GapMind for catabolism of small carbon sources

 

Protein 3609759 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)

Length: 275 amino acids

Source: Dino in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuG med ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) 35% 99% 188.3 ABC transporter for L-Fucose, permease component 2 31% 173.3
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) 34% 95% 174.5 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
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) 34% 95% 174.5 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 31% 97% 173.3 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 96% 166.4 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 31% 99% 166 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 33% 96% 162.2 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
D-mannitol catabolism mtlG lo ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized) 33% 100% 161.4 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
D-sorbitol (glucitol) catabolism mtlG lo ABC transporter for D-Sorbitol, permease component 1 (characterized) 32% 89% 160.6 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
glycerol catabolism glpQ lo ABC transporter for Glycerol, permease component 2 (characterized) 31% 97% 159.1 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 31% 99% 146.7 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 35% 188.3

Sequence Analysis Tools

View 3609759 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

MTGKQRKQFWSAVHAVLIIAAMFVMLVPILWIFLAAFKSHVDVYQLKLFFTPTLENFGTV
FDDPYRLGEKLFNSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQFLPAV
VIILPFFIMFRDIGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVDGSSR
LQVIWNIVLPMAAPGLLTSGIFCFIIAWNEFLFALILTNKDAVTLPIGLALFKGEEGDLW
NLLSAAGIIIMAPMFVLALMIRKYFVQGMTMGAVR

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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