GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Alkalihalobacterium alkalinitrilicum DSM 22532

Found 94 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component BK574_RS19640 BK574_RS23345
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase BK574_RS16270 BK574_RS16265
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
acetate actP: cation/acetate symporter ActP BK574_RS19385
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
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)
asparagine ans: asparaginase BK574_RS25620 BK574_RS10085
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose bgl: cellobiase BK574_RS02405
citrate citM: citrate:cation:H+ symporter CitM BK574_RS07120
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BK574_RS11415 BK574_RS18745
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BK574_RS11420 BK574_RS01585
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BK574_RS01585 BK574_RS18740
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BK574_RS11425
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase BK574_RS02500 BK574_RS09650
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BK574_RS04445 BK574_RS05870
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
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
gluconate gntK: D-gluconate kinase BK574_RS09405
gluconate gntT: gluconate:H+ symporter GntT BK574_RS14425
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) BK574_RS22665
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate dmeA: L-glutamate transporter DmeA BK574_RS00415 BK574_RS03130
histidine hutG: N-formiminoglutamate formiminohydrolase BK574_RS19045
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component BK574_RS20910 BK574_RS21085
histidine PA5505: L-histidine ABC transporter, substrate-binding component BK574_RS21095 BK574_RS20920
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BK574_RS19095 BK574_RS14045
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BK574_RS25480 BK574_RS11480
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BK574_RS23295 BK574_RS11610
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) BK574_RS02405
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BK574_RS25480 BK574_RS11480
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BK574_RS23295 BK574_RS08370
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BK574_RS14015 BK574_RS02990
lysine cadA: lysine decarboxylase BK574_RS18815
lysine davD: glutarate semialdehyde dehydrogenase BK574_RS05090 BK574_RS21850
lysine davT: 5-aminovalerate aminotransferase BK574_RS23575 BK574_RS14870
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase BK574_RS23575 BK574_RS07925
lysine patD: 5-aminopentanal dehydrogenase BK574_RS16255 BK574_RS03925
mannitol mt2d: mannitol 2-dehydrogenase BK574_RS15565 BK574_RS08120
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase
mannose manP: mannose PTS system, EII-CBA components BK574_RS21980
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase BK574_RS02545 BK574_RS15635
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 BK574_RS25200 BK574_RS19135
myoinositol iolT: myo-inositol:H+ symporter
NAG nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP BK574_RS22665
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 BK574_RS03985 BK574_RS08220
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BK574_RS10695 BK574_RS09250
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BK574_RS10695 BK574_RS09250
phenylacetate paaK: phenylacetate-CoA ligase BK574_RS06940 BK574_RS05580
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BK574_RS12730 BK574_RS06125
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase BK574_RS05200
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase BK574_RS05195 BK574_RS15760
phenylalanine QDPR: 6,7-dihydropteridine reductase BK574_RS07990
proline putP: proline:Na+ symporter BK574_RS09125 BK574_RS08755
propionate pccA: propionyl-CoA carboxylase, alpha subunit BK574_RS23295 BK574_RS11610
putrescine gabT: gamma-aminobutyrate transaminase BK574_RS15860 BK574_RS14945
putrescine patA: putrescine aminotransferase (PatA/SpuC) BK574_RS15860 BK574_RS14945
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BK574_RS03925 BK574_RS16255
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like)
rhamnose LRA1: L-rhamnofuranose dehydrogenase BK574_RS23330 BK574_RS26210
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BK574_RS15565 BK574_RS25175
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase BK574_RS15585 BK574_RS23410
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase BK574_RS25175 BK574_RS00935
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BK574_RS11740 BK574_RS11745
threonine tdcC: L-threonine:H+ symporter TdcC
trehalose treC: trehalose-6-phosphate hydrolase BK574_RS15500 BK574_RS15505
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC
tryptophan mhpD: 2-hydroxypentadienoate hydratase BK574_RS16270 BK574_RS16265
tryptophan tnaT: tryptophan:Na+ symporter TnaT BK574_RS21030
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BK574_RS14045 BK574_RS19095
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BK574_RS25480 BK574_RS11480
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BK574_RS03985 BK574_RS21830
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BK574_RS14435 BK574_RS20040
valine pccA: propionyl-CoA carboxylase, alpha subunit BK574_RS23295 BK574_RS11610
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) BK574_RS21980
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BK574_RS14505 BK574_RS04440
xylose xylA: xylose isomerase
xylose xylB: xylulokinase BK574_RS09405
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