GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Haloterrigena daqingensis JX313

Found 153 low-confidence and 62 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 BB347_RS14775 BB347_RS11345
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component BB347_RS14770
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase BB347_RS14470 BB347_RS07830
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 BB347_RS13565
acetate actP: cation/acetate symporter ActP BB347_RS03535
alanine cycA: L-alanine symporter CycA
arabinose araE: L-arabinose:H+ symporter
arabinose xacC: L-arabinono-1,4-lactonase
arabinose xacD: L-arabinonate dehydratase BB347_RS05410 BB347_RS08605
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase
arabinose xacF: alpha-ketoglutarate semialdehyde dehydrogenase BB347_RS14690 BB347_RS02620
arginine gabD: succinate semialdehyde dehydrogenase BB347_RS14690 BB347_RS05680
arginine gabT: gamma-aminobutyrate transaminase BB347_RS07365 BB347_RS14645
arginine patA: putrescine aminotransferase (PatA/SpuC) BB347_RS07365 BB347_RS14645
arginine patD: gamma-aminobutyraldehyde dehydrogenase BB347_RS14690 BB347_RS05680
arginine rocE: L-arginine permease
asparagine ans: asparaginase BB347_RS06060 BB347_RS11200
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase BB347_RS10270
citrate SLC13A5: citrate:Na+ symporter BB347_RS08520
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BB347_RS13945 BB347_RS14205
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 rocA: 1-pyrroline-5-carboxylate dehydrogenase BB347_RS14690 BB347_RS02620
citrulline rocD: ornithine aminotransferase BB347_RS08970 BB347_RS07365
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BB347_RS14425 BB347_RS14285
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 BB347_RS10070 BB347_RS08930
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
deoxyinosine deoB: phosphopentomutase BB347_RS07985 BB347_RS02380
deoxyinosine deoD: deoxyinosine phosphorylase BB347_RS11110 BB347_RS07925
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase BB347_RS17375 BB347_RS02445
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BB347_RS14535 BB347_RS01505
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase BB347_RS08265
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme BB347_RS14420
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BB347_RS14690 BB347_RS11295
fucose fucA: L-fuculose-phosphate aldolase FucA BB347_RS09575
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 galE: UDP-glucose 4-epimerase BB347_RS08880 BB347_RS16920
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase BB347_RS10135 BB347_RS01000
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
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) BB347_RS08085 BB347_RS02940
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 BB347_RS14690 BB347_RS02620
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase BB347_RS14730
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BB347_RS01000 BB347_RS10135
glucuronate udh: D-glucuronate dehydrogenase BB347_RS12925
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase BB347_RS07370
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 BB347_RS02745 BB347_RS02635
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BB347_RS13030
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BB347_RS13025
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BB347_RS11510 BB347_RS14695
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BB347_RS10975 BB347_RS09235
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BB347_RS04550
L-lactate lctO: L-lactate oxidase or 2-monooxygenase BB347_RS09095
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galE: UDP-glucose 4-epimerase BB347_RS08880 BB347_RS16920
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase BB347_RS10270
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase BB347_RS17375 BB347_RS02445
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BB347_RS13030
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BB347_RS13025
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase BB347_RS02745 BB347_RS02635
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BB347_RS04550
leucine liuC: 3-methylglutaconyl-CoA hydratase BB347_RS14695 BB347_RS09135
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BB347_RS02695 BB347_RS04580
leucine liuE: hydroxymethylglutaryl-CoA lyase BB347_RS17870
lysine davA: 5-aminovaleramidase BB347_RS04555
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase BB347_RS14690 BB347_RS05680
lysine davT: 5-aminovalerate aminotransferase BB347_RS07365 BB347_RS08970
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BB347_RS09135 BB347_RS14695
lysine gcdG: succinyl-CoA:glutarate CoA-transferase BB347_RS13070 BB347_RS14755
lysine lysP: L-lysine:H+ symporter LysP
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 manA: mannose-6-phosphate isomerase BB347_RS14320 BB347_RS02380
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 BB347_RS17040 BB347_RS08330
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BB347_RS08085 BB347_RS02940
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 BB347_RS14695 BB347_RS01645
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BB347_RS12295 BB347_RS11630
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BB347_RS12295 BB347_RS11330
phenylacetate paaK: phenylacetate-CoA ligase BB347_RS07185 BB347_RS04115
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BB347_RS04120
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase BB347_RS17375 BB347_RS02445
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase BB347_RS13085 BB347_RS06825
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase BB347_RS00380
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase BB347_RS14690 BB347_RS02620
propionate pccA: propionyl-CoA carboxylase, alpha subunit BB347_RS04550
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase BB347_RS14690 BB347_RS05680
putrescine gabT: gamma-aminobutyrate transaminase BB347_RS07365 BB347_RS14645
putrescine patA: putrescine aminotransferase (PatA/SpuC) BB347_RS07365 BB347_RS14645
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BB347_RS14690 BB347_RS05680
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase BB347_RS06655 BB347_RS10975
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase BB347_RS14430 BB347_RS14730
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BB347_RS14535 BB347_RS08015
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase BB347_RS13085 BB347_RS06825
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BB347_RS11495 BB347_RS11480
sucrose scrK: fructokinase BB347_RS11100
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BB347_RS06980 BB347_RS06975
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) BB347_RS14690 BB347_RS11295
thymidine deoB: phosphopentomutase BB347_RS07985 BB347_RS02380
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase BB347_RS10270
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE
trehalose thuF: trehalose ABC transporter, permease component 1 (ThuF) BB347_RS07090 BB347_RS05075
trehalose thuG: trehalose ABC transporter, permease component 2 (ThuG) BB347_RS05070 BB347_RS07095
trehalose treF: trehalase BB347_RS08595
tryptophan aroP: tryptophan:H+ symporter AroP
tyrosine aacS: acetoacetyl-CoA synthetase BB347_RS17375 BB347_RS02445
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase BB347_RS13085 BB347_RS06825
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BB347_RS02745 BB347_RS02635
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BB347_RS14695 BB347_RS07165
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BB347_RS13030
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BB347_RS13025
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BB347_RS09135 BB347_RS14695
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BB347_RS10570
valine pccA: propionyl-CoA carboxylase, alpha subunit BB347_RS04550
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose dopDH: 2,5-dioxopentanonate dehydrogenase BB347_RS14690 BB347_RS02620
xylose kdaD: 2-keto-3-deoxy-D-arabinonate dehydratase
xylose xad: D-xylonate dehydratase BB347_RS08605 BB347_RS14735
xylose xylC: xylonolactonase
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