GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_2414 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_2414 simple sugar transport system permease protein

Length: 358 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araWsh hi Inner-membrane translocator (characterized, see rationale) 47% 87% 295 Galactofuranose transporter permease protein YtfT 50% 277.7
D-galactose catabolism ytfT hi Galactofuranose transporter permease protein YtfT (characterized) 50% 90% 277.7 Fructose import permease protein FruF 37% 219.5
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 37% 94% 219.5 Galactofuranose transporter permease protein YtfT 50% 277.7
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 37% 94% 219.5 Galactofuranose transporter permease protein YtfT 50% 277.7
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 35% 91% 167.2 Galactofuranose transporter permease protein YtfT 50% 277.7
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 35% 91% 167.2 Galactofuranose transporter permease protein YtfT 50% 277.7
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 33% 92% 166.4 Galactofuranose transporter permease protein YtfT 50% 277.7
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 33% 98% 159.8 Galactofuranose transporter permease protein YtfT 50% 277.7
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 32% 91% 157.5 Galactofuranose transporter permease protein YtfT 50% 277.7
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 35% 91% 149.4 Galactofuranose transporter permease protein YtfT 50% 277.7
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 32% 97% 144.1 Galactofuranose transporter permease protein YtfT 50% 277.7
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 32% 97% 144.1 Galactofuranose transporter permease protein YtfT 50% 277.7
myo-inositol catabolism iatP lo Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 33% 88% 141.7 Galactofuranose transporter permease protein YtfT 50% 277.7
D-cellobiose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
D-glucose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
lactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
D-maltose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
sucrose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
trehalose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 92% 127.9 Galactofuranose transporter permease protein YtfT 50% 277.7
L-rhamnose catabolism rhaP lo RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 32% 87% 122.9 Galactofuranose transporter permease protein YtfT 50% 277.7
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 32% 95% 114 Galactofuranose transporter permease protein YtfT 50% 277.7
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 32% 92% 102.4 Galactofuranose transporter permease protein YtfT 50% 277.7

Sequence Analysis Tools

View N515DRAFT_2414 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

MAETTGTMAASSAISSRWGRGLRRCLAHPLLWPLLTLILLLAGNGLFNPGFLALQWRDGH
LYGNLIDIAHRAAPLALVSLGMTLVIALRGLDISVGAVLAIAATVAAWTIGHVSNDGLLP
LWLAIAAALAAGALCGLWNGWLVVGAGMQPIVATLILMVAGRGIAQSISGGQILTLYYAP
YSFLGNGFVLGLPFSLFVVAAVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAIT
LGAYVFCGIAAALAGLLVSSNVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSL
LGALIIQALTTTIYAIGVPPQVNLAVKAVLVFAVMLLQSPLCRGQLRALLRLRAERRA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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