GapMind for catabolism of small carbon sources

 

Protein 3607127 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)

Length: 272 amino acids

Source: Dino in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0549 hi ABC transporter for Xylitol, permease component 2 (characterized) 100% 100% 530 ABC transporter for D-mannitol and D-mannose, permease component 2 41% 213.4
D-mannitol catabolism mtlG med ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized) 41% 99% 213.4 ABC transporter for Xylitol, permease component 2 100% 530.0
D-sorbitol (glucitol) catabolism mtlG med MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 42% 93% 210.7 ABC transporter for Xylitol, permease component 2 100% 530.0
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% 94% 190.7 ABC transporter for Xylitol, permease component 2 100% 530.0
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% 94% 190.7 ABC transporter for Xylitol, permease component 2 100% 530.0
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% 94% 190.7 ABC transporter for Xylitol, permease component 2 100% 530.0
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 35% 94% 177.6 ABC transporter for Xylitol, permease component 2 100% 530.0
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 36% 92% 174.5 ABC transporter for Xylitol, permease component 2 100% 530.0
glycerol catabolism glpQ lo GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 94% 170.2 ABC transporter for Xylitol, permease component 2 100% 530.0
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 92% 142.9 ABC transporter for Xylitol, permease component 2 100% 530.0
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 31% 100% 133.7 ABC transporter for Xylitol, permease component 2 100% 530.0
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 31% 100% 133.7 ABC transporter for Xylitol, permease component 2 100% 530.0
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
D-maltose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
sucrose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
trehalose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 62% 115.5 ABC transporter for Xylitol, permease component 2 100% 530.0
putrescine catabolism potC lo spermidine/putrescine ABC transporter, permease protein PotC (characterized) 32% 82% 98.2 ABC transporter for Xylitol, permease component 2 100% 530.0

Sequence Analysis Tools

View 3607127 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MTSTRSLFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALF
EDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLA
LPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTI
MRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKI
MATSTLIVIPVLIFALIASKQLVRGLTMGAVK

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, 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