GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Paraburkholderia bryophila 376MFSha3.1

Found 11 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase H281DRAFT_01504 H281DRAFT_05723
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H281DRAFT_02161 H281DRAFT_06096
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H281DRAFT_04062 H281DRAFT_06397
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H281DRAFT_04061 H281DRAFT_04452
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component H281DRAFT_06476 H281DRAFT_00221
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 H281DRAFT_06475 H281DRAFT_00222
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 H281DRAFT_00223 H281DRAFT_06474
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component H281DRAFT_01522 H281DRAFT_00224
citrulline arcC: carbamate kinase
citrulline aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) H281DRAFT_06480 H281DRAFT_06479
D-serine cycA: D-serine:H+ symporter CycA H281DRAFT_04042 H281DRAFT_01668
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit H281DRAFT_01474 H281DRAFT_05399
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit H281DRAFT_05400 H281DRAFT_01475
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) H281DRAFT_01976 H281DRAFT_01853
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
isoleucine prpC: 2-methylcitrate synthase H281DRAFT_06634 H281DRAFT_06327
lactose lacP: lactose permease LacP
lysine davA: 5-aminovaleramidase H281DRAFT_03146 H281DRAFT_05434
lysine davB: L-lysine 2-monooxygenase
lysine hisM: L-lysine ABC transporter, permease component 1 (HisM) H281DRAFT_00222 H281DRAFT_06475
lysine hisQ: L-lysine ABC transporter, permease component 2 (HisQ) H281DRAFT_00223 H281DRAFT_06474
mannitol mt2d: mannitol 2-dehydrogenase H281DRAFT_01519 H281DRAFT_02952
mannitol mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE H281DRAFT_04159
mannitol mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) H281DRAFT_04158 H281DRAFT_03746
mannitol mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) H281DRAFT_04157 H281DRAFT_05890
mannitol mtlK: polyol ABC transporter, ATP component MtlK/SmoG H281DRAFT_04155 H281DRAFT_02629
propionate prpC: 2-methylcitrate synthase H281DRAFT_06634 H281DRAFT_06327
putrescine puuB: gamma-glutamylputrescine oxidase H281DRAFT_03219 H281DRAFT_06337
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) H281DRAFT_01222 H281DRAFT_01120
rhamnose rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) H281DRAFT_01221 H281DRAFT_02714
rhamnose rhaT': L-rhamnose ABC transporter, ATPase component RhaT H281DRAFT_01223 H281DRAFT_03380
sucrose ams: sucrose hydrolase (invertase) H281DRAFT_02777 H281DRAFT_06049
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) H281DRAFT_02161 H281DRAFT_06096
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) H281DRAFT_04062 H281DRAFT_06397
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) H281DRAFT_04061 H281DRAFT_04452
thymidine deoA: thymidine phosphorylase DeoA H281DRAFT_05998
thymidine deoB: phosphopentomutase
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA H281DRAFT_01075 H281DRAFT_01653
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB H281DRAFT_01076
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC H281DRAFT_01077 H281DRAFT_04056
tryptophan pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase H281DRAFT_01504 H281DRAFT_05723
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) H281DRAFT_04062 H281DRAFT_06397
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H281DRAFT_02161 H281DRAFT_02405
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) H281DRAFT_04061 H281DRAFT_05513
valine prpC: 2-methylcitrate synthase H281DRAFT_06634 H281DRAFT_06327
xylitol PS417_12055: xylitol ABC transporter, substrate-binding component
xylitol PS417_12065: xylitol ABC transporter, ATPase component H281DRAFT_03380 H281DRAFT_01223

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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