GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_5114 in Pseudomonas fluorescens FW300-N1B4

Annotation: Maltose/maltodextrin ABC transporter, permease protein MalG

Length: 280 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism thuG hi Sugar ABC transporter permease (characterized, see rationale) 100% 100% 546.2 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 288.9
D-maltose catabolism thuG hi ABC transporter for D-Trehalose, permease component 2 (characterized) 68% 97% 380.6 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 288.9
trehalose catabolism thuG hi ABC transporter for D-Trehalose, permease component 2 (characterized) 68% 97% 380.6 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 288.9
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 35% 100% 177.6 ABC transporter for D-Trehalose, permease component 2 68% 380.6
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 34% 96% 176.8 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 34% 92% 160.2 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-mannitol catabolism mtlG lo ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized) 33% 98% 153.3 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-sorbitol (glucitol) catabolism mtlG lo MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 31% 98% 151.8 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 87% 150.2 ABC transporter for D-Trehalose, permease component 2 68% 380.6
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 34% 86% 149.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 34% 86% 149.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 34% 95% 146.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 34% 92% 145.2 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 34% 92% 145.2 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-cellobiose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-glucose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
lactose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-maltose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-mannose catabolism TT_C0326 lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
sucrose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
trehalose catabolism gtsC lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 31% 100% 144.4 ABC transporter for D-Trehalose, permease component 2 68% 380.6
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) 31% 100% 131.3 ABC transporter for D-Trehalose, permease component 2 68% 380.6
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) 31% 100% 131.3 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 121.7 ABC transporter for D-Trehalose, permease component 2 68% 380.6
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 121.7 ABC transporter for D-Trehalose, permease component 2 68% 380.6
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 121.7 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 97% 117.9 ABC transporter for D-Trehalose, permease component 2 68% 380.6
D-cellobiose catabolism cebG lo CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 31% 95% 114 ABC transporter for D-Trehalose, permease component 2 68% 380.6

Sequence Analysis Tools

View Pf1N1B4_5114 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

MNLRLLKKALLRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYA
AVLNQASFLRAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQ
VAVLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGAS
PWVTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPH
ELPWGLLMAASVVVTVPLVILVLIFQRRIVSGLTAGALKG

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