GapMind for catabolism of small carbon sources

 

Protein WP_110753064.1 in Phyllobacterium leguminum ORS 1419

Annotation: NCBI__GCF_003217235.1:WP_110753064.1

Length: 296 amino acids

Source: GCF_003217235.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuF med MalF, component of Maltose/trehalose porter (characterized) 36% 90% 200.3 Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR 32% 185.3
trehalose catabolism thuF med MalF, component of Maltose/trehalose porter (characterized) 36% 90% 200.3 Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR 32% 185.3
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 32% 97% 177.6 MalF, component of Maltose/trehalose porter 36% 200.3
sucrose catabolism thuF lo Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 35% 94% 176.4 MalF, component of Maltose/trehalose porter 36% 200.3
L-fucose catabolism SM_b21104 lo ABC transporter for L-Fucose, permease component 1 (characterized) 31% 96% 166.8 MalF, component of Maltose/trehalose porter 36% 200.3
xylitol catabolism Dshi_0548 lo ABC transporter for Xylitol, permease component 1 (characterized) 32% 96% 165.6 MalF, component of Maltose/trehalose porter 36% 200.3
D-cellobiose catabolism cebF lo CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 30% 99% 157.9 MalF, component of Maltose/trehalose porter 36% 200.3
xylitol catabolism HSERO_RS17005 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 32% 95% 147.5 MalF, component of Maltose/trehalose porter 36% 200.3
D-mannitol catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 30% 93% 143.3 MalF, component of Maltose/trehalose porter 36% 200.3
D-sorbitol (glucitol) catabolism mtlF lo SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) 30% 93% 143.3 MalF, component of Maltose/trehalose porter 36% 200.3
D-maltose catabolism aglF lo ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) 30% 83% 127.1 MalF, component of Maltose/trehalose porter 36% 200.3
sucrose catabolism aglF lo ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) 30% 83% 127.1 MalF, component of Maltose/trehalose porter 36% 200.3
trehalose catabolism aglF lo ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized) 30% 83% 127.1 MalF, component of Maltose/trehalose porter 36% 200.3

Sequence Analysis Tools

View WP_110753064.1 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

MAPSAKPGKSLIKPSYWPFVLPALITVGAVIVFPWLFTLWMSVHQWQLGGIKSFVGFDNF
IRLAGDARFWDSMWHTIVYTVLSVVAPMVLGTIAALVFDSKLPMRGLLRGIFVMPMMATP
VAVALVWTMMYHPQLGVLNYLLSLVGIGPQEWIFNQNTVIPSLVAVETWQWTPLVMLIVL
GGLASMPRDPFESAEIDGANGWQKFRYITLPMILPFIMVAVIIRSIDALKSFDIIYAMTQ
GGPGTASETINIYLYNVAFSYYDIGYASAIAVVFFIIIIAMSLILLALRQRTKWGN

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