Potential Gaps in catabolism of small carbon sources in Novosphingobium aromaticivorans DSM 12444
Found 82 low-confidence and 35 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | SARO_RS10545 | SARO_RS13230 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | SARO_RS07960 | |
alanine | snatA: L-alanine symporter SnatA | SARO_RS01345 | |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | SARO_RS16065 | |
arginine | adiA: arginine decarboxylase (AdiA/SpeA) | | |
arginine | patD: gamma-aminobutyraldehyde dehydrogenase | SARO_RS14550 | SARO_RS19930 |
arginine | rocE: L-arginine permease | | |
asparagine | ans: asparaginase | | |
cellobiose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
citrate | citA: citrate:H+ symporter CitA | SARO_RS10545 | SARO_RS00790 |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | SARO_RS05745 | SARO_RS11475 |
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 | rocD: ornithine aminotransferase | SARO_RS13120 | SARO_RS14875 |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
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 | SARO_RS05490 | |
deoxyinosine | deoB: phosphopentomutase | SARO_RS02415 | SARO_RS16840 |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | SARO_RS19160 | SARO_RS14535 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | SARO_RS17880 | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | SARO_RS00750 | |
deoxyribose | deoP: deoxyribose transporter | SARO_RS12220 | |
fructose | glcP: fructose:H+ symporter GlcP | SARO_RS16065 | |
fucose | fucU: L-fucose mutarotase FucU | SARO_RS12215 | |
galactose | galE: UDP-glucose 4-epimerase | SARO_RS16630 | SARO_RS08110 |
galactose | galP: galactose:H+ symporter GalP | SARO_RS16065 | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | SARO_RS19260 | |
gluconate | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | SARO_RS12135 | |
glucose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | uxaC: D-glucuronate isomerase | SARO_RS19260 | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | Bap2: L-isoleucine permease Bap2 | | |
L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
L-malate | sdlC: L-malate:Na+ symporter SdlC | SARO_RS12910 | |
lactose | galE: UDP-glucose 4-epimerase | SARO_RS16630 | SARO_RS08110 |
lactose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
lactose | lacP: lactose permease LacP | | |
leucine | leuT: L-leucine:Na+ symporter LeuT | | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | SARO_RS04305 | SARO_RS07105 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | SARO_RS00880 | |
lysine | davA: 5-aminovaleramidase | SARO_RS15710 | |
lysine | davB: L-lysine 2-monooxygenase | | |
lysine | davD: glutarate semialdehyde dehydrogenase | SARO_RS17165 | SARO_RS14885 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
maltose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
mannitol | mt2d: mannitol 2-dehydrogenase | SARO_RS19265 | SARO_RS09380 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | gluP: mannose:Na+ symporter | SARO_RS04365 | SARO_RS12220 |
mannose | man-isomerase: D-mannose isomerase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
myoinositol | iolT: myo-inositol:H+ symporter | SARO_RS16065 | |
myoinositol | uxaE: D-tagaturonate epimerase | | |
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 | SARO_RS04305 | SARO_RS18985 |
phenylacetate | paaK: phenylacetate-CoA ligase | SARO_RS06055 | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | SARO_RS18110 | SARO_RS06415 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | SARO_RS14020 | |
propionate | putP: propionate transporter; proline:Na+ symporter | | |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | SARO_RS14550 | SARO_RS19930 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
rhamnose | rhaM: L-rhamnose mutarotase | | |
ribose | rbsK: ribokinase | SARO_RS00750 | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | snatA: L-serine transporter | SARO_RS01345 | |
sorbitol | sdh: sorbitol dehydrogenase | SARO_RS19125 | SARO_RS07815 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
succinate | sdc: succinate:Na+ symporter Sdc | SARO_RS12910 | |
sucrose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | SARO_RS09270 | SARO_RS09275 |
threonine | ltaE: L-threonine aldolase | SARO_RS16590 | SARO_RS11270 |
threonine | snatA: L-threonine transporter snatA | SARO_RS01345 | |
thymidine | deoA: thymidine phosphorylase DeoA | SARO_RS18780 | |
thymidine | deoB: phosphopentomutase | SARO_RS02415 | SARO_RS16840 |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
trehalose | glk: glucokinase | SARO_RS09495 | SARO_RS09440 |
trehalose | treF: trehalase | SARO_RS09470 | SARO_RS07540 |
tryptophan | andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | SARO_RS16995 | SARO_RS01080 |
tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | kyn: kynureninase | | |
tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
tryptophan | kynB: kynurenine formamidase | SARO_RS13615 | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
valine | acdH: isobutyryl-CoA dehydrogenase | SARO_RS04295 | SARO_RS08250 |
valine | Bap2: L-valine permease Bap2 | | |
xylitol | PLT5: xylitol:H+ symporter PLT5 | SARO_RS16065 | |
xylitol | xdhA: xylitol dehydrogenase | SARO_RS19090 | SARO_RS12445 |
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