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 (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