GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Haloglycomyces albus DSM 45210

Found 109 low-confidence and 59 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 adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
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 HALAL_RS0115415
arginine arcC: carbamate kinase
arginine ocd: ornithine cyclodeaminase
arginine put1: proline dehydrogenase HALAL_RS0107260
arginine rocE: L-arginine permease
asparagine glt: aspartate:proton symporter Glt HALAL_RS0106530
aspartate glt: aspartate:proton symporter Glt HALAL_RS0106530
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HALAL_RS0102760 HALAL_RS0113980
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HALAL_RS0102765 HALAL_RS0104120
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline ocd: ornithine cyclodeaminase
citrulline put1: proline dehydrogenase HALAL_RS0107260
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase HALAL_RS0110800 HALAL_RS0107050
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 HALAL_RS0108905 HALAL_RS0109860
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component HALAL_RS0100340 HALAL_RS0100350
deoxyinosine deoB: phosphopentomutase HALAL_RS0110755 HALAL_RS0100830
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 HALAL_RS0100330
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 HALAL_RS0100325
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HALAL_RS0108330 HALAL_RS0101795
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme HALAL_RS0113565
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
fructose glcP: fructose:H+ symporter GlcP HALAL_RS0113840
fructose scrK: fructokinase HALAL_RS0101660 HALAL_RS0114515
fucose aldA: lactaldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
fucose fucA: L-fuculose-phosphate aldolase FucA
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 galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase HALAL_RS0102095
galactose pgmA: alpha-phosphoglucomutase HALAL_RS0110755 HALAL_RS0101005
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase HALAL_RS0114520
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase HALAL_RS0114515
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 nagB: glucosamine 6-phosphate deaminase (isomerizing) HALAL_RS0115970 HALAL_RS0105325
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT HALAL_RS0106530
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) HALAL_RS0107415 HALAL_RS0113770
histidine hutG': N-formylglutamate amidohydrolase
histidine PA5503: L-histidine ABC transporter, ATPase component HALAL_RS0113980 HALAL_RS0102760
histidine PA5504: L-histidine ABC transporter, permease component HALAL_RS0102360
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALAL_RS0105530 HALAL_RS0116060
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase HALAL_RS0110635 HALAL_RS0102000
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HALAL_RS0113050 HALAL_RS0101795
isoleucine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HALAL_RS0107805
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit HALAL_RS0104645
L-lactate lctO: L-lactate oxidase or 2-monooxygenase HALAL_RS0103385
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase HALAL_RS0102095
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) HALAL_RS0100400
lactose pgmA: alpha-phosphoglucomutase HALAL_RS0110755 HALAL_RS0101005
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALAL_RS0105530 HALAL_RS0116060
leucine leuT: L-leucine:Na+ symporter LeuT HALAL_RS0115700 HALAL_RS0115765
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HALAL_RS0104645
leucine liuC: 3-methylglutaconyl-CoA hydratase HALAL_RS0102000 HALAL_RS0104455
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit HALAL_RS0107640 HALAL_RS0100970
lysine bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit HALAL_RS0104340 HALAL_RS0107635
lysine ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit
lysine ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit
lysine etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit HALAL_RS0116135
lysine etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit HALAL_RS0116140
lysine kamA: L-lysine 2,3-aminomutase HALAL_RS0113570
lysine kdd: 3,5-diaminohexanoate dehydrogenase HALAL_RS0113575
lysine lysP: L-lysine:H+ symporter LysP
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 HALAL_RS0107690
myoinositol iolT: myo-inositol:H+ symporter HALAL_RS0113840
myoinositol mmsA: malonate-semialdehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) HALAL_RS0115970 HALAL_RS0105325
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 HALAL_RS0104000
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase HALAL_RS0110635
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase HALAL_RS0110640 HALAL_RS0107190
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase HALAL_RS0110640 HALAL_RS0107190
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa HALAL_RS0101385
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine hmgA: homogentisate dioxygenase HALAL_RS0108625
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase HALAL_RS0107260
propionate mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HALAL_RS0107805
propionate pccA: propionyl-CoA carboxylase, alpha subunit HALAL_RS0104645
putrescine patA: putrescine aminotransferase (PatA/SpuC) HALAL_RS0112700 HALAL_RS0102620
putrescine patD: gamma-aminobutyraldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase HALAL_RS0112015 HALAL_RS0110770
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 serP: L-serine permease SerP
sorbitol scrK: fructokinase HALAL_RS0101660 HALAL_RS0114515
sorbitol sdh: sorbitol dehydrogenase HALAL_RS0100575 HALAL_RS0101795
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dauA: succinate:H+ symporter DauA HALAL_RS0105760
sucrose ams: sucrose hydrolase (invertase) HALAL_RS0103065
threonine adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) HALAL_RS0102625 HALAL_RS0112015
thymidine deoB: phosphopentomutase HALAL_RS0110755 HALAL_RS0100830
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase HALAL_RS0102420 HALAL_RS0103065
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine hmgA: homogentisate dioxygenase HALAL_RS0108625
tyrosine maiA: maleylacetoacetate isomerase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase HALAL_RS0103255
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component HALAL_RS0105530 HALAL_RS0116060
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase HALAL_RS0110635
valine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit HALAL_RS0107805
valine mmsA: methylmalonate-semialdehyde dehydrogenase HALAL_RS0110770 HALAL_RS0112015
valine mmsB: 3-hydroxyisobutyrate dehydrogenase HALAL_RS0114690
valine pccA: propionyl-CoA carboxylase, alpha subunit HALAL_RS0104645
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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