GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Nocardiopsis lucentensis DSM 44048

Found 69 low-confidence and 67 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP D471_RS0128695 D471_RS0103990
4-hydroxybenzoate pcaH: protocatechuate 3,4-dioxygenase, alpha subunit D471_RS0117445 D471_RS0117450
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) D471_RS0117460
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter D471_RS0107095
arginine rocE: L-arginine permease D471_RS0105135
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB D471_RS32895
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC D471_RS0103690 D471_RS0103675
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component D471_RS0100160 D471_RS0110910
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 D471_RS0100155
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 D471_RS0100155 D471_RS0110900
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA D471_RS0105135
D-alanine dadA: D-alanine dehydrogenase D471_RS0104545
D-lactate glcE: D-lactate dehydrogenase, FAD-linked subunit 2 (GlcE) D471_RS0111095 D471_RS0120670
D-lactate glcF: D-lactate dehydrogenase, FeS subunit GlcF
D-lactate larD: D,L-lactic acid transporter D471_RS0115830
D-serine cycA: D-serine:H+ symporter CycA D471_RS0105135
D-serine dsdA: D-serine ammonia-lyase D471_RS0112815 D471_RS0112340
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component D471_RS0107160
deoxyinosine deoB: phosphopentomutase D471_RS0107130 D471_RS0110440
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 D471_RS0107185
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 D471_RS0107185
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase D471_RS0106110 D471_RS0128820
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) D471_RS0120610 D471_RS0118875
fucose aldA: lactaldehyde dehydrogenase D471_RS0107105 D471_RS0122805
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU D471_RS0124225
galactose galK: galactokinase (-1-phosphate forming) D471_RS0101900
galactose galP: galactose:H+ symporter GalP D471_RS0107095
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose pgmA: alpha-phosphoglucomutase D471_RS0107130 D471_RS0100635
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase D471_RS0126250
galacturonate gli: D-galactarolactone isomerase
galacturonate udh: D-galacturonate dehydrogenase
gluconate gntT: gluconate:H+ symporter GntT D471_RS0115765
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) D471_RS0100490 D471_RS0129340
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucosamine ptsC: N-acetylglucosamine phosphotransferase system, EII-C component PtsC D471_RS0100505
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase D471_RS0126250
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) D471_RS0102200 D471_RS0120660
histidine hutG': N-formylglutamate amidohydrolase
histidine hutH: histidine ammonia-lyase D471_RS0109810
histidine hutU: urocanase D471_RS0109800
histidine PA5503: L-histidine ABC transporter, ATPase component D471_RS0100160 D471_RS0116565
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase D471_RS0107015 D471_RS35705
isoleucine Bap2: L-isoleucine permease Bap2 D471_RS0105135
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component D471_RS0127585 D471_RS0116485
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase D471_RS0108855 D471_RS0103415
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit D471_RS0101775 D471_RS0107025
L-lactate larD: D,L-lactic acid transporter LarD D471_RS0115830
L-lactate lutC: L-lactate dehydrogenase, LutC subunit D471_RS0124150
lactose galK: galactokinase (-1-phosphate forming) D471_RS0101900
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) D471_RS0107340 D471_RS0125015
lactose pgmA: alpha-phosphoglucomutase D471_RS0107130 D471_RS0100635
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component D471_RS0127585 D471_RS0116485
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit D471_RS0107025 D471_RS0101775
leucine liuC: 3-methylglutaconyl-CoA hydratase D471_RS0106555 D471_RS0103415
leucine liuE: hydroxymethylglutaryl-CoA lyase D471_RS0102710
leucine natB: L-leucine ABC transporter, substrate-binding component NatB D471_RS0102655
leucine natC: L-leucine ABC transporter, permease component 1 (NatC)
leucine natD: L-leucine ABC transporter, permease component 2 (NatD) D471_RS0102635 D471_RS0105195
lysine davD: glutarate semialdehyde dehydrogenase D471_RS0113535 D471_RS0127260
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase D471_RS0108630 D471_RS0108855
lysine gcdG: succinyl-CoA:glutarate CoA-transferase D471_RS0120140 D471_RS0124980
lysine lysL: L-lysine transporter LysL D471_RS0103755
mannitol cmtB: mannitol phosphotransferase system, EII-A component CmtB/MtlF D471_RS0114580
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose mannokinase: D-mannose kinase D471_RS0110445 D471_RS0118645
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolE: scyllo-inosose 2-dehydratase D471_RS0110500
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase D471_RS33780
myoinositol iolT: myo-inositol:H+ symporter D471_RS0107095
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) D471_RS0100490 D471_RS0129340
NAG ptsC: N-acetylglucosamine phosphotransferase system, EII-C component PtsC D471_RS0100505
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase D471_RS0108630 D471_RS0126255
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase D471_RS0106115 D471_RS0123245
phenylacetate ppa: phenylacetate permease ppa D471_RS0129210 D471_RS0109765
phenylalanine aroP: L-phenylalanine:H+ symporter AroP D471_RS0105135
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase D471_RS0108630 D471_RS0126255
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase D471_RS0106115 D471_RS0123245
phenylalanine pad-dh: phenylacetaldehyde dehydrogenase D471_RS0112170 D471_RS0107105
propionate pccA: propionyl-CoA carboxylase, alpha subunit D471_RS0101775 D471_RS0107025
putrescine patA: putrescine aminotransferase (PatA/SpuC) D471_RS0118295 D471_RS0110630
rhamnose aldA: lactaldehyde dehydrogenase D471_RS0107105 D471_RS0122805
rhamnose rhaB: L-rhamnulokinase D471_RS35925
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase D471_RS0124225
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) D471_RS0102655
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) D471_RS0102635 D471_RS0127515
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
sorbitol sdh: sorbitol dehydrogenase D471_RS0127265 D471_RS0106840
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) D471_RS0102655
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) D471_RS0102635 D471_RS0127515
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)
thymidine deoB: phosphopentomutase D471_RS0107130 D471_RS0110440
thymidine nupG: thymidine permease NupG/XapB
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE D471_RS0106180
trehalose thuK: trehalose ABC transporter, ATPase component ThuK D471_RS0104225 D471_RS0130575
trehalose treF: trehalase D471_RS0115940 D471_RS0103165
tryptophan tnaA: tryptophanase
tryptophan tnaT: tryptophan:Na+ symporter TnaT D471_RS0126420
tyrosine aroP: L-tyrosine transporter (AroP/FywP) D471_RS0105135
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase D471_RS0107015 D471_RS0128745
valine Bap2: L-valine permease Bap2 D471_RS0105135
valine bch: 3-hydroxyisobutyryl-CoA hydrolase D471_RS35700 D471_RS0106555
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component D471_RS0127585 D471_RS0116485
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase D471_RS0108630 D471_RS0108855
valine mmsA: methylmalonate-semialdehyde dehydrogenase D471_RS0100055 D471_RS0110495
valine mmsB: 3-hydroxyisobutyrate dehydrogenase D471_RS0116100 D471_RS42355
valine pccA: propionyl-CoA carboxylase, alpha subunit D471_RS0101775 D471_RS0107025
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase D471_RS0114585 D471_RS0118875
xylose xdhA: xylitol dehydrogenase D471_RS0114585 D471_RS0118875
xylose xylT: D-xylose transporter D471_RS0107095
xylose xyrA: xylitol reductase D471_RS0115115 D471_RS0106015

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