS00745
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit EK17_RS04015 EK17_RS01335
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) EK17_RS03210 EK17_RS03300
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) EK17_RS03305 EK17_RS03215
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) EK17_RS03225 EK17_RS03315
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK EK17_RS01270 EK17_RS03230
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) EK17_RS03220 EK17_RS01290
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 EK17_RS00745 EK17_RS01785
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase EK17_RS00745 EK17_RS01785
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase EK17_RS08780 EK17_RS00755
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase EK17_RS08780 EK17_RS00755
phenylalanine paaZ1: oxepin-CoA hydrolase EK17_RS00745
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline HSERO_RS00870: proline ABC transporter, substrate-binding component EK17_RS03230
proline HSERO_RS00885: proline ABC transporter, permease component 1 EK17_RS03225 EK17_RS03315
proline HSERO_RS00890: proline ABC transporter, permease component 2 EK17_RS03220 EK17_RS01290
proline HSERO_RS00895: proline ABC transporter, ATPase component 1 EK17_RS03215 EK17_RS03305
proline HSERO_RS00900: proline ABC transporter, ATPase component 2 EK17_RS03210 EK17_RS03300
proline put1: proline dehydrogenase EK17_RS03485
propionate pccA: propionyl-CoA carboxylase, alpha subunit EK17_RS05865 EK17_RS01750
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase EK17_RS06045
putrescine gabT: gamma-aminobutyrate transaminase EK17_RS05995 EK17_RS07835
putrescine patA: putrescine aminotransferase (PatA/SpuC) EK17_RS07835 EK17_RS05995
putrescine patD: gamma-aminobutyraldehyde dehydrogenase EK17_RS06045 EK17_RS08750
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
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
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase EK17_RS06155 EK17_RS02605
serine snatA: L-serine transporter EK17_RS02595
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase EK17_RS00290 EK17_RS05395
sucrose ams: sucrose hydrolase (invertase)
sucrose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
threonine pccA: propionyl-CoA carboxylase, alpha subunit EK17_RS05865 EK17_RS01750
threonine snatA: L-threonine transporter snatA EK17_RS02595
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) EK17_RS08750 EK17_RS06045
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase EK17_RS02620
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase EK17_RS08525 EK17_RS08775
valine bch: 3-hydroxyisobutyryl-CoA hydrolase EK17_RS00745
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) EK17_RS01270 EK17_RS03230
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) EK17_RS04040 EK17_RS03310
valine mmsA: methylmalonate-semialdehyde dehydrogenase EK17_RS06045
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit EK17_RS05865 EK17_RS01750
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
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