GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Ochrobactrum thiophenivorans DSM 7216

Found 60 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase CEV31_RS10450
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
arabinose xacD: L-arabinonate dehydratase CEV31_RS20170 CEV31_RS02600
cellobiose bgl: cellobiase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component CEV31_RS14700 CEV31_RS14695
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1 CEV31_RS11195 CEV31_RS20085
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2 CEV31_RS11190 CEV31_RS20080
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component CEV31_RS19205 CEV31_RS20075
D-lactate larD: D,L-lactic acid transporter CEV31_RS03820
D-serine dsdA: D-serine ammonia-lyase CEV31_RS01255 CEV31_RS19095
deoxyinosine deoB: phosphopentomutase CEV31_RS03255
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase CEV31_RS15270 CEV31_RS18820
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter CEV31_RS08170
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
galactose dgoD: D-galactonate dehydratase CEV31_RS20170 CEV31_RS02600
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagP: N-acetylglucosamine transporter NagP CEV31_RS19855
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase CEV31_RS01035 CEV31_RS05790
L-lactate larD: D,L-lactic acid transporter LarD CEV31_RS03820
lactose dgoD: D-galactonate dehydratase CEV31_RS20170 CEV31_RS02600
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine lysN: 2-aminoadipate transaminase CEV31_RS01885 CEV31_RS08835
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase CEV31_RS07780 CEV31_RS20510
maltose susB: alpha-glucosidase (maltase)
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE CEV31_RS15290
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) CEV31_RS15285 CEV31_RS07130
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG CEV31_RS15275 CEV31_RS16725
myoinositol PGA1_c07300: myo-inositol ABC transport, substrate-binding component CEV31_RS01785
NAG nagP: N-acetylglucosamine transporter NagP CEV31_RS19855
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 CEV31_RS05620 CEV31_RS09090
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CEV31_RS09090 CEV31_RS05620
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase CEV31_RS15760 CEV31_RS04315
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase CEV31_RS03605 CEV31_RS15765
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase CEV31_RS03605 CEV31_RS15765
phenylacetate paaK: phenylacetate-CoA ligase CEV31_RS07230
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase CEV31_RS05620
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine fahA: fumarylacetoacetate hydrolase CEV31_RS06805 CEV31_RS17405
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) CEV31_RS03685 CEV31_RS13110
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK CEV31_RS05815 CEV31_RS03655
phenylalanine maiA: maleylacetoacetate isomerase CEV31_RS10425
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine QDPR: 6,7-dihydropteridine reductase CEV31_RS09725
propionate putP: propionate transporter; proline:Na+ symporter
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) CEV31_RS15585
putrescine puuB: gamma-glutamylputrescine oxidase CEV31_RS15615 CEV31_RS19040
putrescine puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase CEV31_RS06610 CEV31_RS16975
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase CEV31_RS16855
rhamnose rhaM: L-rhamnose mutarotase CEV31_RS06785
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) CEV31_RS05815 CEV31_RS03660
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) CEV31_RS03685 CEV31_RS13110
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CEV31_RS03670 CEV31_RS14820
sorbitol mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK CEV31_RS15275 CEV31_RS16725
sucrose ams: sucrose hydrolase (invertase)
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) CEV31_RS05815 CEV31_RS03660
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) CEV31_RS03685 CEV31_RS13110
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) CEV31_RS03670 CEV31_RS14820
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase CEV31_RS03255
thymidine nupG: thymidine permease NupG/XapB
tryptophan aroP: tryptophan:H+ symporter AroP CEV31_RS20665 CEV31_RS18290
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) CEV31_RS20665 CEV31_RS18290
tyrosine fahA: fumarylacetoacetate hydrolase CEV31_RS06805 CEV31_RS17405
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase CEV31_RS10425
valine acdH: isobutyryl-CoA dehydrogenase CEV31_RS05790 CEV31_RS01035
valine mmsA: methylmalonate-semialdehyde dehydrogenase CEV31_RS03890 CEV31_RS04895
xylitol xdhA: xylitol dehydrogenase CEV31_RS18365 CEV31_RS15265

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