GapMind for catabolism of small carbon sources

 

Protein WP_047214614.1 in Pandoraea thiooxydans ATSB16

Annotation: NCBI__GCF_001931675.1:WP_047214614.1

Length: 253 amino acids

Source: GCF_001931675.1 in NCBI

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism glnQ med 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) 58% 97% 266.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 54% 98% 251.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 51% 97% 247.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 51% 89% 226.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 80% 140.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 84% 135.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 106.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 106.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 106.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 86% 106.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 54% 266.5

Sequence Analysis Tools

View WP_047214614.1 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

MSGSAIVQIRDLTKSFGDHVVLKGIDFEVEPSQVVVIIGPSGSGKSTFLRCCNGLEVAER
GVIDICGTRLLDNGRLLPDKALNRLRTEVGMVFQSFNLFPHLSVLDNITIGPRKLRGMSH
EAARQEARALLQKVGLSEKADAMPGRLSGGQKQRVAIARALAMRPKVMLFDEPTSALDPE
LVGEVLQVMKLLAKEGMTMMVVTHEMGFAREVADVVVVMDGGGIVEAGPPSQIFSQPREA
RTRSFLQAVISRE

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