GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Rhizorhabdus wittichii RW1

Found 90 low-confidence and 33 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase SWIT_RS05455 SWIT_RS22605
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK SWIT_RS21460
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
alanine cycA: L-alanine symporter CycA SWIT_RS03485
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease SWIT_RS03485
asparagine ans: asparaginase SWIT_RS14155 SWIT_RS10740
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase SWIT_RS08215 SWIT_RS05865
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component SWIT_RS13320 SWIT_RS00070
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 SWIT_RS13325
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase SWIT_RS06125
D-alanine cycA: D-alanine:H+ symporter CycA SWIT_RS03485
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA SWIT_RS03485
D-serine dsdA: D-serine ammonia-lyase SWIT_RS12115 SWIT_RS08040
deoxyinosine deoB: phosphopentomutase SWIT_RS00410
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase SWIT_RS07050
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit SWIT_RS20095 SWIT_RS19550
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit SWIT_RS20090 SWIT_RS23205
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribose garK: glycerate 2-kinase
fructose Slc2a5: fructose:H+ symporter
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 exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase SWIT_RS09530
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) SWIT_RS22990
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase SWIT_RS09530
glucuronate uxuB: D-mannonate dehydrogenase SWIT_RS09525
glutamate gltP: L-glutamate:cation symporter GltP/GltT SWIT_RS14595 SWIT_RS13355
isoleucine Bap2: L-isoleucine permease Bap2 SWIT_RS03485
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
lactose lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) SWIT_RS12205
lactose lacC': periplasmic lactose 3-dehydrogenase, LacC subunit SWIT_RS09570
lactose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuC: 3-methylglutaconyl-CoA hydratase SWIT_RS11725 SWIT_RS03865
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit SWIT_RS10915 SWIT_RS14645
leucine liuE: hydroxymethylglutaryl-CoA lyase SWIT_RS11725
lysine cadA: lysine decarboxylase SWIT_RS16155
lysine lysP: L-lysine:H+ symporter LysP SWIT_RS03485
lysine patA: cadaverine aminotransferase SWIT_RS21305 SWIT_RS07135
lysine patD: 5-aminopentanal dehydrogenase SWIT_RS08545 SWIT_RS08815
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase SWIT_RS09525 SWIT_RS23215
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase SWIT_RS17360 SWIT_RS22725
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase SWIT_RS16685
myoinositol iolM: 2-inosose 4-dehydrogenase SWIT_RS25905
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase SWIT_RS09605
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase SWIT_RS09525
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) SWIT_RS22990
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate ppa: phenylacetate permease ppa SWIT_RS09585
phenylalanine ARO10: phenylpyruvate decarboxylase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP SWIT_RS03485
proline CCNA_00435: proline transporter SWIT_RS22305 SWIT_RS13040
propionate putP: propionate transporter; proline:Na+ symporter
putrescine patA: putrescine aminotransferase (PatA/SpuC) SWIT_RS21305 SWIT_RS07135
putrescine patD: gamma-aminobutyraldehyde dehydrogenase SWIT_RS08815 SWIT_RS03735
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose LRA1: L-rhamnofuranose dehydrogenase SWIT_RS07495 SWIT_RS25640
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase SWIT_RS15600 SWIT_RS21815
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase SWIT_RS13045
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter SWIT_RS14540
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) SWIT_RS13650 SWIT_RS13645
threonine snatA: L-threonine transporter snatA SWIT_RS14540
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase SWIT_RS00410
thymidine deoC: deoxyribose-5-phosphate aldolase
trehalose glk: glucokinase SWIT_RS08215 SWIT_RS05865
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase SWIT_RS23890 SWIT_RS07320
tyrosine aroP: L-tyrosine transporter (AroP/FywP) SWIT_RS03485
valine Bap2: L-valine permease Bap2 SWIT_RS03485
valine bch: 3-hydroxyisobutyryl-CoA hydrolase SWIT_RS03305 SWIT_RS18205
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase SWIT_RS25905
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