GapMind for catabolism of small carbon sources

 

Protein WP_050656201.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_050656201.1

Length: 321 amino acids

Source: GCF_002893965.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuF hi Trehalose transport system permease protein SugA (characterized) 73% 100% 446.8 PalF, component of Platinose (isomaltulose) (6-O-α-D-glucopyranosyl-D-fructofuranose) porter 35% 189.9
D-maltose catabolism thuF med Trehalose/maltose transport system permease protein MalF (characterized) 41% 95% 206.5 Trehalose transport system permease protein SugA 73% 446.8
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) 40% 97% 198 Trehalose transport system permease protein SugA 73% 446.8
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 33% 97% 154.5 Trehalose transport system permease protein SugA 73% 446.8
xylitol catabolism Dshi_0548 lo ABC transporter for Xylitol, permease component 1 (characterized) 32% 97% 150.2 Trehalose transport system permease protein SugA 73% 446.8
L-fucose catabolism SM_b21104 lo ABC transporter for L-Fucose, permease component 1 (characterized) 30% 94% 131 Trehalose transport system permease protein SugA 73% 446.8
lactose catabolism lacF lo ABC transporter for Lactose, permease component 1 (characterized) 30% 93% 126.7 Trehalose transport system permease protein SugA 73% 446.8
trehalose catabolism treT lo TreT, component of Trehalose porter (characterized) 30% 96% 116.3 Trehalose transport system permease protein SugA 73% 446.8
L-arabinose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 57% 55.5 Trehalose transport system permease protein SugA 73% 446.8
D-fructose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 57% 55.5 Trehalose transport system permease protein SugA 73% 446.8
sucrose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 57% 55.5 Trehalose transport system permease protein SugA 73% 446.8
D-xylose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 57% 55.5 Trehalose transport system permease protein SugA 73% 446.8

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MTIDSENSGAAPTVATASPEPKHSAKTKMSDGKAAERRLGLWLVAPAAILMIAVTAYPVV
YAVWLSLQRYDLRFPDQRKFVWFDNYVSVLTDGYWWQAFAVTTSITVVSVVIEFVLGLTI
ALVMHRTIVGKGLVRTVVLIPYGIVTVAAAYSWYYAWTPGTGYLANLLPDGSAPLTDQIP
SLAIIVLAEVWKTTPFMALLLLAGLALVPDDLLKAAQVDGAGAWTRLVRIILPLMKPAIL
VALLFRTLDAFRIFDNIYVLTKGANDTGSVSILGYDNLFKAFNLGIGSAISVLIFVCVAV
IAFIFIKLFGASAPGSDTEGR

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