GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Sedimenticola selenatireducens DSM 17993

Found 110 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
acetate actP: cation/acetate symporter ActP
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) A3GO_RS0114190 A3GO_RS0114160
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) A3GO_RS0114215 A3GO_RS0114165
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) A3GO_RS0114175 A3GO_RS0114425
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) A3GO_RS0106830 A3GO_RS0106835
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA A3GO_RS0106845 A3GO_RS0104265
arginine rocF: arginase A3GO_RS24575
asparagine ans: asparaginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component A3GO_RS0106845 A3GO_RS0104265
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 A3GO_RS0106830 A3GO_RS0106835
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 A3GO_RS0106835 A3GO_RS0106830
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component A3GO_RS0106840
citrulline arcC: carbamate kinase
D-alanine AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 A3GO_RS0114175 A3GO_RS0114425
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase A3GO_RS0118715 A3GO_RS0117900
deoxyinosine deoB: phosphopentomutase A3GO_RS26720 A3GO_RS24860
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase A3GO_RS0105425
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase A3GO_RS0115810
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase A3GO_RS0117290
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase A3GO_RS0115130 A3GO_RS0114560
fucose fucA: L-fuculose-phosphate aldolase FucA A3GO_RS0121690
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 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 A3GO_RS0115130 A3GO_RS0114560
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase A3GO_RS0102965
galacturonate udh: D-galacturonate dehydrogenase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
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) A3GO_RS0103505
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garK: glycerate 2-kinase A3GO_RS0117290
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase A3GO_RS0102965
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) A3GO_RS0114215 A3GO_RS0114165
glutamate braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) A3GO_RS0114210 A3GO_RS0114170
glutamate braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) A3GO_RS0114175 A3GO_RS0114425
glycerol glpF: glycerol facilitator glpF
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) A3GO_RS0114215 A3GO_RS0114165
histidine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) A3GO_RS0114210 A3GO_RS0114170
histidine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) A3GO_RS0114175 A3GO_RS0114425
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase A3GO_RS0109385 A3GO_RS0118285
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) A3GO_RS0114215 A3GO_RS0114165
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
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) A3GO_RS0114215 A3GO_RS0114165
lysine davA: 5-aminovaleramidase A3GO_RS0113290 A3GO_RS0105545
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase A3GO_RS0110380 A3GO_RS0109800
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase A3GO_RS0108695 A3GO_RS0114400
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) A3GO_RS0106830 A3GO_RS0106835
lysine hisP: L-lysine ABC transporter, ATPase component HisP A3GO_RS0106845 A3GO_RS0104265
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) A3GO_RS0106835 A3GO_RS0106830
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
mannitol mt2d: mannitol 2-dehydrogenase A3GO_RS0109385 A3GO_RS0118285
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase A3GO_RS0108450 A3GO_RS26720
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 A3GO_RS0113465 A3GO_RS0110470
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) A3GO_RS0103505
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) A3GO_RS0114215 A3GO_RS0114165
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK A3GO_RS0114190 A3GO_RS0114160
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase A3GO_RS0108935 A3GO_RS0110520
putrescine patA: putrescine aminotransferase (PatA/SpuC) A3GO_RS0110380 A3GO_RS0108935
putrescine patD: gamma-aminobutyraldehyde dehydrogenase A3GO_RS0117140 A3GO_RS0115130
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase A3GO_RS0115130 A3GO_RS0114560
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 rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) A3GO_RS0114190 A3GO_RS0114160
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) A3GO_RS0114215 A3GO_RS0114165
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) A3GO_RS0114175 A3GO_RS0114425
sorbitol sdh: sorbitol dehydrogenase A3GO_RS0104110 A3GO_RS0118285
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) A3GO_RS0114190 A3GO_RS0114160
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) A3GO_RS0114215 A3GO_RS0114165
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) A3GO_RS0114175 A3GO_RS0114425
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) A3GO_RS0118780 A3GO_RS24555
threonine ltaE: L-threonine aldolase A3GO_RS0100345
thymidine deoA: thymidine phosphorylase DeoA A3GO_RS0110755
thymidine deoB: phosphopentomutase A3GO_RS26720 A3GO_RS24860
thymidine deoC: deoxyribose-5-phosphate aldolase
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
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 A3GO_RS0114180 A3GO_RS0114200
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 A3GO_RS0114170 A3GO_RS0114210
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 A3GO_RS0114165 A3GO_RS0114215
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component A3GO_RS0114190
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase A3GO_RS0114405 A3GO_RS0108710
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) A3GO_RS0114215 A3GO_RS0114165
valine mmsB: 3-hydroxyisobutyrate dehydrogenase A3GO_RS23760 A3GO_RS0115125
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