GapMind for catabolism of small carbon sources

 

Protein WP_012409870.1 in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Annotation: NCBI__GCF_000020025.1:WP_012409870.1

Length: 278 amino acids

Source: GCF_000020025.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 34% 95% 166.4 L-arabinose transport system permease protein AraQ 36% 186.0
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) 34% 96% 161.4 L-arabinose transport system permease protein AraQ 36% 186.0
lactose catabolism lacG lo ABC transporter for Lactose, permease component 2 (characterized) 33% 94% 160.2 L-arabinose transport system permease protein AraQ 36% 186.0
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% 97% 149.4 L-arabinose transport system permease protein AraQ 36% 186.0
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% 97% 149.4 L-arabinose transport system permease protein AraQ 36% 186.0
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% 97% 149.4 L-arabinose transport system permease protein AraQ 36% 186.0
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 32% 99% 138.7 L-arabinose transport system permease protein AraQ 36% 186.0
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 32% 99% 138.7 L-arabinose transport system permease protein AraQ 36% 186.0
D-cellobiose catabolism msdC2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 30% 92% 127.9 L-arabinose transport system permease protein AraQ 36% 186.0
L-arabinose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 31% 98% 122.5 L-arabinose transport system permease protein AraQ 36% 186.0
D-fructose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 31% 98% 122.5 L-arabinose transport system permease protein AraQ 36% 186.0
sucrose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 31% 98% 122.5 L-arabinose transport system permease protein AraQ 36% 186.0
D-xylose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 31% 98% 122.5 L-arabinose transport system permease protein AraQ 36% 186.0
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 62% 120.2 L-arabinose transport system permease protein AraQ 36% 186.0
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 62% 120.2 L-arabinose transport system permease protein AraQ 36% 186.0
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 62% 120.2 L-arabinose transport system permease protein AraQ 36% 186.0

Sequence Analysis Tools

View WP_012409870.1 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

MLNWKKSRSQNLLMYALLGAIALVMLFPLLWLISTALKSPTENILQSPPQLLPSQPTLDN
FFSVWNSLPFGQYLYNSTLVSVLTVGLNLLFCALAAYPLARLSFVGRDWIFVAIVSTIMI
PFQIVMIPLYILTVQLGLRNSYLGMIFPSLASAFGIFLLRQAFMSVPKEIEEAARMDGSS
ELGLWWHVMLPAVRPALVTLAIFVFIGAWSDFLWPLIVIQDENLYTLPLGVAKLAGTFSL
DWRLVAAGSVIAIAPVLLLFLFLQRYIVPTDTGSGVKG

This GapMind analysis is from Apr 09 2024. 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