GapMind for catabolism of small carbon sources

 

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:

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