GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Cereibacter sphaeroides ATCC 17029

Found 65 low-confidence and 50 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase RSPH17029_RS18910 RSPH17029_RS10985
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 RSPH17029_RS14715
alanine snatA: L-alanine symporter SnatA RSPH17029_RS07790
arabinose araE: L-arabinose:H+ symporter
arabinose xacB: L-arabinose 1-dehydrogenase RSPH17029_RS00190 RSPH17029_RS09145
arabinose xacD: L-arabinonate dehydratase RSPH17029_RS09155 RSPH17029_RS18285
arabinose xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase RSPH17029_RS15630
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
arginine odc: L-ornithine decarboxylase RSPH17029_RS03580
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB RSPH17029_RS15400
citrate tctC: citrate/Na+ symporter, substrate-binding component TctC RSPH17029_RS17585
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase RSPH17029_RS03580
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 RSPH17029_RS17505 RSPH17029_RS15650
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 RSPH17029_RS10180 RSPH17029_RS17505
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component RSPH17029_RS10165 RSPH17029_RS17510
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component RSPH17029_RS02000 RSPH17029_RS18145
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 RSPH17029_RS18140 RSPH17029_RS02005
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component RSPH17029_RS02015 RSPH17029_RS18130
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase RSPH17029_RS04715
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase RSPH17029_RS17955 RSPH17029_RS08755
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) RSPH17029_RS20315 RSPH17029_RS04355
fucose fucD: L-fuconate dehydratase RSPH17029_RS01345
fucose fuconolactonase: L-fucono-1,5-lactonase
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galP: galactose:H+ symporter GalP
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase RSPH17029_RS20915 RSPH17029_RS18320
galacturonate gli: D-galactarolactone isomerase
galacturonate udh: D-galacturonate dehydrogenase
gluconate gntA: gluconate TRAP transporter, small permease component RSPH17029_RS17125
gluconate gntC: gluconate TRAP transporter, periplasmic solute-binding component RSPH17029_RS17115 RSPH17029_RS10770
gluconate gntK: D-gluconate kinase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) RSPH17029_RS05915
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dctQ: D-glucuronate TRAP transporter, small permease component
glucuronate kdgK: 2-keto-3-deoxygluconate kinase RSPH17029_RS10785 RSPH17029_RS13575
glucuronate uxaC: D-glucuronate isomerase RSPH17029_RS10775
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) RSPH17029_RS18135 RSPH17029_RS02010
histidine aapP: L-histidine ABC transporter, ATPase component AapP RSPH17029_RS02015 RSPH17029_RS18130
histidine hutG': N-formylglutamate amidohydrolase RSPH17029_RS00345
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) RSPH17029_RS17970 RSPH17029_RS20325
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RSPH17029_RS17965
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) RSPH17029_RS04845 RSPH17029_RS17975
L-lactate Shew_2731: L-lactate:Na+ symporter, large component RSPH17029_RS11235
L-lactate Shew_2732: L-lactate:Na+ symporter, small component RSPH17029_RS11240
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) RSPH17029_RS07690
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) RSPH17029_RS17970 RSPH17029_RS20325
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RSPH17029_RS17965
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) RSPH17029_RS04845 RSPH17029_RS17975
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
lysine davA: 5-aminovaleramidase RSPH17029_RS11495 RSPH17029_RS17110
lysine davB: L-lysine 2-monooxygenase
lysine fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
myoinositol iatA: myo-inositol ABC transporter, ATPase component IatA RSPH17029_RS17460 RSPH17029_RS14655
myoinositol ibpA: myo-inositol ABC transporter, substrate-binding component IbpA
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) RSPH17029_RS05915
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
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase RSPH17029_RS00050 RSPH17029_RS16015
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
phenylacetate paaK: phenylacetate-CoA ligase RSPH17029_RS04830 RSPH17029_RS18475
phenylacetate paaZ1: oxepin-CoA hydrolase RSPH17029_RS05960 RSPH17029_RS06550
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa RSPH17029_RS19600
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine fahA: fumarylacetoacetate hydrolase RSPH17029_RS09140
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase RSPH17029_RS18110 RSPH17029_RS19405
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate mctC: propionate:H+ symporter RSPH17029_RS19600
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) RSPH17029_RS05415 RSPH17029_RS19040
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) RSPH17029_RS05410 RSPH17029_RS19035
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) RSPH17029_RS05405
rhamnose LRA1: L-rhamnofuranose dehydrogenase RSPH17029_RS05260 RSPH17029_RS04240
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase RSPH17029_RS01345 RSPH17029_RS18320
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine snatA: L-serine transporter RSPH17029_RS07790
sucrose ams: sucrose hydrolase (invertase) RSPH17029_RS00200 RSPH17029_RS13100
threonine snatA: L-threonine transporter snatA RSPH17029_RS07790
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase RSPH17029_RS00200 RSPH17029_RS13100
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase RSPH17029_RS09140
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase RSPH17029_RS18110 RSPH17029_RS19405
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) RSPH17029_RS17970 RSPH17029_RS20325
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RSPH17029_RS17965
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) RSPH17029_RS04845 RSPH17029_RS17975
valine mmsA: methylmalonate-semialdehyde dehydrogenase RSPH17029_RS08140 RSPH17029_RS04350
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase RSPH17029_RS18305 RSPH17029_RS17935
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 10 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