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 (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