GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_3494 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_3494 sodium transport system ATP-binding protein

Length: 244 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 32% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 94% 113.6 ABC-type Na+ transporter (EC 7.2.2.4) 44% 201.1

Sequence Analysis Tools

View N515DRAFT_3494 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

MIEVKDLHKAFGAIKAVDGVGFSARDGQITGLLGPNGAGKTTTLRMLYTLMKPDRGQILV
DGIDAAADPLAVRRQLGVLPDARGLYKRLTARENIDYFARLHGLPENELASRREALVKAL
EMEEIADRRTEGFSQGQRVKTAIARALIHDPRNVILDEPTNGLDVMATRALRQFMLKLKA
EGRCVLFSSHIMQEVAALCDRIVVIAHGRVVADETPQALREQTGETNLEDAFVKIIGSEE
GLAA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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