Potential Gaps in catabolism of small carbon sources in Pseudarthrobacter sulfonivorans Ar51
Found 41 low-confidence and 72 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | AU252_RS10750 | |
4-hydroxybenzoate | pcaD: 3-oxoadipate enol-lactone hydrolase | AU252_RS16275 | AU252_RS10755 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | AU252_RS04970 | AU252_RS22885 |
arginine | gabT: gamma-aminobutyrate transaminase | AU252_RS16125 | AU252_RS02890 |
arginine | gbamidase: guanidinobutyramidase | AU252_RS04565 | AU252_RS09230 |
arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | AU252_RS01555 | AU252_RS22410 |
arginine | rocE: L-arginine permease | AU252_RS04790 | AU252_RS08100 |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | AU252_RS13905 | AU252_RS15210 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AU252_RS09255 | AU252_RS15205 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AU252_RS13390 | AU252_RS09255 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | citrullinase: putative citrullinase | AU252_RS13110 | AU252_RS06335 |
citrulline | gabT: gamma-aminobutyrate transaminase | AU252_RS16125 | AU252_RS02890 |
citrulline | odc: L-ornithine decarboxylase | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-lactate | D-LDH: D-lactate dehydrogenase | AU252_RS06485 | AU252_RS16225 |
D-lactate | larD: D,L-lactic acid transporter | AU252_RS21085 | |
D-serine | dsdA: D-serine ammonia-lyase | AU252_RS04295 | AU252_RS13625 |
deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | AU252_RS04435 | |
deoxyinosine | deoB: phosphopentomutase | AU252_RS03935 | AU252_RS06775 |
deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | AU252_RS04425 | |
deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | AU252_RS04420 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AU252_RS13405 | AU252_RS01350 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AU252_RS05895 | AU252_RS20980 |
deoxyribose | deoP: deoxyribose transporter | | |
fructose | scrK: fructokinase | AU252_RS09170 | AU252_RS08575 |
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 | AU252_RS14775 | |
galacturonate | PS417_04205: D-galacturonate transporter | AU252_RS13435 | |
galacturonate | udh: D-galacturonate dehydrogenase | | |
galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
gluconate | gntT: gluconate:H+ symporter GntT | AU252_RS04805 | AU252_RS08420 |
glucosamine | crr: N-acetylglucosamine phosphotransferase system, EII-A component Crr | AU252_RS11915 | |
glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | AU252_RS16240 | AU252_RS14180 |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
glucuronate | uxaC: D-glucuronate isomerase | AU252_RS07655 | |
glucuronate | uxuA: D-mannonate dehydratase | AU252_RS07640 | AU252_RS14175 |
glucuronate | uxuB: D-mannonate dehydrogenase | AU252_RS07650 | |
glutamate | gltP: L-glutamate:cation symporter GltP/GltT | AU252_RS03850 | AU252_RS13765 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | AU252_RS17445 | AU252_RS21080 |
histidine | hutH: histidine ammonia-lyase | AU252_RS08055 | AU252_RS12375 |
isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AU252_RS15600 | AU252_RS02340 |
isoleucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | AU252_RS02335 | AU252_RS03920 |
isoleucine | natB: L-isoleucine ABC transporter, substrate-binding component NatB | AU252_RS04345 | |
isoleucine | natC: L-isoleucine ABC transporter, permease component 1 (NatC) | AU252_RS04330 | |
isoleucine | natD: L-isoleucine ABC transporter, permease component 2 (NatD) | AU252_RS04325 | |
L-lactate | larD: D,L-lactic acid transporter LarD | AU252_RS21085 | |
lactose | lacP: lactose permease LacP | | |
leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AU252_RS15600 | AU252_RS02340 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | AU252_RS00745 | AU252_RS00825 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | AU252_RS01445 | AU252_RS01285 |
leucine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | AU252_RS02335 | AU252_RS03920 |
leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | AU252_RS04345 | |
leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | AU252_RS04330 | |
leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | AU252_RS04325 | |
lysine | davD: glutarate semialdehyde dehydrogenase | AU252_RS01005 | AU252_RS04095 |
lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | AU252_RS02130 | AU252_RS07090 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | AU252_RS00300 | AU252_RS01440 |
lysine | lysP: L-lysine:H+ symporter LysP | AU252_RS04790 | AU252_RS13875 |
lysine | patA: cadaverine aminotransferase | AU252_RS02890 | AU252_RS16125 |
mannose | manP: mannose PTS system, EII-CBA components | AU252_RS08305 | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | AU252_RS05915 | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | AU252_RS06000 | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | AU252_RS06020 | AU252_RS08415 |
NAG | crr: N-acetylglucosamine phosphotransferase system, EII-A component Crr | AU252_RS11915 | |
phenylacetate | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | AU252_RS15440 | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AU252_RS07800 | AU252_RS00885 |
phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | AU252_RS02130 | AU252_RS07090 |
phenylacetate | ppa: phenylacetate permease ppa | AU252_RS03465 | AU252_RS03490 |
phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | AU252_RS15440 | |
phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AU252_RS07800 | AU252_RS00885 |
phenylalanine | paaH: 3-hydroxyadipyl-CoA dehydrogenase | AU252_RS02130 | AU252_RS07090 |
phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | AU252_RS01160 | AU252_RS01555 |
proline | put1: proline dehydrogenase | AU252_RS11615 | AU252_RS09435 |
proline | putA: L-glutamate 5-semialdeyde dehydrogenase | AU252_RS22410 | AU252_RS01555 |
putrescine | gabT: gamma-aminobutyrate transaminase | AU252_RS16125 | AU252_RS02890 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | rhaM: L-rhamnose mutarotase | AU252_RS14775 | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | AU252_RS04345 | |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | AU252_RS04325 | AU252_RS00670 |
serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | AU252_RS04330 | AU252_RS00900 |
sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | AU252_RS06475 | AU252_RS13340 |
sorbitol | scrK: fructokinase | AU252_RS09170 | AU252_RS08575 |
threonine | lpd: dihydrolipoyl dehydrogenase | AU252_RS02335 | AU252_RS03920 |
threonine | RR42_RS28305: L-threonine:H+ symporter | AU252_RS15260 | AU252_RS08100 |
thymidine | deoB: phosphopentomutase | AU252_RS03935 | AU252_RS06775 |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | treF: trehalase | AU252_RS06490 | AU252_RS14285 |
tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | AU252_RS22725 | |
tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | AU252_RS22720 | |
tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | AU252_RS22715 | |
tryptophan | kyn: kynureninase | AU252_RS03235 | |
tryptophan | kynB: kynurenine formamidase | AU252_RS09345 | |
tryptophan | xylE: catechol 2,3-dioxygenase | AU252_RS19380 | AU252_RS22415 |
tryptophan | xylF: 2-hydroxymuconate semialdehyde hydrolase | AU252_RS17320 | AU252_RS22250 |
tyrosine | fahA: fumarylacetoacetate hydrolase | AU252_RS19175 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | AU252_RS07810 | AU252_RS00745 |
valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | AU252_RS15600 | AU252_RS02340 |
valine | lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component | AU252_RS02335 | AU252_RS03920 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | AU252_RS07815 | AU252_RS22410 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AU252_RS07805 | AU252_RS13575 |
valine | natB: L-valine ABC transporter, substrate-binding component NatB | AU252_RS04345 | |
valine | natC: L-valine ABC transporter, permease component 1 (NatC) | AU252_RS04330 | |
valine | natD: L-valine ABC transporter, permease component 2 (NatD) | AU252_RS04325 | |
xylitol | PLT5: xylitol:H+ symporter PLT5 | AU252_RS05985 | |
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