GapMind for catabolism of small carbon sources

 

Protein WP_038021225.1 in Tatumella morbirosei LMG 23360

Annotation: NCBI__GCF_000757425.2:WP_038021225.1

Length: 360 amino acids

Source: GCF_000757425.2 in NCBI

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism manP lo protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 45% 53% 294.3 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
D-fructose catabolism fruA lo PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) 46% 57% 273.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
sucrose catabolism fruA lo PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized) 46% 57% 273.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
D-fructose catabolism fruII-ABC lo The fructose-specific PTS Enzyme IIABC FruA (characterized) 40% 52% 249.2 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
sucrose catabolism fruII-ABC lo The fructose-specific PTS Enzyme IIABC FruA (characterized) 40% 52% 249.2 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
D-fructose catabolism fruII-C lo PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 39% 96% 248.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
sucrose catabolism fruII-C lo PTS system, fructose subfamily, IIC subunit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 39% 96% 248.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9
xylitol catabolism fruI lo The fructose inducible fructose/xylitol porter, FruI (characterized) 35% 55% 196.4 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9

Sequence Analysis Tools

View WP_038021225.1 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

MSELTLILKNTRQHLMTGVSYMIPFVVSGGILLAVAVMFYGKGAVPDAESAANLKKLFDI
GVAGLTLMVPFLAAYIGYSISERSALAPCAIAAWVGNSFGAGFFGALIAGIIGGIVVYYL
KKIPVHKVLRSVMPIFVIPVIGTLITAGIMMWGLGEPVGMLTKSLTVWLQGMQQGSVVIL
AVIMGLMLAFDMGGPVNKVAYAFMLICVAQGVYHVVAIAAVSICIPPLGLGLATLIGRRN
FSAEEQEAGKAALVMGCVGVTEGAIPFAASDPLRVIPSIMLGSVSGAVVAALTGAECYAG
WGGLIVLPVVSGKFGYLLAVVTGMVVTALCVNLLKHLSRHKVSAAPAAEEDLDLDFEIHP

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