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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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