Potential Gaps in catabolism of small carbon sources in Polaromonas naphthalenivorans CJ2
Found 85 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | PNAP_RS02410 | |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | PNAP_RS10580 | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | PNAP_RS10865 | PNAP_RS19290 |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | PNAP_RS16005 | PNAP_RS08255 |
alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | PNAP_RS16000 | PNAP_RS08260 |
alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | PNAP_RS15995 | PNAP_RS17570 |
arabinose | araE: L-arabinose:H+ symporter | | |
arabinose | xacB: L-arabinose 1-dehydrogenase | PNAP_RS06215 | PNAP_RS11540 |
arabinose | xacC: L-arabinono-1,4-lactonase | PNAP_RS07950 | PNAP_RS00605 |
arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | PNAP_RS19290 | PNAP_RS10865 |
arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | PNAP_RS16000 | PNAP_RS08260 |
arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | PNAP_RS18010 | PNAP_RS15995 |
arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | PNAP_RS15990 | PNAP_RS17565 |
asparagine | glt: aspartate:proton symporter Glt | PNAP_RS18735 | PNAP_RS04900 |
aspartate | glt: aspartate:proton symporter Glt | PNAP_RS18735 | PNAP_RS04900 |
cellobiose | bgl: cellobiase | | |
citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | PNAP_RS06180 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | PNAP_RS10325 | PNAP_RS05130 |
citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | PNAP_RS20255 | PNAP_RS05125 |
citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | PNAP_RS05125 | PNAP_RS10320 |
citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
citrulline | arcC: carbamate kinase | | |
D-alanine | cycA: D-alanine:H+ symporter CycA | | |
D-serine | cycA: D-serine:H+ symporter CycA | | |
deoxyinosine | deoB: phosphopentomutase | | |
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 | PNAP_RS11540 | PNAP_RS13705 |
deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyribose | deoK: deoxyribokinase | | |
deoxyribose | deoP: deoxyribose transporter | | |
fucose | aldA: lactaldehyde dehydrogenase | PNAP_RS15070 | PNAP_RS13310 |
fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
galactose | galE: UDP-glucose 4-epimerase | PNAP_RS13580 | PNAP_RS05275 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
galactose | PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component | PNAP_RS18460 | PNAP_RS01135 |
galacturonate | exuT: D-galacturonate transporter ExuT | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PNAP_RS02660 | |
glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
glutamate | gltP: L-glutamate:cation symporter GltP/GltT | PNAP_RS18735 | PNAP_RS04900 |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | PNAP_RS01625 | |
glycerol | glpF: glycerol facilitator glpF | | |
histidine | Ac3H11_2554: ABC transporter for L-Histidine, permease component 2 | PNAP_RS05125 | PNAP_RS10320 |
histidine | Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2 | PNAP_RS05120 | PNAP_RS17190 |
histidine | Ac3H11_2561: L-histidine ABC transporter, permease component 1 | PNAP_RS00210 | PNAP_RS02710 |
histidine | Ac3H11_2562: L-histidine ABC transporter, substrate-binding component 1 | | |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | PNAP_RS14375 | |
lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
lysine | davD: glutarate semialdehyde dehydrogenase | PNAP_RS13165 | PNAP_RS07980 |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | PNAP_RS15060 | PNAP_RS13135 |
lysine | patD: 5-aminopentanal dehydrogenase | PNAP_RS15070 | PNAP_RS13165 |
maltose | susB: alpha-glucosidase (maltase) | | |
mannitol | mt2d: mannitol 2-dehydrogenase | PNAP_RS10390 | PNAP_RS11540 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | man-isomerase: D-mannose isomerase | | |
myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | PNAP_RS10375 | |
myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | PNAP_RS19335 | PNAP_RS09965 |
myoinositol | iolT: myo-inositol:H+ symporter | | |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PNAP_RS02660 | |
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 | PNAP_RS09595 | PNAP_RS18065 |
phenylacetate | paaK: phenylacetate-CoA ligase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | PNAP_RS14710 | |
phenylacetate | ppa: phenylacetate permease ppa | PNAP_RS02400 | PNAP_RS16395 |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | PNAP_RS07330 | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | PNAP_RS06535 | |
propionate | lctP: propionate permease | PNAP_RS17340 | |
putrescine | gabT: gamma-aminobutyrate transaminase | PNAP_RS13135 | PNAP_RS14300 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | PNAP_RS15070 | PNAP_RS13165 |
putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | PNAP_RS14295 | PNAP_RS15685 |
rhamnose | aldA: lactaldehyde dehydrogenase | PNAP_RS15070 | PNAP_RS13310 |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PNAP_RS06215 | PNAP_RS11540 |
rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
rhamnose | LRA3: L-rhamnonate dehydratase | PNAP_RS10380 | PNAP_RS07975 |
rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | PNAP_RS07985 | |
rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
ribose | rbsK: ribokinase | | |
sorbitol | sdh: sorbitol dehydrogenase | PNAP_RS06215 | PNAP_RS13545 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | ams: sucrose hydrolase (invertase) | | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | PNAP_RS10865 | PNAP_RS19290 |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | PNAP_RS16005 | PNAP_RS08255 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | PNAP_RS16000 | PNAP_RS08260 |
threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | PNAP_RS15995 | PNAP_RS17570 |
thymidine | deoA: thymidine phosphorylase DeoA | PNAP_RS05400 | |
thymidine | deoB: phosphopentomutase | | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | treF: trehalase | PNAP_RS02610 | |
tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | PNAP_RS10600 | PNAP_RS25675 |
tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | PNAP_RS10595 | |
tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | PNAP_RS10590 | PNAP_RS20840 |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | catB: muconate cycloisomerase | PNAP_RS10630 | |
tryptophan | pcaD: 3-oxoadipate enol-lactone hydrolase | PNAP_RS10640 | PNAP_RS15820 |
tyrosine | hmgA: homogentisate dioxygenase | | |
valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | PNAP_RS10865 | PNAP_RS19290 |
valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | PNAP_RS16000 | PNAP_RS08260 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | PNAP_RS18995 | PNAP_RS07980 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | PNAP_RS07990 | PNAP_RS01355 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | PNAP_RS18440 | PNAP_RS02600 |
xylose | gtsD: xylose ABC transporter, ATPase component GtsD | PNAP_RS18460 | PNAP_RS01135 |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
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