GapMind for catabolism of small carbon sources

 

Protein WP_017620408.1 in Nocardiopsis gilva YIM 90087

Annotation: NCBI__GCF_002263495.1:WP_017620408.1

Length: 303 amino acids

Source: GCF_002263495.1 in NCBI

Candidate for 2 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
lactose catabolism lacG med LacG, component of Lactose porter (characterized) 30% 98% 144.1 ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR 31% 137.9
D-cellobiose catabolism msdC2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 34% 66% 117.9 LacG, component of Lactose porter 30% 144.1

Sequence Analysis Tools

View WP_017620408.1 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

MTGTRTDPGTPSSSSPPAPRPARPVAKRRVGRRTRTVLRYALLLLIMAISVGPFLWQLST
ALKGIGEDIYASPPRFVPADPTLGNFVRVGEVLPVWGYVWNSVRVALATVVLNVVGASLA
GYALARLRFRGRRAALGVFILALLVPGEAIMVAQFLMMRSVHLNDTLVAVVLPGMVGALN
VLLMYNAFLAQSTQIDEAAMIDGANAWQRFTRVALPSVKGTIAVVAIFAFMGAWDDFLWP
LIVLSDPDYYTLTIGLNYLKGTFVGDQRLIAAGTIIAVAPLILLFLTLQRYFFRGVNEGA
IKG

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