GapMind for catabolism of small carbon sources

 

Protein WP_043919941.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043919941.1

Length: 286 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0549 med ABC transporter for Xylitol, permease component 2 (characterized) 38% 96% 187.2 ABC transporter for D-Trehalose, permease component 2 40% 186.0
D-maltose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 40% 97% 186 ABC transporter for Xylitol, permease component 2 38% 187.2
sucrose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 40% 97% 186 ABC transporter for Xylitol, permease component 2 38% 187.2
trehalose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 40% 97% 186 ABC transporter for Xylitol, permease component 2 38% 187.2
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 97% 152.9 ABC transporter for Xylitol, permease component 2 38% 187.2
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 34% 92% 152.5 ABC transporter for Xylitol, permease component 2 38% 187.2
D-cellobiose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
D-glucose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
lactose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
D-maltose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
D-mannose catabolism TT_C0326 lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
sucrose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
trehalose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 32% 99% 137.5 ABC transporter for Xylitol, permease component 2 38% 187.2
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 99% 135.2 ABC transporter for Xylitol, permease component 2 38% 187.2
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 99% 135.2 ABC transporter for Xylitol, permease component 2 38% 187.2
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 88% 132.1 ABC transporter for Xylitol, permease component 2 38% 187.2
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 88% 132.1 ABC transporter for Xylitol, permease component 2 38% 187.2

Sequence Analysis Tools

View WP_043919941.1 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

MERRANPAFYALLVALVLMAVGPIWLMLATSLKLNVDIISGTSALFFVPTLNNYETVLCD
YLWYEPEHVRRCDRTFGRALVNSLIVSTVATFLTLILGCMAAYALVRFRFMGRGVTSLTT
LLVRMVPPAVLLVPVFGIWTFQYGLDGSRAGLVLVYVAMNLPFVIWILQSFIVQVPIQLE
EAARMDGAGPFRTFFLVVLPLIKPGLAAAAIFTFRIAWNEFLLANALADRNTRTVPVVIV
NSITEYDIDWGVIMATGMLLAIPPILFTLVASRQIITGMTAGAVKG

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