GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Photobacterium jeanii R-40508

Found 77 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine astE: succinylglutamate desuccinylase A3K86_RS04085
cellobiose bgl: cellobiase A3K86_RS10950 A3K86_RS20840
citrate SLC13A5: citrate:Na+ symporter
citrulline rocD: ornithine aminotransferase A3K86_RS14790 A3K86_RS04565
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component A3K86_RS01705
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 A3K86_RS01700
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component A3K86_RS01690 A3K86_RS21200
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase A3K86_RS17175
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase A3K86_RS03820 A3K86_RS03040
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
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 galE: UDP-glucose 4-epimerase A3K86_RS04825 A3K86_RS22330
galactose galP: galactose:H+ symporter GalP
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase A3K86_RS18030
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate edd: phosphogluconate dehydratase A3K86_RS17170
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) A3K86_RS02285 A3K86_RS02900
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter A3K86_RS08435 A3K86_RS17965
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate garR: tartronate semialdehyde reductase A3K86_RS19225 A3K86_RS15910
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase A3K86_RS18020
glucuronate udh: D-glucuronate dehydrogenase
histidine hutG: N-formiminoglutamate formiminohydrolase A3K86_RS04155
histidine hutV: L-histidine ABC transporter, ATPase component HutV A3K86_RS17790 A3K86_RS04635
histidine hutX: L-histidine ABC transporter, substrate-binding component HutX A3K86_RS17800
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-lactate lutC: L-lactate dehydrogenase, LutC subunit A3K86_RS04600
lactose galE: UDP-glucose 4-epimerase A3K86_RS04825 A3K86_RS22330
lactose glk: glucokinase A3K86_RS19100 A3K86_RS03930
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) A3K86_RS04880 A3K86_RS20840
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit A3K86_RS09575
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) A3K86_RS14375 A3K86_RS09065
lysine argT: L-lysine ABC transporter, substrate-binding component ArgT A3K86_RS13005 A3K86_RS01795
lysine hglS: D-2-hydroxyglutarate synthase
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) A3K86_RS13015 A3K86_RS01785
lysine hisP: L-lysine ABC transporter, ATPase component HisP A3K86_RS13000 A3K86_RS01690
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) A3K86_RS13010 A3K86_RS01790
lysine lat: L-lysine 6-aminotransferase A3K86_RS14790 A3K86_RS09055
lysine lysN: 2-aminoadipate transaminase A3K86_RS09055 A3K86_RS14790
maltose glk: glucokinase A3K86_RS19100 A3K86_RS03930
maltose susB: alpha-glucosidase (maltase) A3K86_RS14095 A3K86_RS15650
mannitol mt2d: mannitol 2-dehydrogenase A3K86_RS20580 A3K86_RS05510
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components A3K86_RS18075 A3K86_RS02155
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 A3K86_RS16320
myoinositol iolT: myo-inositol:H+ symporter
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components A3K86_RS02285 A3K86_RS06395
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 A3K86_RS15920 A3K86_RS13455
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase A3K86_RS04680 A3K86_RS17390
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase A3K86_RS17385 A3K86_RS19875
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase A3K86_RS17385 A3K86_RS19875
phenylacetate paaK: phenylacetate-CoA ligase A3K86_RS06195
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase A3K86_RS15920
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
putrescine gabT: gamma-aminobutyrate transaminase A3K86_RS09055 A3K86_RS14790
putrescine patA: putrescine aminotransferase (PatA/SpuC) A3K86_RS09055 A3K86_RS14790
putrescine patD: gamma-aminobutyraldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
pyruvate actP: large subunit of pyruvate transporter (actP-like) A3K86_RS09840
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) A3K86_RS09845
rhamnose aldA: lactaldehyde dehydrogenase A3K86_RS19720 A3K86_RS14375
rhamnose LRA1: L-rhamnofuranose dehydrogenase A3K86_RS16360 A3K86_RS05510
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase A3K86_RS18030 A3K86_RS18020
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsA: D-ribose ABC transporter, ATPase component RbsA A3K86_RS19615
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB A3K86_RS19605
ribose rbsC: D-ribose ABC transporter, permease component RbsC A3K86_RS19610 A3K86_RS15090
sorbitol sdh: sorbitol dehydrogenase A3K86_RS05510 A3K86_RS20580
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) A3K86_RS20815 A3K86_RS14095
trehalose glk: glucokinase A3K86_RS19100 A3K86_RS03930
trehalose treC: trehalose-6-phosphate hydrolase A3K86_RS14095
tryptophan tnaA: tryptophanase
valine acdH: isobutyryl-CoA dehydrogenase A3K86_RS15925 A3K86_RS15945
valine bch: 3-hydroxyisobutyryl-CoA hydrolase A3K86_RS15915 A3K86_RS21225
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase A3K86_RS15920 A3K86_RS17390
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) A3K86_RS02155 A3K86_RS18075
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase A3K86_RS20580
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 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