GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Halopiger salifodinae KCY07-B2

Found 124 low-confidence and 72 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 LT39_RS09665 LT39_RS05195
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component LT39_RS05205
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase LT39_RS07720 LT39_RS07770
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK LT39_RS07700
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase LT39_RS11520
acetate actP: cation/acetate symporter ActP
alanine cycA: L-alanine symporter CycA
arabinose xacC: L-arabinono-1,4-lactonase
arabinose xacD: L-arabinonate dehydratase LT39_RS12220 LT39_RS04010
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arginine gabT: gamma-aminobutyrate transaminase LT39_RS09315 LT39_RS17915
arginine patA: putrescine aminotransferase (PatA/SpuC) LT39_RS09315 LT39_RS17915
arginine patD: gamma-aminobutyraldehyde dehydrogenase LT39_RS03980 LT39_RS09545
arginine rocE: L-arginine permease
asparagine ans: asparaginase LT39_RS18365 LT39_RS16160
cellobiose bgl: cellobiase LT39_RS14850 LT39_RS13975
cellobiose glk: glucokinase LT39_RS14210
cellobiose gtsA: glucose ABC transporter, substrate-binding component (GtsA) LT39_RS16405
cellobiose gtsB: glucose ABC transporter, permease component 1 (GtsB) LT39_RS16410 LT39_RS19805
citrate citM: citrate:cation:H+ symporter CitM LT39_RS02045
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component LT39_RS05240 LT39_RS00585
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 LT39_RS05235
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component LT39_RS05250
citrulline arcC: carbamate kinase
citrulline gabT: gamma-aminobutyrate transaminase LT39_RS09315 LT39_RS17915
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) LT39_RS09315 LT39_RS17915
citrulline patD: gamma-aminobutyraldehyde dehydrogenase LT39_RS03980 LT39_RS09545
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase LT39_RS12340 LT39_RS09685
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase LT39_RS02535 LT39_RS02355
deoxyinosine deoB: phosphopentomutase LT39_RS09955 LT39_RS05035
deoxyinosine deoD: deoxyinosine phosphorylase LT39_RS02880 LT39_RS06385
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase LT39_RS02910 LT39_RS18840
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase LT39_RS14405 LT39_RS05905
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme LT39_RS01295
deoxyribose deoK: deoxyribokinase LT39_RS14800 LT39_RS06395
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase LT39_RS04155 LT39_RS07935
fucose fucA: L-fuculose-phosphate aldolase FucA LT39_RS02315
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
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP LT39_RS16075 LT39_RS07700
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 LT39_RS03265 LT39_RS04135
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) LT39_RS13495 LT39_RS10200
glucose glk: glucokinase LT39_RS14210
glucose gtsA: glucose ABC transporter, substrate-binding component (GtsA) LT39_RS16405
glucose gtsB: glucose ABC transporter, permease component 1 (GtsB) LT39_RS16410 LT39_RS19805
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuA: D-mannonate dehydratase LT39_RS03790 LT39_RS04205
glucuronate uxuB: D-mannonate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) LT39_RS20215
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase LT39_RS17920
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 LT39_RS01525 LT39_RS01410
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LT39_RS15940 LT39_RS09400
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LT39_RS09390 LT39_RS15935
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase LT39_RS10065 LT39_RS00050
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase LT39_RS17515 LT39_RS17715
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit LT39_RS20420
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase LT39_RS14210
lactose lacP: lactose permease LacP LT39_RS16075 LT39_RS07700
lactose lacZ: lactase (homomeric) LT39_RS20035 LT39_RS04160
leucine aacS: acetoacetyl-CoA synthetase LT39_RS02910 LT39_RS18840
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LT39_RS15940 LT39_RS09400
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LT39_RS09390 LT39_RS15935
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase LT39_RS01525 LT39_RS01410
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit LT39_RS20420
leucine liuC: 3-methylglutaconyl-CoA hydratase LT39_RS05925 LT39_RS10065
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit LT39_RS19540 LT39_RS16580
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine davA: 5-aminovaleramidase LT39_RS01375
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase LT39_RS09545 LT39_RS14635
lysine davT: 5-aminovalerate aminotransferase LT39_RS09315 LT39_RS17915
lysine gcdG: succinyl-CoA:glutarate CoA-transferase LT39_RS09680 LT39_RS04055
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase LT39_RS14210
maltose gtsA: glucose ABC transporter, substrate-binding component (GtsA) LT39_RS16405
maltose gtsB: glucose ABC transporter, permease component 1 (GtsB) LT39_RS16410 LT39_RS19805
maltose susB: alpha-glucosidase (maltase) LT39_RS12245 LT39_RS07910
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose man-isomerase: D-mannose isomerase
mannose scrK: fructokinase LT39_RS18665 LT39_RS06395
mannose TT_C0327: mannose ABC transporter, permease component 1
mannose TT_C0328: mannose ABC transporter, substrate-binding component LT39_RS16405
myoinositol iolG: myo-inositol 2-dehydrogenase LT39_RS07755 LT39_RS16400
myoinositol iolM: 2-inosose 4-dehydrogenase LT39_RS07740 LT39_RS01720
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter LT39_RS16075 LT39_RS07700
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase LT39_RS03790 LT39_RS04205
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) LT39_RS13495 LT39_RS10200
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 LT39_RS10065 LT39_RS00050
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase LT39_RS14505 LT39_RS01195
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase LT39_RS14505 LT39_RS01195
phenylacetate paaK: phenylacetate-CoA ligase LT39_RS18840 LT39_RS00320
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase LT39_RS18835 LT39_RS10065
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 LT39_RS10065 LT39_RS00050
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase LT39_RS14505 LT39_RS01195
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase LT39_RS14505 LT39_RS01195
phenylalanine paaK: phenylacetate-CoA ligase LT39_RS18840 LT39_RS00320
phenylalanine paaZ1: oxepin-CoA hydrolase LT39_RS18835 LT39_RS10065
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine PPDCalpha: phenylpyruvate decarboxylase, alpha subunit LT39_RS15945 LT39_RS12500
phenylalanine PPDCbeta: phenylpyruvate decarboxylase, beta subunit LT39_RS15940 LT39_RS09400
proline put1: proline dehydrogenase LT39_RS20215
proline putA: L-glutamate 5-semialdeyde dehydrogenase LT39_RS07935 LT39_RS04155
proline putP: proline:Na+ symporter LT39_RS05680
propionate lctP: propionate permease LT39_RS07665
propionate pccA: propionyl-CoA carboxylase, alpha subunit LT39_RS20420
putrescine gabT: gamma-aminobutyrate transaminase LT39_RS09315 LT39_RS17915
putrescine patA: putrescine aminotransferase (PatA/SpuC) LT39_RS09315 LT39_RS17915
putrescine patD: gamma-aminobutyraldehyde dehydrogenase LT39_RS03980 LT39_RS09545
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate MCT4: pyruvate symporter MCT4 (SLC16A3) LT39_RS16495
rhamnose LRA1: L-rhamnofuranose dehydrogenase LT39_RS00180 LT39_RS14405
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase LT39_RS12145 LT39_RS07820
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase LT39_RS20235 LT39_RS01720
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase LT39_RS14800 LT39_RS06395
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol scrK: fructokinase LT39_RS18665 LT39_RS06395
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 LT39_RS16075 LT39_RS07700
sucrose ams: sucrose hydrolase (invertase) LT39_RS16995
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) LT39_RS04305 LT39_RS04310
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase LT39_RS09955 LT39_RS05035
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase LT39_RS14210
trehalose gtsA: glucose ABC transporter, substrate-binding component (GtsA) LT39_RS16405
trehalose gtsB: glucose ABC transporter, permease component 1 (GtsB) LT39_RS16410 LT39_RS19805
trehalose treF: trehalase LT39_RS10680
tryptophan aroP: tryptophan:H+ symporter AroP
tyrosine aacS: acetoacetyl-CoA synthetase LT39_RS02910 LT39_RS18840
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase LT39_RS07800 LT39_RS04565
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase LT39_RS01525 LT39_RS01410
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase LT39_RS00050
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LT39_RS15940 LT39_RS09400
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LT39_RS09390 LT39_RS15935
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit LT39_RS20420
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) LT39_RS14805
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase LT39_RS07835 LT39_RS19820
xylose xad: D-xylonate dehydratase LT39_RS04795 LT39_RS19815
xylose xylC: xylonolactonase
xylose xylT: D-xylose transporter LT39_RS16075 LT39_RS07700

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