GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_2051 in Pseudomonas fluorescens FW300-N2E2

Annotation: Amino acid ABC transporter, permease protein

Length: 220 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism AO353_21720 hi ABC transporter for D-Glucosamine, permease component 1 (characterized) 100% 100% 436.4 Glutamine ABC transporter permease and substrate binding protein 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 36% 141.4
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 81% 137.5 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 81% 137.5 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 81% 137.5 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 52% 124.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 52% 124.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 30% 63% 112.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-asparagine catabolism aatQ lo Glutamate/aspartate import permease protein GltJ (characterized) 31% 88% 104.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-aspartate catabolism aatQ lo Glutamate/aspartate import permease protein GltJ (characterized) 31% 88% 104.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-glutamate catabolism gltJ lo Glutamate/aspartate import permease protein GltJ (characterized) 31% 88% 104.8 ABC transporter for D-Glucosamine, permease component 1 100% 436.4
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 30% 73% 89.7 ABC transporter for D-Glucosamine, permease component 1 100% 436.4

Sequence Analysis Tools

View Pf6N2E2_2051 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MYESPSWLHELWVARDTLWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRF
YVDLIRGTPVFVLVLACFYMAPALGWQIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRG
QMEASQAIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQ
IIARTFMTLEFYLFAGFLFFIINYAIELLGRHIEKRVALP

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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