GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Knoellia flava TL1

Found 92 low-confidence and 86 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 adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
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 N798_RS08300
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) N798_RS14385 N798_RS04795
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) N798_RS14375 N798_RS04780
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) N798_RS14370 N798_RS04785
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose gguA: L-arabinose ABC transporter, ATPase component GguA N798_RS01380 N798_RS02050
arabinose gguB: L-arabinose ABC transporter, permease component GguB N798_RS01375
arginine arcA: arginine deiminase
arginine arcC: carbamate kinase N798_RS05150
arginine put1: proline dehydrogenase N798_RS13430 N798_RS16010
arginine rocE: L-arginine permease
asparagine glt: aspartate:proton symporter Glt N798_RS03995
aspartate glt: aspartate:proton symporter Glt N798_RS03995
cellobiose mglC: glucose ABC transporter, permease component (MglC) N798_RS01375 N798_RS02395
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC N798_RS16750
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component N798_RS06050 N798_RS02785
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 N798_RS06055
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 N798_RS02800
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component N798_RS06060
citrulline put1: proline dehydrogenase N798_RS13430 N798_RS16010
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase N798_RS10165 N798_RS16845
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase N798_RS09475 N798_RS08920
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component N798_RS06900
deoxyinosine deoB: phosphopentomutase N798_RS09775
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 N798_RS06895
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 N798_RS06890
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase N798_RS01845 N798_RS14640
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase N798_RS08100
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme N798_RS00500
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
fructose scrK: fructokinase N798_RS06095
fucose aldA: lactaldehyde dehydrogenase N798_RS09790 N798_RS09860
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 galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose gguA: galactose ABC transporter, ATPase component GguA N798_RS01380 N798_RS02050
galactose gguB: galactose ABC transporter, permease component GguB N798_RS01375
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase N798_RS04170 N798_RS09860
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase N798_RS15405
galacturonate udh: D-galacturonate dehydrogenase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) N798_RS09425
glucose mglC: glucose ABC transporter, permease component (MglC) N798_RS01375 N798_RS02395
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase N798_RS04170 N798_RS09860
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase N798_RS15405
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) N798_RS11290
glycerol glpF: glycerol facilitator glpF N798_RS04980
histidine Ga0059261_1577: L-histidine transporter N798_RS02150 N798_RS15860
histidine hutG': N-formylglutamate amidohydrolase
histidine hutH: histidine ammonia-lyase N798_RS01590
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N798_RS14890 N798_RS08170
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase N798_RS02330 N798_RS04830
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) N798_RS14385 N798_RS04795
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) N798_RS14390
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit N798_RS09750 N798_RS16330
L-lactate lutC: L-lactate dehydrogenase, LutC subunit N798_RS07070
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) N798_RS06065
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N798_RS14890 N798_RS08170
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit N798_RS09750 N798_RS16330
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit N798_RS09655 N798_RS09605
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) N798_RS14385 N798_RS04795
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) N798_RS14390
lysine bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit N798_RS09545 N798_RS09660
lysine ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit N798_RS10985
lysine ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit N798_RS10990
lysine etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit N798_RS16595
lysine etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit N798_RS16590
lysine kamA: L-lysine 2,3-aminomutase N798_RS12280
lysine lysP: L-lysine:H+ symporter LysP
maltose mglC: glucose ABC transporter, permease component (MglC) N798_RS01375 N798_RS02395
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase N798_RS06095
mannose mannokinase: D-mannose kinase N798_RS07950 N798_RS16475
myoinositol iolE: scyllo-inosose 2-dehydratase N798_RS06775
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase N798_RS06780 N798_RS14905
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase N798_RS03035
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) N798_RS09425
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 N798_RS15390
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase N798_RS16580 N798_RS14785
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase N798_RS00930 N798_RS00620
phenylacetate paaK: phenylacetate-CoA ligase N798_RS16630
phenylacetate paaZ1: oxepin-CoA hydrolase N798_RS14785 N798_RS02330
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa N798_RS12935
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) N798_RS14370 N798_RS04785
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) N798_RS14385
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK N798_RS14390
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase N798_RS12925
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase N798_RS06205
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline HSERO_RS00870: proline ABC transporter, substrate-binding component N798_RS14390
proline HSERO_RS00890: proline ABC transporter, permease component 2 N798_RS14380
proline HSERO_RS00900: proline ABC transporter, ATPase component 2 N798_RS14370 N798_RS04785
proline put1: proline dehydrogenase N798_RS13430 N798_RS16010
propionate pccA: propionyl-CoA carboxylase, alpha subunit N798_RS09750 N798_RS16330
putrescine gabT: gamma-aminobutyrate transaminase N798_RS11945 N798_RS02465
putrescine patA: putrescine aminotransferase (PatA/SpuC) N798_RS11945 N798_RS09075
putrescine patD: gamma-aminobutyraldehyde dehydrogenase N798_RS09860 N798_RS09790
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase N798_RS09790 N798_RS09860
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
serine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 N798_RS14370 N798_RS04785
serine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 N798_RS14380
serine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 N798_RS14385
serine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component N798_RS14390
sorbitol mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF N798_RS01750 N798_RS10270
sorbitol mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK N798_RS04700 N798_RS00345
sorbitol scrK: fructokinase N798_RS06095
sorbitol sdh: sorbitol dehydrogenase N798_RS01760 N798_RS01765
sucrose mglC: glucose ABC transporter, permease component (MglC) N798_RS01375 N798_RS02395
threonine adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) N798_RS14385 N798_RS04795
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) N798_RS14375 N798_RS04780
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) N798_RS14370 N798_RS04785
thymidine adh: acetaldehyde dehydrogenase (not acylating) N798_RS09860 N798_RS04170
thymidine deoB: phosphopentomutase N798_RS09775
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 N798_RS14370 N798_RS04785
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 N798_RS14380
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 N798_RS14385
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component N798_RS14390
tyrosine maiA: maleylacetoacetate isomerase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase N798_RS14785 N798_RS01860
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component N798_RS14890 N798_RS08170
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) N798_RS14385 N798_RS04795
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
valine mmsA: methylmalonate-semialdehyde dehydrogenase N798_RS06805 N798_RS09860
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit N798_RS09750 N798_RS16330
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component
xylitol PS417_12065: xylitol ABC transporter, ATPase component N798_RS01380 N798_RS02050
xylitol xdhA: xylitol dehydrogenase N798_RS01765 N798_RS10430
xylose xylH: ABC transporter for xylose, permease component xylH N798_RS01375 N798_RS02395

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