GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhodospirillum centenum SW SW; ATCC 51521

Found 97 low-confidence and 70 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 RC1_RS17665 RC1_RS09455
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 RC1_RS14925
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RC1_RS04995 RC1_RS05000
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RC1_RS08780
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RC1_RS08790 RC1_RS08795
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase RC1_RS14990
arabinose araE: L-arabinose:H+ symporter
arginine adiA: arginine decarboxylase (AdiA/SpeA)
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RC1_RS08780
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RC1_RS08785
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RC1_RS08790 RC1_RS12190
asparagine bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) RC1_RS14935
asparagine bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) RC1_RS14940
asparagine bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) RC1_RS14945 RC1_RS14340
aspartate bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB) RC1_RS14935
aspartate bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC) RC1_RS14940
aspartate bztD: aspartate/asparagine ABC transporter, ATPase component (BztD) RC1_RS14945 RC1_RS14340
cellobiose bgl: cellobiase
cellobiose SemiSWEET: Sugar transporter SemiSWEET RC1_RS12330
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component RC1_RS14340 RC1_RS14945
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 RC1_RS12980 RC1_RS12975
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 RC1_RS12975 RC1_RS12980
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component RC1_RS12965
citrulline citrullinase: putative citrullinase RC1_RS03115
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 RC1_RS08785
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP RC1_RS15805
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase RC1_RS03695 RC1_RS15150
deoxyinosine deoB: phosphopentomutase RC1_RS08135 RC1_RS08600
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase RC1_RS07525 RC1_RS18990
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme RC1_RS16890
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) RC1_RS07605 RC1_RS16075
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase RC1_RS06940 RC1_RS07630
fucose fucA: L-fuculose-phosphate aldolase FucA RC1_RS14990
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
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase RC1_RS12210 RC1_RS22390
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase RC1_RS07630 RC1_RS18020
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase RC1_RS07200
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) RC1_RS16035
glucosamine SLC2A2: glucosamine transporter SLC2A2
glucose SemiSWEET: Sugar transporter SemiSWEET RC1_RS12330
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase RC1_RS07630 RC1_RS18020
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase RC1_RS07200
glucuronate udh: D-glucuronate dehydrogenase
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) RC1_RS08780
glutamate braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) RC1_RS08785
glutamate braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) RC1_RS08790 RC1_RS12190
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) RC1_RS01225
glycerol glpF: glycerol facilitator glpF
histidine PA5503: L-histidine ABC transporter, ATPase component RC1_RS16055 RC1_RS14945
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase RC1_RS06450 RC1_RS01895
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) RC1_RS08780
L-lactate Shew_2732: L-lactate:Na+ symporter, small component RC1_RS15405
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase RC1_RS12210 RC1_RS22390
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)
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) RC1_RS08780
lysine argT: L-lysine ABC transporter, substrate-binding component ArgT RC1_RS12965 RC1_RS12970
lysine davA: 5-aminovaleramidase RC1_RS03115
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase RC1_RS02625 RC1_RS11870
lysine gcdG: succinyl-CoA:glutarate CoA-transferase RC1_RS07275 RC1_RS15585
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) RC1_RS12980 RC1_RS12975
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) RC1_RS12975 RC1_RS12980
maltose susB: alpha-glucosidase (maltase) RC1_RS08160 RC1_RS15920
maltose thuK: maltose ABC transporter, ATPase component ThuK RC1_RS17855 RC1_RS06975
mannitol manA: mannose-6-phosphate isomerase RC1_RS00780
mannitol mt1d: mannitol 1-dehydrogenase RC1_RS16075
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase RC1_RS00780
mannose STP6: mannose:H+ symporter
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 RC1_RS19465
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase RC1_RS07630 RC1_RS06940
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) RC1_RS16035
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 RC1_RS12905 RC1_RS03020
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase RC1_RS18865 RC1_RS09350
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase RC1_RS18865 RC1_RS09350
phenylacetate paaK: phenylacetate-CoA ligase RC1_RS17570 RC1_RS16880
phenylacetate paaZ1: oxepin-CoA hydrolase RC1_RS12905 RC1_RS14595
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa RC1_RS12730
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) RC1_RS08780
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK RC1_RS05000 RC1_RS04995
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline AZOBR_RS08240: proline ABC transporter, permease component 2 RC1_RS08785
propionate lctP: propionate permease RC1_RS15805
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) RC1_RS06980
rhamnose aldA: lactaldehyde dehydrogenase RC1_RS06940 RC1_RS07630
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 rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RC1_RS04995 RC1_RS05000
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RC1_RS08780
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RC1_RS08790 RC1_RS08795
sorbitol sdh: sorbitol dehydrogenase RC1_RS18590 RC1_RS07525
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) RC1_RS08160 RC1_RS15920
sucrose thuK: sucrose ABC transporter, ATPase component ThuK RC1_RS17855 RC1_RS06975
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RC1_RS04995 RC1_RS05000
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RC1_RS08780
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RC1_RS08790 RC1_RS08795
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) RC1_RS17505 RC1_RS17500
threonine ltaE: L-threonine aldolase RC1_RS08280 RC1_RS06420
thymidine deoB: phosphopentomutase RC1_RS08135 RC1_RS08600
thymidine nupG: thymidine permease NupG/XapB
trehalose thuK: trehalose ABC transporter, ATPase component ThuK RC1_RS17855 RC1_RS06975
trehalose treF: trehalase RC1_RS08160 RC1_RS15920
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
valine acdH: isobutyryl-CoA dehydrogenase RC1_RS06450 RC1_RS01895
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) RC1_RS08780
valine mmsA: methylmalonate-semialdehyde dehydrogenase RC1_RS18020 RC1_RS07630
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 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