GapMind for catabolism of small carbon sources

 

Protein SMc01979 in Sinorhizobium meliloti 1021

Annotation: SMc01979 sugar transport system permease ABC transporter protein

Length: 277 amino acids

Source: Smeli in FitnessBrowser

Candidate for 20 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) 38% 96% 206.8 Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake 40% 196.8
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 36% 97% 199.5 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 38% 206.8
D-maltose catabolism thuG lo Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) 40% 90% 196.8 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 38% 206.8
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 37% 96% 189.5 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 38% 206.8
sucrose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 35% 99% 176.4 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 38% 206.8
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 31% 99% 158.7 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 38% 206.8
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 31% 99% 158.7 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 38% 206.8
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 90% 154.1 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 38% 206.8
D-maltose catabolism malG_Sm lo MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 34% 99% 150.2 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 38% 206.8
trehalose catabolism malG lo MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 34% 99% 150.2 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 38% 206.8
D-sorbitol (glucitol) catabolism mtlG lo ABC transporter for D-Sorbitol, permease component 1 (characterized) 33% 94% 149.4 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 38% 206.8
D-cellobiose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
D-glucose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
lactose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
D-maltose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
sucrose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
trehalose catabolism gtsC lo GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 33% 94% 143.7 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 38% 206.8
D-maltose catabolism malG lo ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) 33% 98% 143.3 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 38% 206.8
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 34% 92% 140.6 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 38% 206.8
trehalose catabolism treU lo TreU, component of Trehalose porter (characterized) 31% 97% 121.3 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 38% 206.8

Sequence Analysis Tools

View SMc01979 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

MRAKQAFLTIAHRLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDF
VLRHSAFPVFFRNSLIVSGSTAVIVTILASLSGYALSRFRFRGKYWLVTLMLLTQMFPLV
MLVAPIFKILSPLGLTNSLTGLVVVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQ
FVAFRQIILPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPVGLLSFVSKFSVD
FGQMMAAGVLALIPACLFFLLIQRYLVQGLTAGAVKG

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 (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 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