GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_1668 in Pseudomonas fluorescens FW300-N2E2

Annotation: Xylonate dehydratase (EC 4.2.1.82)

Length: 594 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xad hi Xylonate dehydratase (EC 4.2.1.82) (characterized) 100% 100% 1202.2 L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 46% 483.0
L-arabinose catabolism xacD med L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized) 46% 97% 483 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
D-galactose catabolism dgoD med L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized) 46% 97% 483 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
lactose catabolism dgoD med L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized) 46% 97% 483 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
D-cellobiose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
D-gluconate catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
D-glucose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
lactose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
D-maltose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
sucrose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2
trehalose catabolism edd lo phosphogluconate dehydratase (characterized) 31% 82% 194.9 Xylonate dehydratase (EC 4.2.1.82) 100% 1202.2

Sequence Analysis Tools

View Pf6N2E2_1668 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSDTPKHRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPC
NRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLD
GVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAG
EIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYA
TGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDW
QRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVS
NSLTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFE
ARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID
SLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMA
QRRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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