GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhodobacter ovatus JA234

Found 112 low-confidence and 45 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 CRO07_RS05315 CRO07_RS11935
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 CRO07_RS12710
alanine snatA: L-alanine symporter SnatA CRO07_RS09050
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase CRO07_RS10595
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
arginine rocD: ornithine aminotransferase CRO07_RS11670 CRO07_RS09520
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline arcC: carbamate kinase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 CRO07_RS14445 CRO07_RS13060
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 CRO07_RS13065
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component CRO07_RS13050 CRO07_RS02960
citrulline rocD: ornithine aminotransferase CRO07_RS11670 CRO07_RS09520
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component CRO07_RS02945
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 CRO07_RS02950
D-alanine Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 CRO07_RS02955 CRO07_RS14445
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component CRO07_RS02960 CRO07_RS14455
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 CRO07_RS00460
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component CRO07_RS00330
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 CRO07_RS00320 CRO07_RS16110
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 CRO07_RS12920 CRO07_RS00315
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CRO07_RS11135 CRO07_RS04670
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) CRO07_RS11675 CRO07_RS00175
fucose aldA: lactaldehyde dehydrogenase CRO07_RS00170 CRO07_RS10080
fucose fucA: L-fuculose-phosphate aldolase FucA CRO07_RS14710
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 CRO07_RS03645 CRO07_RS11110
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase CRO07_RS11540
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntA: gluconate TRAP transporter, small permease component CRO07_RS06720
gluconate gntC: gluconate TRAP transporter, periplasmic solute-binding component CRO07_RS06725 CRO07_RS11160
gluconate gntK: D-gluconate kinase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) CRO07_RS10700
glucose MFS-glucose: glucose transporter, MFS superfamily
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 CRO07_RS13230
glucuronate garR: tartronate semialdehyde reductase CRO07_RS14265 CRO07_RS00680
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component CRO07_RS15225 CRO07_RS14455
histidine PA5504: L-histidine ABC transporter, permease component CRO07_RS15220
histidine PA5505: L-histidine ABC transporter, substrate-binding component CRO07_RS15215 CRO07_RS15230
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) CRO07_RS11685 CRO07_RS08900
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) CRO07_RS00585 CRO07_RS15930
L-lactate Shew_2731: L-lactate:Na+ symporter, large component CRO07_RS05565
L-lactate Shew_2732: L-lactate:Na+ symporter, small component CRO07_RS05570
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase CRO07_RS03645 CRO07_RS11110
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) CRO07_RS11685 CRO07_RS08900
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) CRO07_RS00585 CRO07_RS15930
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
lysine davA: 5-aminovaleramidase CRO07_RS08480 CRO07_RS07285
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase CRO07_RS04985 CRO07_RS12290
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase CRO07_RS00265 CRO07_RS02660
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
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 CRO07_RS12785 CRO07_RS07770
myoinositol iolT: myo-inositol:H+ symporter
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) CRO07_RS10700
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 CRO07_RS07050 CRO07_RS17650
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CRO07_RS00265 CRO07_RS02660
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CRO07_RS06990 CRO07_RS03135
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CRO07_RS06990 CRO07_RS03135
phenylacetate paaK: phenylacetate-CoA ligase CRO07_RS06260 CRO07_RS11145
phenylacetate paaZ1: oxepin-CoA hydrolase CRO07_RS01150
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa CRO07_RS16135
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
propionate mctC: propionate:H+ symporter CRO07_RS16135
putrescine gabD: succinate semialdehyde dehydrogenase CRO07_RS10080 CRO07_RS00170
putrescine patA: putrescine aminotransferase (PatA/SpuC) CRO07_RS11670 CRO07_RS13090
putrescine patD: gamma-aminobutyraldehyde dehydrogenase CRO07_RS00170 CRO07_RS06630
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) CRO07_RS08555 CRO07_RS11195
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) CRO07_RS08560
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF)
rhamnose LRA1: L-rhamnofuranose dehydrogenase CRO07_RS04670 CRO07_RS11530
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase CRO07_RS04670 CRO07_RS03130
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine snatA: L-serine transporter CRO07_RS09050
sorbitol sdh: sorbitol dehydrogenase CRO07_RS11570 CRO07_RS11525
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
threonine snatA: L-threonine transporter snatA CRO07_RS09050
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase CRO07_RS08120
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) CRO07_RS11685 CRO07_RS08900
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) CRO07_RS00585 CRO07_RS15930
valine mmsA: methylmalonate-semialdehyde dehydrogenase CRO07_RS08740 CRO07_RS00170
xylitol PLT5: xylitol:H+ symporter PLT5
xylose xylT: D-xylose transporter
xylose xyrA: xylitol reductase CRO07_RS07255

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