GapMind for catabolism of small carbon sources

 

Protein WP_011382725.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS01410 cobalt ABC transporter

Length: 264 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 91% 168.7 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 64% 314.3
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 87% 147.5 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 64% 314.3
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 36% 89% 104 Cobalt import ATP-binding protein CbiO; Energy-coupling factor transporter ATP-binding protein CbiO; ECF transporter A component CbiO; EC 7.2.2.- 64% 314.3

Sequence Analysis Tools

View WP_011382725.1 at NCBI

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

MILEAAGLTYRYPGGVAALSGLDLGVERGRRLAVLGPNGAGKTTLLLHLNGTLKPSAGTV
RLGGEIMGYSRAALTGWRRRVGLVLQEPDDQLFAATVAEDVSFGPLNLGLSEAETRRRVE
AALDALGISDLAGRATHMLSFGQKKRVAIAGALAMEPEVLLLDEPLAGLDHQGGKRLLAA
LDALARAGTTLVFTTHEVDLAHGFADRVALFRDGRVIAQGEAAEVLSDRECLAACGLEMP
LLLELGVRTRDEALALLAVGRKVY

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