GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_4848 in Pseudomonas fluorescens FW300-N1B4

Annotation: Various polyols ABC transporter, permease component 2

Length: 276 amino acids

Source: pseudo1_N1B4 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
D-mannitol catabolism mtlG hi ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized) 98% 100% 539.7 ABC transporter for D-Sorbitol, permease component 1 66% 362.5
D-sorbitol (glucitol) catabolism mtlG hi ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 (characterized) 98% 100% 537.7
xylitol catabolism Dshi_0549 med ABC transporter for Xylitol, permease component 2 (characterized) 42% 96% 209.9 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
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) 33% 99% 161.8 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
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) 33% 99% 161.8 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
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) 33% 99% 161.8 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 31% 100% 152.9 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 99% 151 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
glycerol catabolism glpQ lo ABC transporter for Glycerol, permease component 2 (characterized) 30% 100% 146.7 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 31% 100% 136.7 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 30% 96% 104.8 ABC transporter for D-mannitol and D-mannose, permease component 2 98% 539.7

Sequence Analysis Tools

View Pf1N1B4_4848 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

MTLQQSRRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLENYL
HINERSDYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPP
VGVLMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGAT
LWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSQAAPLTALIASYSSPEGLF
WAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK

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, 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