GapMind for catabolism of small carbon sources

 

Protein WP_068006705.1 in Pseudovibrio axinellae Ad2

Annotation: NCBI__GCF_001623255.1:WP_068006705.1

Length: 275 amino acids

Source: GCF_001623255.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuG hi ABC transporter for D-Trehalose, permease component 2 (characterized) 66% 98% 368.6 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 319.7
sucrose catabolism thuG hi ABC transporter for D-Trehalose, permease component 2 (characterized) 66% 98% 368.6 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 319.7
trehalose catabolism thuG hi ABC transporter for D-Trehalose, permease component 2 (characterized) 66% 98% 368.6 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 57% 319.7
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 33% 96% 175.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 31% 100% 160.2 ABC transporter for D-Trehalose, permease component 2 66% 368.6
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 30% 88% 159.8 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 30% 88% 159.8 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-sorbitol (glucitol) catabolism mtlG lo ABC transporter for D-Sorbitol, permease component 1 (characterized) 33% 88% 154.5 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 34% 99% 153.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 34% 99% 153.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 34% 100% 151 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-mannitol catabolism mtlG lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 (characterized) 33% 99% 150.6 ABC transporter for D-Trehalose, permease component 2 66% 368.6
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 32% 97% 149.4 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 32% 97% 149.4 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 33% 99% 148.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 90% 146.4 ABC transporter for D-Trehalose, permease component 2 66% 368.6
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) 35% 99% 132.1 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 64% 131.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 64% 131.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 64% 131.3 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-cellobiose catabolism SMc04257 lo ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 32% 91% 130.2 ABC transporter for D-Trehalose, permease component 2 66% 368.6
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 30% 98% 121.7 ABC transporter for D-Trehalose, permease component 2 66% 368.6

Sequence Analysis Tools

View WP_068006705.1 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

MNRQLKTVLFYALVVVVVVFSVFPFYYAIITSFRSGQELFNPSALPTSFDLSSYFAIFNE
QPFGRNILNSVIVATSVVVLSLIIAVTASYALARVHFRGRGLLLMTILSVSMFPQVAILS
GMYELIRSMGLYNSLPGLIIPNTVLTLPFTVWVLTTFMKELPKELEEAAVVDGASPLTIV
RRIFLPLMWPAMVTTGLLAFIGAWNEFLFALTFTLSNEVRTVPVAIALMSGASKYELPWG
NIMAASVLVTVPIVVLVLVFQRKIVAGLTAGAVKG

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