GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Paraburkholderia phymatum STM815

Found 12 low-confidence and 38 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BPHY_RS00550 BPHY_RS32955
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BPHY_RS02955 BPHY_RS15515
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BPHY_RS02960
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BPHY_RS02970 BPHY_RS15485
arginine odc: L-ornithine decarboxylase BPHY_RS32090 BPHY_RS11130
arginine puuB: gamma-glutamylputrescine oxidase BPHY_RS18185 BPHY_RS32820
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BPHY_RS09100 BPHY_RS11025
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BPHY_RS09105 BPHY_RS11020
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BPHY_RS11015 BPHY_RS09110
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BPHY_RS19095 BPHY_RS09055
citrulline odc: L-ornithine decarboxylase BPHY_RS32090 BPHY_RS11130
citrulline puuB: gamma-glutamylputrescine oxidase BPHY_RS18185 BPHY_RS32820
D-serine cycA: D-serine:H+ symporter CycA BPHY_RS03010 BPHY_RS31005
D-serine dsdA: D-serine ammonia-lyase BPHY_RS19110 BPHY_RS28470
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BPHY_RS20500 BPHY_RS33885
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter BPHY_RS11080 BPHY_RS17575
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme BPHY_RS16660
deoxyribose deoP: deoxyribose transporter
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) BPHY_RS01460
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
lactose lacP: lactose permease LacP
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) BPHY_RS11020 BPHY_RS09105
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) BPHY_RS11015 BPHY_RS09110
lysine patA: cadaverine aminotransferase BPHY_RS31375 BPHY_RS09090
lysine patD: 5-aminopentanal dehydrogenase BPHY_RS28155 BPHY_RS23615
maltose susB: alpha-glucosidase (maltase) BPHY_RS26235 BPHY_RS15920
mannitol mt2d: mannitol 2-dehydrogenase BPHY_RS02500 BPHY_RS33955
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE BPHY_RS02460
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) BPHY_RS02465 BPHY_RS11940
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) BPHY_RS02470 BPHY_RS33175
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG BPHY_RS02480 BPHY_RS11955
putrescine puuB: gamma-glutamylputrescine oxidase BPHY_RS18185 BPHY_RS32820
rhamnose LRA2: L-rhamnono-gamma-lactonase
sucrose ams: sucrose hydrolase (invertase) BPHY_RS30225 BPHY_RS30235
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BPHY_RS00550 BPHY_RS32955
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BPHY_RS02955 BPHY_RS15515
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BPHY_RS02960
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BPHY_RS02970 BPHY_RS15485
thymidine deoA: thymidine phosphorylase DeoA BPHY_RS31915
thymidine deoB: phosphopentomutase
thymidine nupG: thymidine permease NupG/XapB
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BPHY_RS26785
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB BPHY_RS26780
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC BPHY_RS30415 BPHY_RS26775
tryptophan pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase BPHY_RS19030 BPHY_RS13665
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) BPHY_RS02955 BPHY_RS15515
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BPHY_RS00550 BPHY_RS15375
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) BPHY_RS02960

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