GapMind for catabolism of small carbon sources

 

Protein WP_068861912.1 in Porphyrobacter dokdonensis DSW-74

Annotation: NCBI__GCF_001677335.1:WP_068861912.1

Length: 236 amino acids

Source: GCF_001677335.1 in NCBI

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 44% 83% 156.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 78% 142.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 61% 146.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
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) 40% 83% 138.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 86% 137.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 86% 137.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 84% 124.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 84% 124.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 53% 105.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 48% 179.9

Sequence Analysis Tools

View WP_068861912.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MTSPSLAISARNLTLTLGSDSAPITILRGIDLDIPHGQVVALLGPSGSGKSSLMAVLSGL
ERASGGSLTVAGADFVGLDEDGLATARRGRIGIVLQAFHLLPTMTAAENVATPMELAGME
NAQARAIAELEAVGLGHRTGHYPTQLSGGEQQRVAIARATAPRPGLIFADEPTGNLDAAT
GEEIINLLFARRAETGATLLIITHDAGLAARCERVLTMADGVIVSDTAGNPVAAGA

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