GapMind for catabolism of small carbon sources

 

Protein WP_004115187.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004115187.1

Length: 310 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuF 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) 36% 92% 182.2 ABC-type maltose transporter (EC 7.5.2.1) 35% 181.8
D-glucosamine (chitosamine) catabolism SM_b21220 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 35% 96% 180.3 Maltose transport system permease protein malF aka TT_C1628, 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 37% 182.6
D-maltose catabolism thuF lo Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) 32% 95% 149.8 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 36% 182.2
D-sorbitol (glucitol) catabolism mtlF lo ABC transporter for D-Sorbitol, permease component 2 (characterized) 31% 89% 142.5 Maltose transport system permease protein malF aka TT_C1628, 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 37% 182.6
D-maltose catabolism malF_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 89% 137.9 Maltose transport system permease protein malF aka TT_C1628, 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 37% 182.6

Sequence Analysis Tools

View WP_004115187.1 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

MTSIADTLDGRHDRRPWLKRLADASEPYLYSAPALILIIAVMLVPLAIGVSYAFRDIQLL
NPFSGGFIGLQHFRDLAKDGAFYWALKNTLWWTGASVALQFIFGLILALLLDKPFAGRSI
VQALVFLPWAVPSFLAGLNWSWLFNPVIGPIPHWLYALGLMSEPTNILSDPQYAMWGPIV
ANVWWGIPFFAITLLAALQAIPRDLYEAASIDGAGWFERFRSITLPFLAPTIAITVLLRT
VWVSNFADLIIVMTGGGPADRTQIVASYIFTQAFRRLDFGYASAIALVLLVLLLAYSMLI
ILLRQTLLKD

This GapMind analysis is from Sep 24 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:

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