GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Methylocystis bryophila S285

Found 121 low-confidence and 41 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP B1812_RS09575
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase B1812_RS07870 B1812_RS18210
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine ans: asparaginase
asparagine glt: aspartate:proton symporter Glt B1812_RS05970
aspartate glt: aspartate:proton symporter Glt B1812_RS05970
cellobiose SemiSWEET: Sugar transporter SemiSWEET B1812_RS14175
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B1812_RS18275 B1812_RS06065
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 B1812_RS01090
citrulline arcC: carbamate kinase
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
deoxyinosine deoB: phosphopentomutase B1812_RS19160
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase B1812_RS10685
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase B1812_RS02990 B1812_RS16415
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter B1812_RS02940
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) B1812_RS03375 B1812_RS18230
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase B1812_RS13395 B1812_RS07050
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
fucose fucU: L-fucose mutarotase FucU
galactose galE: UDP-glucose 4-epimerase B1812_RS17270 B1812_RS09540
galactose galP: galactose:H+ symporter GalP
galactose pgmA: alpha-phosphoglucomutase B1812_RS02305 B1812_RS19160
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase B1812_RS12430
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) B1812_RS10365
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose SemiSWEET: Sugar transporter SemiSWEET B1812_RS14175
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase B1812_RS10880 B1812_RS13395
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase B1812_RS00335
glucuronate udh: D-glucuronate dehydrogenase
glutamate aspA: L-aspartate ammonia-lyase B1812_RS10595 B1812_RS08730
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpF: glycerol facilitator glpF B1812_RS19760
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B1812_RS02625 B1812_RS02990
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose galE: UDP-glucose 4-epimerase B1812_RS17270 B1812_RS09540
lactose lacP: lactose permease LacP
lactose pgmA: alpha-phosphoglucomutase B1812_RS02305 B1812_RS19160
leucine leuT: L-leucine:Na+ symporter LeuT
lysine lat: L-lysine 6-aminotransferase B1812_RS21480 B1812_RS12405
lysine lysN: 2-aminoadipate transaminase B1812_RS18690 B1812_RS21480
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase B1812_RS11125 B1812_RS02130
maltose SemiSWEET: Sugar transporter SemiSWEET B1812_RS14175
maltose susB: alpha-glucosidase (maltase)
mannitol mak: mannose kinase B1812_RS05150
mannitol manA: mannose-6-phosphate isomerase B1812_RS02400
mannitol mt1d: mannitol 1-dehydrogenase B1812_RS03375
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase B1812_RS02400
mannose manP: mannose PTS system, EII-CBA components
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 B1812_RS11350
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) B1812_RS10365
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 B1812_RS05255 B1812_RS16295
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B1812_RS05255 B1812_RS17255
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B1812_RS02620 B1812_RS16320
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase B1812_RS02620 B1812_RS16320
phenylacetate paaK: phenylacetate-CoA ligase B1812_RS14630 B1812_RS03790
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase B1812_RS00705
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase B1812_RS13565
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase B1812_RS10880 B1812_RS13395
putrescine gabT: gamma-aminobutyrate transaminase B1812_RS09075 B1812_RS21480
putrescine patA: putrescine aminotransferase (PatA/SpuC) B1812_RS19660 B1812_RS09075
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B1812_RS13395 B1812_RS07050
putrescine potA: putrescine ABC transporter, ATPase component (PotA/PotG) B1812_RS01630 B1812_RS18275
rhamnose aldA: lactaldehyde dehydrogenase B1812_RS13395 B1812_RS07050
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
serine serP: L-serine permease SerP
sorbitol scrK: fructokinase B1812_RS05150 B1812_RS12430
sorbitol sdh: sorbitol dehydrogenase B1812_RS02990 B1812_RS13135
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase)
sucrose SemiSWEET: Sugar transporter SemiSWEET B1812_RS14175
threonine ltaE: L-threonine aldolase B1812_RS20455 B1812_RS07220
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B1812_RS19160
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose SemiSWEET: Sugar transporter SemiSWEET B1812_RS14175
trehalose treF: trehalase B1812_RS07660 B1812_RS09170
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase B1812_RS17380
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase B1812_RS16310 B1812_RS16285
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B1812_RS16315
valine mmsA: methylmalonate-semialdehyde dehydrogenase B1812_RS16250 B1812_RS10880
valine mmsB: 3-hydroxyisobutyrate dehydrogenase B1812_RS03585 B1812_RS14205
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
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:

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:

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:

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