GapMind for catabolism of small carbon sources

 

Protein WP_015928110.1 in Methylobacterium nodulans ORS 2060

Annotation: NCBI__GCF_000022085.1:WP_015928110.1

Length: 292 amino acids

Source: GCF_000022085.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuG lo Maltose transport system permease protein malG aka TT_C1629, 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) 38% 95% 182.6 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
sucrose catabolism thuG lo Maltose transport system permease protein malG aka TT_C1629, 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) 38% 95% 182.6 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
trehalose catabolism thuG lo Maltose transport system permease protein malG aka TT_C1629, 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) 38% 95% 182.6 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 34% 100% 162.5 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 32% 97% 156.8 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-mannitol catabolism mtlG lo MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 32% 98% 152.5 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-sorbitol (glucitol) catabolism mtlG lo MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 32% 98% 152.5 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 32% 97% 146.4 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 32% 98% 136 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 31% 85% 118.2 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 31% 85% 118.2 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-maltose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
sucrose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
trehalose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 100.9 Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV 36% 184.1

Sequence Analysis Tools

View WP_015928110.1 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

MAQATADHSEGMAYLETLPRRLVTVYLPLTIILVVLLFPFYWMALTSIKPDDQLIDMETY
NPFFVVSPTLKHITKLLFETQYPLWLWNTMLVSVAATVLSLFASVLAAYAIVRIRYRGAA
AVGGAIFLAYLVPPSILFIPLATIIQAYGLFDSPLALILVYPTILIPFSTWLLMGYFKTI
PYELEECALIDGAGRWQILTRIILPLAVPGLISAGIFSLTLCWNEFIYALTFLSSTPNKT
VPVAVVSEFVDGDIYRWGSLMAGALVGSLPLVILYSFFVEHYVSAMTGAVKE

This GapMind analysis is from Apr 09 2024. 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