GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Brevibacterium jeotgali SJ5-8

Found 130 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP BJEO58_RS11445 BJEO58_RS07950
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase BJEO58_RS04930
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase BJEO58_RS08425
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate actP: cation/acetate symporter ActP
alanine alsT: L-alanine symporter AlsT/DagA BJEO58_RS05770 BJEO58_RS12205
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine aruH: L-arginine:pyruvate transaminase BJEO58_RS07370 BJEO58_RS10030
arginine aruI: 2-ketoarginine decarboxylase BJEO58_RS08980 BJEO58_RS03915
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
arginine kauB: 4-guanidinobutyraldehyde dehydrogenase BJEO58_RS09005 BJEO58_RS05335
asparagine dauA: dicarboxylic acid transporter DauA BJEO58_RS06775
aspartate dauA: dicarboxylic acid transporter DauA BJEO58_RS06775
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase BJEO58_RS13700
citrate SLC13A5: citrate:Na+ symporter BJEO58_RS12955
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BJEO58_RS06850 BJEO58_RS04205
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BJEO58_RS10150 BJEO58_RS06845
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase
citrulline patA: putrescine aminotransferase (PatA/SpuC) BJEO58_RS05345 BJEO58_RS07400
D-alanine cycA: D-alanine:H+ symporter CycA BJEO58_RS06510
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BJEO58_RS04575 BJEO58_RS11240
D-serine cycA: D-serine:H+ symporter CycA BJEO58_RS06510
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
deoxyinosine bmpA: deoxyinosine ABC transporter, substrate-binding component BJEO58_RS09185
deoxyinosine deoB: phosphopentomutase BJEO58_RS09135
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 BJEO58_RS09175
deoxyinosine nupC': deoxyinosine ABC transporter, permease component 2 BJEO58_RS09170
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BJEO58_RS14305 BJEO58_RS08150
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme BJEO58_RS13895
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BJEO58_RS09005 BJEO58_RS12670
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 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 BJEO58_RS06110 BJEO58_RS05335
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BJEO58_RS03445
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)
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase BJEO58_RS06110 BJEO58_RS05335
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BJEO58_RS03445
glucuronate udh: D-glucuronate dehydrogenase
glutamate gluD: L-glutamate ABC transporter, permease component 2 (GluD) BJEO58_RS03180 BJEO58_RS06845
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) BJEO58_RS07995
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase BJEO58_RS08975
histidine permease: L-histidine permease BJEO58_RS06510
isoleucine Bap2: L-isoleucine permease Bap2 BJEO58_RS06510
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BJEO58_RS13400 BJEO58_RS08650
L-lactate lutC: L-lactate dehydrogenase, LutC subunit BJEO58_RS00835
L-malate sdlC: L-malate:Na+ symporter SdlC BJEO58_RS12955
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase BJEO58_RS13700
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BJEO58_RS13400 BJEO58_RS08650
leucine leuT: L-leucine:Na+ symporter LeuT BJEO58_RS06490
leucine liuC: 3-methylglutaconyl-CoA hydratase BJEO58_RS03580 BJEO58_RS08900
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BJEO58_RS00860 BJEO58_RS10090
lysine cadA: lysine decarboxylase
lysine davD: glutarate semialdehyde dehydrogenase BJEO58_RS06110 BJEO58_RS12670
lysine lysP: L-lysine:H+ symporter LysP BJEO58_RS06510
lysine patA: cadaverine aminotransferase BJEO58_RS04770 BJEO58_RS05345
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase) BJEO58_RS08360
mannitol mak: mannose kinase
mannitol mt1d: mannitol 1-dehydrogenase BJEO58_RS01820
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS 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
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
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 BJEO58_RS01640
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BJEO58_RS05920 BJEO58_RS08110
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BJEO58_RS05920 BJEO58_RS08110
phenylacetate paaK: phenylacetate-CoA ligase BJEO58_RS10625 BJEO58_RS05940
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BJEO58_RS03580 BJEO58_RS03525
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP BJEO58_RS06510
phenylalanine fahA: fumarylacetoacetate hydrolase BJEO58_RS04110 BJEO58_RS05470
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase BJEO58_RS06810
phenylalanine QDPR: 6,7-dihydropteridine reductase BJEO58_RS06935
proline davD: glutarate semialdehyde dehydrogenase BJEO58_RS06110 BJEO58_RS12670
proline prdA: D-proline reductase, prdA component
proline prdB: D-proline reductase, prdB component
proline prdC: D-proline reductase, electron transfer component PrdC
proline prdF: proline racemase
putrescine patA: putrescine aminotransferase (PatA/SpuC) BJEO58_RS05345 BJEO58_RS07400
putrescine puuP: putrescine:H+ symporter PuuP/PlaP BJEO58_RS09325
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase BJEO58_RS09005 BJEO58_RS12670
rhamnose LRA1: L-rhamnofuranose dehydrogenase BJEO58_RS06010 BJEO58_RS08150
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase BJEO58_RS08425
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BJEO58_RS14305 BJEO58_RS10640
succinate dauA: succinate:H+ symporter DauA BJEO58_RS06775
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) BJEO58_RS09005 BJEO58_RS03430
thymidine deoB: phosphopentomutase BJEO58_RS09135
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase BJEO58_RS13700
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP BJEO58_RS06510
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) BJEO58_RS06510
tyrosine fahA: fumarylacetoacetate hydrolase BJEO58_RS04110 BJEO58_RS05470
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine Bap2: L-valine permease Bap2 BJEO58_RS06510
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BJEO58_RS08895 BJEO58_RS08900
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BJEO58_RS13400 BJEO58_RS08650
valine mmsA: methylmalonate-semialdehyde dehydrogenase BJEO58_RS07395 BJEO58_RS13455
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BJEO58_RS08510
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BJEO58_RS11150
xylose xylA: xylose isomerase
xylose xylB: xylulokinase BJEO58_RS08130
xylose xylT: D-xylose transporter

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