GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_3233 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_3233 xylose ABC transporter membrane protein

Length: 380 amino acids

Source: Dyella79 in FitnessBrowser

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-xylose catabolism xylH hi Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized) 52% 95% 377.5 Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production 38% 241.1
L-arabinose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-cellobiose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-galactose catabolism gguB lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-glucose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
lactose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-maltose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
sucrose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
trehalose catabolism mglC lo GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 38% 92% 256.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 35% 85% 159.5 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 74% 141.4 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 52% 123.2 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 36% 53% 90.9 Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas 52% 377.5

Sequence Analysis Tools

View N515DRAFT_3233 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

MQAQSIQQLFARYKILALLLAVAAIWVFFHVATGGDFVTARNVSNLFRQMAITGMLACGM
VFVIIAGEIDLSVGSLLGLLGGVVAVLTVNQGWSTPVAIVAVLGLGVLIGLFNGFWVTRL
RVPSFIVGLGGMLAFRGVLLGTTHSATIAPVPADLVYLGQGYVSPLWSTVLGVAIFAVVV
ALAVLRRRRRAQLQIRQLPWWADLLKVVAIGAALGVFVATLNSYGGIPLPVLILVALLAV
FSYLASQTVLGRHIYAVGGNLEATRLSGVNVARVKLVVFGIMGLMCAFAGIVNTARLAAG
SPSAGTNGELDAIAACFIGGASMRGGAGTVHGALIGALVMASLDNGMSMMDVDTYWQYIV
KGAILVLAVWVDVLSRPQRD

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