GapMind for catabolism of small carbon sources

 

Protein WP_106712916.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106712916.1

Length: 316 amino acids

Source: GCF_003010955.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism SMc04257 hi ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 75% 95% 464.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 51% 290.4
D-cellobiose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-glucose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
lactose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-maltose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
sucrose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
trehalose catabolism gtsC med Sugar ABC transporter permease (characterized, see rationale) 46% 99% 290.8 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-galactose catabolism PfGW456L13_1896 med ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 51% 98% 290.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-xylose catabolism gtsC med ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 50% 100% 289.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-mannose catabolism TT_C0326 med 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) 41% 99% 230.7 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
L-arabinose catabolism xacI lo Xylose/arabinose import permease protein XacI (characterized, see rationale) 30% 92% 134.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5
D-cellobiose catabolism msdC2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 66% 94.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 75% 464.5

Sequence Analysis Tools

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

MGNAGIPSRETPRRWFKMSSSLASFEPRGRRPKRLMSPASIMIYSVLFVAAIYYLIPLYV
MVMTSLKGMPEIRIGNIFSPPVEVTFQPWATAWNSACTGLYCEGIKVGFFNSMKILVPSV
ILSIIIASVNGYALSNWRFKGSELFFTALIFGAFIPYQVMLYPLVIITRQLGIFGTLTGV
IVIHTIFGMPILTLLFRNYFVSLPPELFKAARVDGAGFWRIFLQIMLPMSLPIFVVAVIL
QVTGIWNDFLFGVIFAGTKNFPMTVQLNNIVNSTQGVKEYNVNMAATILTGAVPLLVYFF
SGKYFVRGIAAGAVKG

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