GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Magnetospirillum magneticum AMB-1

Found 103 low-confidence and 66 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
4-hydroxybenzoate pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase AMB_RS13850 AMB_RS04295
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AMB_RS15010
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AMB_RS09135 AMB_RS08455
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AMB_RS09125 AMB_RS08465
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AMB_RS09120 AMB_RS10230
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AMB_RS09135 AMB_RS08455
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMB_RS09130 AMB_RS14460
arginine rocD: ornithine aminotransferase AMB_RS04150 AMB_RS08515
arginine rocF: arginase
asparagine ans: asparaginase AMB_RS00215 AMB_RS00600
cellobiose SemiSWEET: Sugar transporter SemiSWEET AMB_RS06675
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component AMB_RS10565 AMB_RS06945
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
citrulline arcC: carbamate kinase
citrulline rocD: ornithine aminotransferase AMB_RS04150 AMB_RS08515
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 AMB_RS09130 AMB_RS14460
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine deoB: phosphopentomutase AMB_RS02965
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase AMB_RS20840
deoxyinosine nupC: deoxyinosine:H+ symporter NupC AMB_RS20720
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase AMB_RS13470 AMB_RS10625
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter AMB_RS16025
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase AMB_RS16380
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) AMB_RS10835 AMB_RS10625
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase AMB_RS01425 AMB_RS06710
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 galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase AMB_RS06710 AMB_RS04160
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase AMB_RS12805
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase AMB_RS19870
gluconate gntT: gluconate:H+ symporter GntT
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose SemiSWEET: Sugar transporter SemiSWEET AMB_RS06675
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 AMB_RS04095 AMB_RS12805
glucuronate garR: tartronate semialdehyde reductase AMB_RS18155
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AMB_RS09135 AMB_RS08455
glutamate braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMB_RS09130 AMB_RS14460
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) AMB_RS09135 AMB_RS08455
histidine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) AMB_RS09130 AMB_RS14460
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) AMB_RS09135 AMB_RS08455
isoleucine mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
isoleucine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) AMB_RS11280 AMB_RS01115
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) AMB_RS09135 AMB_RS08455
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine davA: 5-aminovaleramidase AMB_RS08115
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase AMB_RS01605 AMB_RS04150
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
lysine lysP: L-lysine:H+ symporter LysP
maltose SemiSWEET: Sugar transporter SemiSWEET AMB_RS06675
maltose susB: alpha-glucosidase (maltase) AMB_RS13755
mannitol mt2d: mannitol 2-dehydrogenase AMB_RS04300 AMB_RS08070
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase AMB_RS00190
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 AMB_RS00635 AMB_RS00695
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase AMB_RS06985
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase AMB_RS04115 AMB_RS06710
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
phenylacetate pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase AMB_RS13850 AMB_RS04295
phenylalanine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
phenylalanine iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit AMB_RS16330
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) AMB_RS09135 AMB_RS08455
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK AMB_RS15010
phenylalanine pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase AMB_RS13850 AMB_RS04295
proline AZOBR_RS08240: proline ABC transporter, permease component 2 AMB_RS09130 AMB_RS14460
propionate lctP: propionate permease AMB_RS20875
propionate mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
propionate mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
putrescine gabD: succinate semialdehyde dehydrogenase AMB_RS06710 AMB_RS04160
putrescine patA: putrescine aminotransferase (PatA/SpuC) AMB_RS08515 AMB_RS04150
putrescine patD: gamma-aminobutyraldehyde dehydrogenase AMB_RS06710 AMB_RS04115
rhamnose aldA: lactaldehyde dehydrogenase AMB_RS01425 AMB_RS06710
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase AMB_RS01425
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase AMB_RS16380
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) AMB_RS15010
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AMB_RS09135 AMB_RS08455
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AMB_RS09125 AMB_RS08465
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AMB_RS09120 AMB_RS10230
serine sdaB: L-serine ammonia-lyase
sorbitol sdh: sorbitol dehydrogenase AMB_RS13035 AMB_RS10625
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) AMB_RS15010
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AMB_RS09135 AMB_RS08455
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AMB_RS09125 AMB_RS08465
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AMB_RS09120 AMB_RS10230
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) AMB_RS03940 AMB_RS03935
threonine ltaE: L-threonine aldolase AMB_RS11815
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase AMB_RS02965
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC AMB_RS20720
trehalose SemiSWEET: Sugar transporter SemiSWEET AMB_RS06675
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1 AMB_RS08465 AMB_RS09125
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 AMB_RS09130 AMB_RS08460
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 AMB_RS09135 AMB_RS08455
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component AMB_RS15010
tyrosine fahA: fumarylacetoacetate hydrolase AMB_RS14215 AMB_RS04120
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase AMB_RS19950 AMB_RS20760
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) AMB_RS09135 AMB_RS08455
valine mcm-large: methylmalonyl-CoA mutase, large (catalytic) subunit AMB_RS01570
valine mcm-small: methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AMB_RS01570
valine mmsA: methylmalonate-semialdehyde dehydrogenase AMB_RS04115 AMB_RS06710
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
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 Sep 17 2021. 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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