GapMind for catabolism of small carbon sources

 

Protein WP_043917711.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043917711.1

Length: 344 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK hi ABC transporter for D-Sorbitol, ATPase component (characterized) 60% 100% 385.6 ABC transporter for Xylitol, ATPase component 56% 365.5
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 60% 100% 378.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 56% 100% 365.5 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 100% 362.5 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 58% 100% 362.5 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 97% 342.8 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 97% 342.8 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 97% 342.8 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 97% 342.8 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 54% 98% 340.1 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 54% 97% 335.9 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 51% 97% 321.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 51% 97% 317.4 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 93% 292.4 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 46% 88% 260.8 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 95% 202.6 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 35% 93% 150.2 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 92% 147.1 ABC transporter for D-Sorbitol, ATPase component 60% 385.6
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 92% 147.1 ABC transporter for D-Sorbitol, ATPase component 60% 385.6

Sequence Analysis Tools

View WP_043917711.1 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

MSAQVELVGVEKWFGDAQVIKGVDLAVAAGEFVVFVGPSGCGKSTLLRMIAGLEETSRGQ
ILVEGRDATAEPPSKRGLAMVFQSYALYPHLSVRENVGFPLKAAGMSKDEISARVDEAAR
ALRLTDYLDRRPKDLSGGQRQRVAIGRSIVREPVAFLFDEPLSNLDAALRVEMRYEIAKL
HQQLGTAMIYVTHDQIEAMTLADRIVVLEAGRIAQVGTPRELYLRPRSLFVAQFIGSPKM
NVFTADAVPDLDAPPGAATLGVRPEDLRIAPQGDGGLSGSVDVLEYLGADTFVIVDCGPA
GRITARVPGEAGLAPGEAVALEFDRSALHAFDEKGVAVDVPARS

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