GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Polaromonas naphthalenivorans CJ2

Found 85 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP PNAP_RS02410
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK PNAP_RS10580
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) PNAP_RS10865 PNAP_RS19290
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PNAP_RS16005 PNAP_RS08255
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PNAP_RS16000 PNAP_RS08260
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PNAP_RS15995 PNAP_RS17570
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase PNAP_RS06215 PNAP_RS11540
arabinose xacC: L-arabinono-1,4-lactonase PNAP_RS07950 PNAP_RS00605
arginine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC PNAP_RS19290 PNAP_RS10865
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) PNAP_RS16000 PNAP_RS08260
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) PNAP_RS18010 PNAP_RS15995
arginine braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) PNAP_RS15990 PNAP_RS17565
asparagine glt: aspartate:proton symporter Glt PNAP_RS18735 PNAP_RS04900
aspartate glt: aspartate:proton symporter Glt PNAP_RS18735 PNAP_RS04900
cellobiose bgl: cellobiase
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC PNAP_RS06180
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component PNAP_RS10325 PNAP_RS05130
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 PNAP_RS20255 PNAP_RS05125
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 PNAP_RS05125 PNAP_RS10320
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
D-serine cycA: D-serine:H+ symporter CycA
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase PNAP_RS11540 PNAP_RS13705
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
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 PNAP_RS15070 PNAP_RS13310
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
galactose galE: UDP-glucose 4-epimerase PNAP_RS13580 PNAP_RS05275
galactose galK: galactokinase (-1-phosphate forming)
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose PfGW456L13_1897: ABC transporter for D-Galactose and D-Glucose, ATPase component PNAP_RS18460 PNAP_RS01135
galacturonate exuT: D-galacturonate transporter ExuT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) PNAP_RS02660
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glutamate gltP: L-glutamate:cation symporter GltP/GltT PNAP_RS18735 PNAP_RS04900
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) PNAP_RS01625
glycerol glpF: glycerol facilitator glpF
histidine Ac3H11_2554: ABC transporter for L-Histidine, permease component 2 PNAP_RS05125 PNAP_RS10320
histidine Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2 PNAP_RS05120 PNAP_RS17190
histidine Ac3H11_2561: L-histidine ABC transporter, permease component 1 PNAP_RS00210 PNAP_RS02710
histidine Ac3H11_2562: L-histidine ABC transporter, substrate-binding component 1
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
lactose klh: periplasmic 3'-ketolactose hydrolase
lactose lacA': periplasmic lactose 3-dehydrogenase, LacA subunit
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) PNAP_RS14375
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit
lysine davD: glutarate semialdehyde dehydrogenase PNAP_RS13165 PNAP_RS07980
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase PNAP_RS15060 PNAP_RS13135
lysine patD: 5-aminopentanal dehydrogenase PNAP_RS15070 PNAP_RS13165
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase PNAP_RS10390 PNAP_RS11540
mannitol PLT5: polyol transporter PLT5
mannose man-isomerase: D-mannose isomerase
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase PNAP_RS10375
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 PNAP_RS19335 PNAP_RS09965
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) PNAP_RS02660
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 PNAP_RS09595 PNAP_RS18065
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PNAP_RS14710
phenylacetate ppa: phenylacetate permease ppa PNAP_RS02400 PNAP_RS16395
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase PNAP_RS07330
phenylalanine QDPR: 6,7-dihydropteridine reductase PNAP_RS06535
propionate lctP: propionate permease PNAP_RS17340
putrescine gabT: gamma-aminobutyrate transaminase PNAP_RS13135 PNAP_RS14300
putrescine patD: gamma-aminobutyraldehyde dehydrogenase PNAP_RS15070 PNAP_RS13165
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) PNAP_RS14295 PNAP_RS15685
rhamnose aldA: lactaldehyde dehydrogenase PNAP_RS15070 PNAP_RS13310
rhamnose LRA1: L-rhamnofuranose dehydrogenase PNAP_RS06215 PNAP_RS11540
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase PNAP_RS10380 PNAP_RS07975
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase PNAP_RS07985
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
sorbitol sdh: sorbitol dehydrogenase PNAP_RS06215 PNAP_RS13545
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase)
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) PNAP_RS10865 PNAP_RS19290
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PNAP_RS16005 PNAP_RS08255
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PNAP_RS16000 PNAP_RS08260
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PNAP_RS15995 PNAP_RS17570
thymidine deoA: thymidine phosphorylase DeoA PNAP_RS05400
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase PNAP_RS02610
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA PNAP_RS10600 PNAP_RS25675
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB PNAP_RS10595
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC PNAP_RS10590 PNAP_RS20840
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan catB: muconate cycloisomerase PNAP_RS10630
tryptophan pcaD: 3-oxoadipate enol-lactone hydrolase PNAP_RS10640 PNAP_RS15820
tyrosine hmgA: homogentisate dioxygenase
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PNAP_RS10865 PNAP_RS19290
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) PNAP_RS16000 PNAP_RS08260
valine mmsA: methylmalonate-semialdehyde dehydrogenase PNAP_RS18995 PNAP_RS07980
valine mmsB: 3-hydroxyisobutyrate dehydrogenase PNAP_RS07990 PNAP_RS01355
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA PNAP_RS18440 PNAP_RS02600
xylose gtsD: xylose ABC transporter, ATPase component GtsD PNAP_RS18460 PNAP_RS01135
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

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.

Links

Downloads

Related tools

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