GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Porphyrobacter dokdonensis DSW-74

Found 110 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP I603_RS03580
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 I603_RS04370
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine astA: arginine N-succinyltransferase I603_RS00795
arginine astC: succinylornithine transaminase I603_RS14155
arginine astE: succinylglutamate desuccinylase
arginine rocE: L-arginine permease
aspartate glt: aspartate:proton symporter Glt I603_RS12595 I603_RS13570
cellobiose glk: glucokinase I603_RS12695 I603_RS05865
citrate SLC13A5: citrate:Na+ symporter I603_RS02475
citrulline citrullinase: putative citrullinase I603_RS11010
citrulline ocd: ornithine cyclodeaminase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component I603_RS07425 I603_RS07065
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase I603_RS05495 I603_RS03095
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase I603_RS05950 I603_RS13060
deoxyinosine deoB: phosphopentomutase I603_RS12545
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase I603_RS06540
deoxyinosine nupC: deoxyinosine:H+ symporter NupC I603_RS11645 I603_RS11035
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase I603_RS09140 I603_RS00745
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter I603_RS08685
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase I603_RS07320 I603_RS01050
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 I603_RS12680
fucose fucU: L-fucose mutarotase FucU
galactose galE: UDP-glucose 4-epimerase I603_RS13660 I603_RS07915
galactose HP1174: Na+-dependent galactose transporter I603_RS12680
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase I603_RS10040
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
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) I603_RS04425
glucose glk: glucokinase I603_RS12695 I603_RS05865
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase I603_RS02320
glucuronate udh: D-glucuronate dehydrogenase I603_RS13385
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase I603_RS07840 I603_RS07060
isoleucine Bap2: L-isoleucine permease Bap2
L-lactate lctO: L-lactate oxidase or 2-monooxygenase I603_RS00540 I603_RS06285
lactose galE: UDP-glucose 4-epimerase I603_RS13660 I603_RS07915
lactose glk: glucokinase I603_RS12695 I603_RS05865
lactose lacP: lactose permease LacP
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase I603_RS07850 I603_RS10115
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit I603_RS07055 I603_RS01520
leucine liuE: hydroxymethylglutaryl-CoA lyase I603_RS12145
lysine davA: 5-aminovaleramidase I603_RS02355
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase I603_RS00545 I603_RS06550
lysine davT: 5-aminovalerate aminotransferase I603_RS14155
lysine lysP: L-lysine:H+ symporter LysP
maltose glk: glucokinase I603_RS12695 I603_RS05865
mannitol mt2d: mannitol 2-dehydrogenase I603_RS10170 I603_RS12090
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter I603_RS12680
mannose man-isomerase: D-mannose isomerase
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
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) I603_RS04425
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 I603_RS07850 I603_RS10325
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase I603_RS07260 I603_RS07435
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase I603_RS07260 I603_RS03105
phenylacetate paaK: phenylacetate-CoA ligase I603_RS09585
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase I603_RS11205 I603_RS10115
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate putP: propionate transporter; proline:Na+ symporter I603_RS00700
putrescine gabT: gamma-aminobutyrate transaminase I603_RS14155
putrescine patA: putrescine aminotransferase (PatA/SpuC) I603_RS14155
putrescine patD: gamma-aminobutyraldehyde dehydrogenase I603_RS07320 I603_RS06550
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate actP: large subunit of pyruvate transporter (actP-like) I603_RS12870
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) I603_RS12875
rhamnose aldA: lactaldehyde dehydrogenase I603_RS07320 I603_RS01050
rhamnose LRA1: L-rhamnofuranose dehydrogenase I603_RS12100 I603_RS12090
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter I603_RS06880
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) I603_RS11690
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) I603_RS12310 I603_RS12305
threonine ltaE: L-threonine aldolase I603_RS09000 I603_RS06420
threonine snatA: L-threonine transporter snatA I603_RS06880
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase I603_RS12545
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC I603_RS11645 I603_RS11035
trehalose glk: glucokinase I603_RS12695 I603_RS05865
trehalose treF: trehalase I603_RS11690 I603_RS13615
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine hmgA: homogentisate dioxygenase
valine acdH: isobutyryl-CoA dehydrogenase I603_RS07840 I603_RS07060
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase I603_RS07845 I603_RS10115
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 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