Potential Gaps in catabolism of small carbon sources in Beijerinckia mobilis UQM 1969
Found 121 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | DL88_RS15060 | DL88_RS13580 |
4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | DL88_RS15065 | DL88_RS15070 |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | DL88_RS15120 | DL88_RS15155 |
alanine | snatA: L-alanine symporter SnatA | DL88_RS13270 | |
arabinose | aldA: (glycol)aldehyde dehydrogenase | DL88_RS10695 | DL88_RS03165 |
arabinose | araE: L-arabinose:H+ symporter | DL88_RS04730 | |
arabinose | KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase | | |
arabinose | xacB: L-arabinose 1-dehydrogenase | DL88_RS16450 | DL88_RS15185 |
arabinose | xacC: L-arabinono-1,4-lactonase | | |
arabinose | xacD: L-arabinonate dehydratase | DL88_RS11215 | DL88_RS13730 |
arginine | rocE: L-arginine permease | | |
arginine | rocF: arginase | | |
asparagine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DL88_RS08835 | DL88_RS05085 |
asparagine | ans: asparaginase | | |
aspartate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DL88_RS08835 | DL88_RS05085 |
cellobiose | bgl: cellobiase | | |
cellobiose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
citrate | SLC13A5: citrate:Na+ symporter | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | DL88_RS08835 | DL88_RS06575 |
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 | DL88_RS13035 | DL88_RS02820 |
citrulline | arcC: carbamate kinase | | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | | |
deoxyinosine | deoB: phosphopentomutase | DL88_RS02395 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | DL88_RS07710 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | DL88_RS06635 | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DL88_RS03920 | DL88_RS16450 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | DL88_RS03920 | DL88_RS16450 |
deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | DL88_RS10405 | DL88_RS01625 |
deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | DL88_RS10400 | DL88_RS01620 |
deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | DL88_RS07020 | DL88_RS10410 |
deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
fructose | fruP: fructose porter FruP | DL88_RS17845 | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucP: L-fucose:H+ symporter FucP | DL88_RS17845 | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galactose | HP1174: Na+-dependent galactose transporter | DL88_RS17845 | |
galactose | pgmA: alpha-phosphoglucomutase | DL88_RS19025 | DL88_RS02395 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
galacturonate | uxaA: D-altronate dehydratase | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | DL88_RS14190 | |
glucose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
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 | DL88_RS11880 | DL88_RS11260 |
glucuronate | garR: tartronate semialdehyde reductase | DL88_RS13040 | DL88_RS16635 |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glutamate | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DL88_RS08835 | DL88_RS05085 |
glutamate | aspA: L-aspartate ammonia-lyase | DL88_RS03785 | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | DL88_RS11650 | DL88_RS18750 |
glycerol | glpK: glycerol kinase | | |
histidine | aapP: L-histidine ABC transporter, ATPase component AapP | DL88_RS08835 | DL88_RS05085 |
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 | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | DL88_RS15185 | DL88_RS07860 |
L-lactate | L-LDH: L-lactate dehydrogenase | DL88_RS18490 | DL88_RS12155 |
lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | DL88_RS10850 | |
lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | DL88_RS10565 | DL88_RS01035 |
lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
lactose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | DL88_RS08835 | DL88_RS05085 |
leucine | liuA: isovaleryl-CoA dehydrogenase | DL88_RS01320 | DL88_RS16625 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | DL88_RS05410 | DL88_RS08080 |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | DL88_RS01245 | DL88_RS16640 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | DL88_RS05405 | |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
lysine | cadA: lysine decarboxylase | DL88_RS12595 | DL88_RS08220 |
lysine | davT: 5-aminovalerate aminotransferase | DL88_RS02255 | DL88_RS04220 |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | DL88_RS03910 | DL88_RS04220 |
lysine | patD: 5-aminopentanal dehydrogenase | DL88_RS04160 | DL88_RS17100 |
maltose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
maltose | susB: alpha-glucosidase (maltase) | DL88_RS01225 | |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | gluP: mannose:Na+ symporter | DL88_RS17845 | |
mannose | man-isomerase: D-mannose isomerase | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | DL88_RS15580 | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | DL88_RS14190 | |
NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
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 | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | DL88_RS01245 | DL88_RS16640 |
phenylacetate | paaK: phenylacetate-CoA ligase | DL88_RS16320 | |
phenylacetate | paaT: phenylacetate transporter Paa | | |
phenylacetate | paaZ1: oxepin-CoA hydrolase | DL88_RS16640 | DL88_RS01245 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | DL88_RS15125 | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | DL88_RS02785 | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
putrescine | gabT: gamma-aminobutyrate transaminase | DL88_RS09505 | DL88_RS04220 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | DL88_RS03910 | DL88_RS09505 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | DL88_RS17100 | DL88_RS04160 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
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 | sdaB: L-serine ammonia-lyase | DL88_RS03720 | |
serine | snatA: L-serine transporter | DL88_RS13270 | |
sorbitol | sdh: sorbitol dehydrogenase | DL88_RS03920 | DL88_RS11290 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | ams: sucrose hydrolase (invertase) | | |
sucrose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | DL88_RS10935 | DL88_RS10940 |
threonine | snatA: L-threonine transporter snatA | DL88_RS13270 | |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | DL88_RS02395 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | MFS-glucose: glucose transporter, MFS superfamily | DL88_RS17845 | DL88_RS04730 |
trehalose | treF: trehalase | DL88_RS02910 | DL88_RS01225 |
tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | DL88_RS14995 | |
tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | DL88_RS15000 | |
tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | DL88_RS15005 | DL88_RS17175 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | kyn: kynureninase | | |
tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
tryptophan | kynB: kynurenine formamidase | | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | DL88_RS15125 | |
valine | acdH: isobutyryl-CoA dehydrogenase | DL88_RS16625 | DL88_RS01320 |
valine | Bap2: L-valine permease Bap2 | | |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | DL88_RS16605 | DL88_RS16620 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | DL88_RS03840 | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
xylose | xylT: D-xylose transporter | DL88_RS04730 | |
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