Potential Gaps in catabolism of small carbon sources in Methylocella silvestris BL2
Found 127 low-confidence and 51 medium-confidence steps on the best paths for 62 pathways.
Pathway | Step | Best candidate | 2nd candidate |
4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MSIL_RS10660 | |
alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MSIL_RS10635 | MSIL_RS00340 |
alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MSIL_RS10640 | |
alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | MSIL_RS10650 | MSIL_RS00325 |
arabinose | araA: L-arabinose isomerase | | |
arabinose | araB: ribulokinase | | |
arabinose | araD: L-ribulose-5-phosphate epimerase | | |
arabinose | araE: L-arabinose:H+ symporter | | |
arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | MSIL_RS00330 | MSIL_RS10645 |
arginine | rocF: arginase | | |
cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
citrate | citT: citrate:succinate antiporter CitT | MSIL_RS08795 | |
citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | MSIL_RS08670 | MSIL_RS09805 |
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 | MSIL_RS05500 | MSIL_RS15415 |
citrulline | arcC: carbamate kinase | | |
D-alanine | AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 | MSIL_RS10645 | MSIL_RS00330 |
D-alanine | AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component | MSIL_RS10660 | |
D-alanine | dadA: D-alanine dehydrogenase | | |
D-serine | dsdA: D-serine ammonia-lyase | MSIL_RS09280 | |
D-serine | dsdX: D-serine transporter DsdX | MSIL_RS15435 | |
deoxyinosine | deoB: phosphopentomutase | MSIL_RS04005 | |
deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
deoxyinosine | deoD: deoxyinosine phosphorylase | MSIL_RS10960 | |
deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | MSIL_RS04625 | MSIL_RS04185 |
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 | | |
fructose | Slc2a5: fructose:H+ symporter | | |
fucose | fucA: L-fuculose-phosphate aldolase FucA | MSIL_RS05785 | |
fucose | fucI: L-fucose isomerase FucI | | |
fucose | fucK: L-fuculose kinase FucK | | |
fucose | fucP: L-fucose:H+ symporter FucP | | |
fucose | fucU: L-fucose mutarotase FucU | | |
galactose | galE: UDP-glucose 4-epimerase | MSIL_RS13830 | MSIL_RS18775 |
galactose | galK: galactokinase (-1-phosphate forming) | | |
galactose | galP: galactose:H+ symporter GalP | | |
galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
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 | | |
glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MSIL_RS03630 | |
glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
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 | MSIL_RS04370 | |
glucuronate | garR: tartronate semialdehyde reductase | MSIL_RS05505 | |
glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
glucuronate | udh: D-glucuronate dehydrogenase | | |
glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
glycerol | glpF: glycerol facilitator glpF | MSIL_RS02545 | |
glycerol | glpK: glycerol kinase | | |
histidine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | MSIL_RS00330 | MSIL_RS10645 |
histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
histidine | hutH: histidine ammonia-lyase | | |
histidine | hutI: imidazole-5-propionate hydrolase | | |
histidine | hutU: urocanase | | |
isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | MSIL_RS04625 | MSIL_RS19175 |
L-lactate | L-LDH: L-lactate dehydrogenase | MSIL_RS12765 | |
lactose | galE: UDP-glucose 4-epimerase | MSIL_RS13830 | MSIL_RS18775 |
lactose | galK: galactokinase (-1-phosphate forming) | | |
lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
lactose | glk: glucokinase | MSIL_RS03150 | MSIL_RS00835 |
lactose | lacP: lactose permease LacP | | |
lactose | lacZ: lactase (homomeric) | | |
leucine | liuA: isovaleryl-CoA dehydrogenase | | |
leucine | liuC: 3-methylglutaconyl-CoA hydratase | MSIL_RS07135 | MSIL_RS08875 |
leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
lysine | cadA: lysine decarboxylase | MSIL_RS05960 | MSIL_RS01155 |
lysine | davD: glutarate semialdehyde dehydrogenase | MSIL_RS17445 | MSIL_RS19705 |
lysine | davT: 5-aminovalerate aminotransferase | MSIL_RS04290 | MSIL_RS08460 |
lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
lysine | lysP: L-lysine:H+ symporter LysP | | |
lysine | patA: cadaverine aminotransferase | MSIL_RS14670 | MSIL_RS08460 |
lysine | patD: 5-aminopentanal dehydrogenase | MSIL_RS19705 | MSIL_RS11965 |
maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
maltose | susB: alpha-glucosidase (maltase) | MSIL_RS01165 | MSIL_RS19910 |
mannitol | manA: mannose-6-phosphate isomerase | MSIL_RS08125 | MSIL_RS05465 |
mannitol | mt1d: mannitol 1-dehydrogenase | MSIL_RS01035 | MSIL_RS09285 |
mannitol | PLT5: polyol transporter PLT5 | | |
mannose | manA: mannose-6-phosphate isomerase | MSIL_RS08125 | MSIL_RS05465 |
mannose | STP6: mannose:H+ symporter | | |
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 | | |
myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | MSIL_RS06150 | |
myoinositol | iolT: myo-inositol:H+ symporter | | |
myoinositol | mmsA: malonate-semialdehyde dehydrogenase | MSIL_RS17445 | MSIL_RS19705 |
NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MSIL_RS03630 | |
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 | paaF: 2,3-dehydroadipyl-CoA hydratase | MSIL_RS04665 | MSIL_RS07135 |
phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | MSIL_RS08880 | MSIL_RS15280 |
phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | MSIL_RS15280 | MSIL_RS08880 |
phenylacetate | paaK: phenylacetate-CoA ligase | MSIL_RS17440 | MSIL_RS01575 |
phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
phenylacetate | ppa: phenylacetate permease ppa | MSIL_RS13365 | |
phenylalanine | fahA: fumarylacetoacetate hydrolase | MSIL_RS16090 | |
phenylalanine | hmgA: homogentisate dioxygenase | | |
phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | MSIL_RS10635 | MSIL_RS00340 |
phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | MSIL_RS10660 | |
phenylalanine | maiA: maleylacetoacetate isomerase | MSIL_RS19970 | MSIL_RS08865 |
phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | MSIL_RS12290 | |
phenylalanine | QDPR: 6,7-dihydropteridine reductase | MSIL_RS15635 | |
propionate | mctC: propionate:H+ symporter | MSIL_RS13365 | |
putrescine | gabT: gamma-aminobutyrate transaminase | MSIL_RS04290 | MSIL_RS08460 |
putrescine | patA: putrescine aminotransferase (PatA/SpuC) | MSIL_RS14670 | MSIL_RS08460 |
putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | MSIL_RS19705 | MSIL_RS11965 |
putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
rhamnose | LRA1: L-rhamnofuranose dehydrogenase | MSIL_RS00315 | MSIL_RS19175 |
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 | rbsK: ribokinase | | |
ribose | rbsU: probable D-ribose transporter RbsU | | |
serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MSIL_RS10660 | |
serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MSIL_RS10635 | MSIL_RS00340 |
serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MSIL_RS10640 | |
serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | MSIL_RS10650 | MSIL_RS00325 |
sorbitol | sdh: sorbitol dehydrogenase | MSIL_RS09315 | MSIL_RS00315 |
sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
sucrose | SUS: sucrose synthase | | |
sucrose | sut: sucrose:proton symporter SUT/SUC | | |
threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | MSIL_RS10660 | |
threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | MSIL_RS10635 | MSIL_RS00340 |
threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | MSIL_RS10640 | |
threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | MSIL_RS10650 | MSIL_RS00325 |
threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | MSIL_RS06240 | MSIL_RS06245 |
threonine | ltaE: L-threonine aldolase | MSIL_RS19680 | MSIL_RS10775 |
thymidine | deoA: thymidine phosphorylase DeoA | | |
thymidine | deoB: phosphopentomutase | MSIL_RS04005 | |
thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
thymidine | nupG: thymidine permease NupG/XapB | | |
trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
trehalose | treF: trehalase | MSIL_RS01165 | MSIL_RS19910 |
tryptophan | andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | MSIL_RS02320 | MSIL_RS07525 |
tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | MSIL_RS07510 | |
tryptophan | aroP: tryptophan:H+ symporter AroP | | |
tryptophan | kyn: kynureninase | | |
tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
tryptophan | kynB: kynurenine formamidase | MSIL_RS10350 | |
tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
tyrosine | fahA: fumarylacetoacetate hydrolase | MSIL_RS16090 | |
tyrosine | hmgA: homogentisate dioxygenase | | |
tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
tyrosine | maiA: maleylacetoacetate isomerase | MSIL_RS19970 | MSIL_RS08865 |
valine | acdH: isobutyryl-CoA dehydrogenase | MSIL_RS08870 | |
valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | MSIL_RS04665 | |
valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | MSIL_RS07135 | MSIL_RS04665 |
valine | mmsA: methylmalonate-semialdehyde dehydrogenase | MSIL_RS17445 | MSIL_RS19705 |
valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | MSIL_RS05505 | MSIL_RS13240 |
xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | MSIL_RS17435 | |
xylose | xylA: xylose isomerase | | |
xylose | xylB: xylulokinase | | |
xylose | xylT: D-xylose transporter | | |
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