GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Dietzia timorensis ID05-A0528

Found 117 low-confidence and 49 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP BJL86_RS12870 BJL86_RS10295
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase BJL86_RS05940 BJL86_RS10690
4-hydroxybenzoate pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) BJL86_RS05920
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK BJL86_RS16575
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter BJL86_RS16305
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase BJL86_RS01995 BJL86_RS10335
arginine rocD: ornithine aminotransferase BJL86_RS07350 BJL86_RS15830
arginine rocE: L-arginine permease BJL86_RS10165 BJL86_RS14755
arginine rocF: arginase
asparagine ans: asparaginase BJL86_RS06925 BJL86_RS06325
asparagine glt: aspartate:proton symporter Glt BJL86_RS05790 BJL86_RS07515
aspartate glt: aspartate:proton symporter Glt BJL86_RS05790 BJL86_RS07515
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BJL86_RS07235 BJL86_RS14905
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BJL86_RS07230
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BJL86_RS11000
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase BJL86_RS01995 BJL86_RS10335
citrulline rocD: ornithine aminotransferase BJL86_RS07350 BJL86_RS15830
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BJL86_RS00530 BJL86_RS09670
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase BJL86_RS06965
deoxyinosine deoB: phosphopentomutase BJL86_RS05065
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BJL86_RS15680 BJL86_RS14825
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase BJL86_RS06280
fucose aldA: lactaldehyde dehydrogenase BJL86_RS04135 BJL86_RS10335
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 BJL86_RS16305
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose pgmA: alpha-phosphoglucomutase BJL86_RS05065 BJL86_RS04440
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase BJL86_RS15820 BJL86_RS01995
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
galacturonate udh: D-galacturonate dehydrogenase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BJL86_RS04450
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase BJL86_RS15820 BJL86_RS01995
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) BJL86_RS04965 BJL86_RS02905
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BJL86_RS11455
L-lactate L-LDH: L-lactate dehydrogenase BJL86_RS11640 BJL86_RS04560
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
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) BJL86_RS09480 BJL86_RS06550
lactose pgmA: alpha-phosphoglucomutase BJL86_RS05065 BJL86_RS04440
leucine leuT: L-leucine:Na+ symporter LeuT BJL86_RS05690
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BJL86_RS11445 BJL86_RS04975
leucine liuC: 3-methylglutaconyl-CoA hydratase BJL86_RS03420 BJL86_RS12100
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BJL86_RS11455
lysine davA: 5-aminovaleramidase
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase BJL86_RS15820 BJL86_RS03515
lysine davT: 5-aminovalerate aminotransferase BJL86_RS15830 BJL86_RS07350
lysine gcdG: succinyl-CoA:glutarate CoA-transferase BJL86_RS02135
lysine lysP: L-lysine:H+ symporter LysP BJL86_RS14755 BJL86_RS10165
mannitol mak: mannose kinase
mannitol mt1d: mannitol 1-dehydrogenase BJL86_RS14875
mannitol PLT5: polyol transporter PLT5
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
myoinositol iolT: myo-inositol:H+ symporter BJL86_RS16305
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BJL86_RS04450
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 BJL86_RS04005 BJL86_RS03420
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BJL86_RS15710 BJL86_RS01865
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BJL86_RS05940 BJL86_RS10690
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BJL86_RS05940 BJL86_RS10690
phenylacetate paaK: phenylacetate-CoA ligase BJL86_RS15280 BJL86_RS12170
phenylacetate paaZ1: oxepin-CoA hydrolase BJL86_RS01865 BJL86_RS15710
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa BJL86_RS04300
phenylalanine fahA: fumarylacetoacetate hydrolase BJL86_RS09645
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase BJL86_RS02355
phenylalanine QDPR: 6,7-dihydropteridine reductase BJL86_RS15350
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase BJL86_RS01995 BJL86_RS10335
putrescine gabT: gamma-aminobutyrate transaminase BJL86_RS15830 BJL86_RS02420
putrescine patA: putrescine aminotransferase (PatA/SpuC) BJL86_RS07350 BJL86_RS02420
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BJL86_RS10335 BJL86_RS03515
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase BJL86_RS04135 BJL86_RS10335
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 serP: L-serine permease SerP BJL86_RS14755
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BJL86_RS12295 BJL86_RS10875
sucrose 1pfk: 1-phosphofructokinase BJL86_RS06280
sucrose ams: sucrose hydrolase (invertase) BJL86_RS05820 BJL86_RS12895
threonine ltaE: L-threonine aldolase BJL86_RS10600
threonine serP1: L-threonine uptake transporter SerP1 BJL86_RS14755
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BJL86_RS05065
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase BJL86_RS05820 BJL86_RS12895
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BJL86_RS05980 BJL86_RS01765
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB BJL86_RS05975
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC BJL86_RS05970
tryptophan catB: muconate cycloisomerase BJL86_RS05990
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase BJL86_RS06265 BJL86_RS15185
tryptophan pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase BJL86_RS05940 BJL86_RS10690
tryptophan pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) BJL86_RS05920
tyrosine fahA: fumarylacetoacetate hydrolase BJL86_RS09645
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine Bap2: L-valine permease Bap2
valine mmsA: methylmalonate-semialdehyde dehydrogenase BJL86_RS12160 BJL86_RS10335
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BJL86_RS12150 BJL86_RS12300
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BJL86_RS11455
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) BJL86_RS06275
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter BJL86_RS16305

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 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