Potential Gaps in catabolism of small carbon sources in Derxia gummosa DSM 723
Found 100 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | dctM: 2-oxoglutarate TRAP transporter, large permease component DctM | H566_RS0106500 | H566_RS0113345 |
2-oxoglutarate | dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ | | |
4-hydroxybenzoate | ligU: 4-oxalomesaconate tautomerase | H566_RS0121285 | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | H566_RS0117030 | |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | H566_RS0102680 | H566_RS0104990 |
alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | H566_RS22525 | H566_RS0104985 |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | H566_RS0102690 | H566_RS0111715 |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | H566_RS0102695 | H566_RS0113085 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | adiA: arginine decarboxylase (AdiA/SpeA) | H566_RS0101800 | |
arginine | rocE: L-arginine permease | | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | H566_RS0119540 | H566_RS0107450 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | H566_RS0119535 | |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | H566_RS0107440 | H566_RS0119535 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
citrulline | odc: L-ornithine decarboxylase | H566_RS0101800 | |
D-alanine | AZOBR_RS08240: D-alanine ABC transporter, permease component 2 | H566_RS22525 | H566_RS0104985 |
D-alanine | AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 | H566_RS0111715 | H566_RS0102690 |
D-alanine | AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 | H566_RS0102695 | H566_RS0104975 |
D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | H566_RS0117030 | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
D-serine | dsdA: D-serine ammonia-lyase | H566_RS0105405 | |
deoxyinosine | deoB: phosphopentomutase | H566_RS0101360 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | H566_RS23450 | H566_RS0112475 |
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 | H566_RS23450 | H566_RS0112475 |
deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | H566_RS23550 | H566_RS0116000 |
deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | | |
deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | H566_RS0106830 | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galacturonate | exuT: D-galacturonate transporter ExuT | H566_RS0114650 | |
galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | H566_RS0119110 | |
galacturonate | uxaA: D-altronate dehydratase | | |
galacturonate | uxaB: tagaturonate reductase | | |
galacturonate | uxaC: D-galacturonate isomerase | | |
gluconate | gntK: D-gluconate kinase | | |
gluconate | gntT: gluconate:H+ symporter GntT | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | H566_RS0114125 | |
glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | H566_RS0107095 | H566_RS0108130 |
glucuronate | exuT: D-glucuronate:H+ symporter ExuT | H566_RS0114650 | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | H566_RS0110445 | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
histidine | hutF: N-formiminoglutamate deiminase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
histidine | PA5503: L-histidine ABC transporter, ATPase component | H566_RS23970 | H566_RS0119540 |
histidine | PA5505: L-histidine ABC transporter, substrate-binding component | H566_RS0108860 | |
isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | H566_RS0120480 | H566_RS0116330 |
leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | H566_RS0110680 | H566_RS0105270 |
leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | H566_RS0106900 | H566_RS0111790 |
lysine | gcdH: glutaryl-CoA dehydrogenase | H566_RS0120480 | H566_RS0116330 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | H566_RS0108125 | H566_RS0102945 |
lysine | patD: 5-aminopentanal dehydrogenase | H566_RS0107095 | H566_RS0101815 |
maltose | susB: alpha-glucosidase (maltase) | H566_RS0104710 | |
mannitol | mt2d: mannitol 2-dehydrogenase | H566_RS0106840 | H566_RS0105240 |
mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | H566_RS0106865 | |
mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | H566_RS0106855 | |
mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | H566_RS0106850 | |
mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | H566_RS23460 | H566_RS0118530 |
mannose | man-isomerase: D-mannose isomerase | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | H566_RS23470 | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | H566_RS0102425 | H566_RS25615 |
myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | H566_RS0119115 | |
myoinositol | PS417_11890: myo-inositol ABC transporter, ATPase component | H566_RS0119125 | H566_RS0119435 |
myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | H566_RS0119120 | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | H566_RS0114125 | |
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 | H566_RS22980 | |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | H566_RS0116355 | H566_RS0118410 |
phenylacetate | paaK: phenylacetate-CoA ligase | H566_RS0103055 | H566_RS0105380 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | H566_RS0112825 | H566_RS0111180 |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | H566_RS0112825 | |
phenylacetate | ppa: phenylacetate permease ppa | H566_RS0121750 | H566_RS0108955 |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | H566_RS0108540 | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | H566_RS0114570 | H566_RS25695 |
propionate | putP: propionate transporter; proline:Na+ symporter | H566_RS0108105 | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | H566_RS0105240 | H566_RS0104000 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | | |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | | |
ribose | rbsK: ribokinase | | |
sorbitol | sdh: sorbitol dehydrogenase | H566_RS0106860 | H566_RS23450 |
sucrose | ams: sucrose hydrolase (invertase) | H566_RS0104710 | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | H566_RS0117030 | |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | H566_RS0102680 | H566_RS0104990 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | H566_RS22525 | H566_RS0104985 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | H566_RS0102690 | H566_RS0111715 |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | H566_RS0102695 | H566_RS0113085 |
threonine | ltaE: L-threonine aldolase | H566_RS0104140 | H566_RS0104925 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | H566_RS0101360 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | treF: trehalase | H566_RS0104710 | H566_RS0113920 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | tnaA: tryptophanase | | |
tyrosine | hmgA: homogentisate dioxygenase | | |
valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | H566_RS0102680 | H566_RS0104990 |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | H566_RS0117030 | H566_RS0104995 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | H566_RS22525 | H566_RS0104985 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | H566_RS24575 | H566_RS0109360 |
valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
xylitol | xdhA: xylitol dehydrogenase | H566_RS0105240 | H566_RS0112475 |
xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | H566_RS0118555 | |
xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | H566_RS0118540 | |
xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | H566_RS0118535 | |
xylose | gtsD: xylose ABC transporter, ATPase component GtsD | H566_RS0118530 | H566_RS23460 |
xylose | xylA: xylose isomerase | | |
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