GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Beijerinckia mobilis UQM 1969

Found 121 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase DL88_RS15060 DL88_RS13580
4-hydroxybenzoate pcaH: protocatechuate 3,4-dioxygenase, alpha subunit DL88_RS15065 DL88_RS15070
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK DL88_RS15120 DL88_RS15155
alanine snatA: L-alanine symporter SnatA DL88_RS13270
arabinose aldA: (glycol)aldehyde dehydrogenase DL88_RS10695 DL88_RS03165
arabinose araE: L-arabinose:H+ symporter DL88_RS04730
arabinose KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase
arabinose xacB: L-arabinose 1-dehydrogenase DL88_RS16450 DL88_RS15185
arabinose xacC: L-arabinono-1,4-lactonase
arabinose xacD: L-arabinonate dehydratase DL88_RS11215 DL88_RS13730
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DL88_RS08835 DL88_RS05085
asparagine ans: asparaginase
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DL88_RS08835 DL88_RS05085
cellobiose bgl: cellobiase
cellobiose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DL88_RS08835 DL88_RS06575
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 DL88_RS13035 DL88_RS02820
citrulline arcC: carbamate kinase
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine deoB: phosphopentomutase DL88_RS02395
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase DL88_RS07710
deoxyinosine nupC: deoxyinosine:H+ symporter NupC DL88_RS06635
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DL88_RS03920 DL88_RS16450
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DL88_RS03920 DL88_RS16450
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit DL88_RS10405 DL88_RS01625
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit DL88_RS10400 DL88_RS01620
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component DL88_RS07020 DL88_RS10410
deoxyribose ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
fructose fruP: fructose porter FruP DL88_RS17845
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP DL88_RS17845
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose HP1174: Na+-dependent galactose transporter DL88_RS17845
galactose pgmA: alpha-phosphoglucomutase DL88_RS19025 DL88_RS02395
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
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) DL88_RS14190
glucose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
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 DL88_RS11880 DL88_RS11260
glucuronate garR: tartronate semialdehyde reductase DL88_RS13040 DL88_RS16635
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DL88_RS08835 DL88_RS05085
glutamate aspA: L-aspartate ammonia-lyase DL88_RS03785
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF DL88_RS11650 DL88_RS18750
glycerol glpK: glycerol kinase
histidine aapP: L-histidine ABC transporter, ATPase component AapP DL88_RS08835 DL88_RS05085
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 ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase DL88_RS15185 DL88_RS07860
L-lactate L-LDH: L-lactate dehydrogenase DL88_RS18490 DL88_RS12155
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit DL88_RS10850
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) DL88_RS10565 DL88_RS01035
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
lactose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
leucine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DL88_RS08835 DL88_RS05085
leucine liuA: isovaleryl-CoA dehydrogenase DL88_RS01320 DL88_RS16625
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DL88_RS05410 DL88_RS08080
leucine liuC: 3-methylglutaconyl-CoA hydratase DL88_RS01245 DL88_RS16640
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit DL88_RS05405
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine cadA: lysine decarboxylase DL88_RS12595 DL88_RS08220
lysine davT: 5-aminovalerate aminotransferase DL88_RS02255 DL88_RS04220
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase DL88_RS03910 DL88_RS04220
lysine patD: 5-aminopentanal dehydrogenase DL88_RS04160 DL88_RS17100
maltose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
maltose susB: alpha-glucosidase (maltase) DL88_RS01225
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter DL88_RS17845
mannose man-isomerase: D-mannose isomerase
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase DL88_RS15580
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) DL88_RS14190
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 paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DL88_RS01245 DL88_RS16640
phenylacetate paaK: phenylacetate-CoA ligase DL88_RS16320
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase DL88_RS16640 DL88_RS01245
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase DL88_RS15125
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase DL88_RS02785
phenylalanine QDPR: 6,7-dihydropteridine reductase
putrescine gabT: gamma-aminobutyrate transaminase DL88_RS09505 DL88_RS04220
putrescine patA: putrescine aminotransferase (PatA/SpuC) DL88_RS03910 DL88_RS09505
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DL88_RS17100 DL88_RS04160
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
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 DL88_RS03720
serine snatA: L-serine transporter DL88_RS13270
sorbitol sdh: sorbitol dehydrogenase DL88_RS03920 DL88_RS11290
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase)
sucrose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) DL88_RS10935 DL88_RS10940
threonine snatA: L-threonine transporter snatA DL88_RS13270
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase DL88_RS02395
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose MFS-glucose: glucose transporter, MFS superfamily DL88_RS17845 DL88_RS04730
trehalose treF: trehalase DL88_RS02910 DL88_RS01225
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA DL88_RS14995
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB DL88_RS15000
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC DL88_RS15005 DL88_RS17175
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase DL88_RS15125
valine acdH: isobutyryl-CoA dehydrogenase DL88_RS16625 DL88_RS01320
valine Bap2: L-valine permease Bap2
valine mmsA: methylmalonate-semialdehyde dehydrogenase DL88_RS16605 DL88_RS16620
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase DL88_RS03840
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter DL88_RS04730

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