GapMind for catabolism of small carbon sources

 

Protein GFF1119 in Marinobacter adhaerens HP15

Annotation: HP15_1097 branched-chain amino acid ABC transporter, ATP-binding protein

Length: 255 amino acids

Source: Marino 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
L-isoleucine catabolism livG med ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 39% 99% 190.3 D-lactate transporter, ATP-binding component 38% 185.7
L-leucine catabolism livG med ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 39% 99% 190.3 D-lactate transporter, ATP-binding component 38% 185.7
L-valine catabolism livG med ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 39% 99% 190.3 D-lactate transporter, ATP-binding component 38% 185.7
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 38% 99% 185.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 37% 100% 174.5 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 95% 120.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 39% 190.3

Sequence Analysis Tools

View GFF1119 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

MANEIILETESLSKHWGGIKALDDISLQFQDKHLHGVVGPNGAGKSTLLNMLCGTLKPTS
GCIFHKGDQIEGMKPWEFVHRGIGRSFQKTNIYVDVTCLENCAIAAQRRFTGSFNLFASR
HSNKLVREGAEKALCQVGLENRVHTVAAEISYGEQRQLELAMVLATDPCILLLDEPMAGM
GHEESQRIIELMNQLKQTYSIVLVEHDMDAIFELSDQLTVLDNGTHLITGTVDEVRNDTR
VKEAYLGKEKEEEAA

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