GapMind for catabolism of small carbon sources

 

Protein WP_047006259.1 in Erythrobacter gangjinensis K7-2

Annotation: NCBI__GCF_001010925.1:WP_047006259.1

Length: 233 amino acids

Source: GCF_001010925.1 in NCBI

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 37% 68% 142.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 89% 141.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 37% 86% 136.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
L-glutamate catabolism gltL lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 37% 86% 136.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 39% 56% 130.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 55% 128.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 57% 127.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 55% 125.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 57% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 55% 123.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 52% 123.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 60% 121.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 60% 121.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 60% 120.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 33% 58% 120.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 58% 119.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 33% 55% 110.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 56% 109.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 43% 182.6

Sequence Analysis Tools

View WP_047006259.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTSPDNAKPVIAAKDLRLTLGEGEAAVEILRGIDLSVQQGETLALLGPSGSGKSSLMSVL
TGLERASGGSLLVAGEDFTALDEDALAMARRGRIGIVLQAFHLLPTMSAVENVATPMELA
GDDAAWEKAAAELESVGLGHRLTHYPTQLSGGEQQRVAIARAIAPRPPLIFADEPTGNLD
TATGTDVENVLFRRRDETGATLIIITHDRKLAERCGRVVTLADGKIASDTAAA

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