GapMind for catabolism of small carbon sources

 

Protein WP_106712778.1 in Phyllobacterium brassicacearum STM 196

Annotation: NCBI__GCF_003010955.1:WP_106712778.1

Length: 505 amino acids

Source: GCF_003010955.1 in NCBI

Candidate for 6 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism ytfR hi galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 59% 98% 583.6 Fructose import ATP-binding protein FruK; EC 7.5.2.- 47% 456.1
L-arabinose catabolism araVsh med ABC transporter related (characterized, see rationale) 52% 99% 507.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 59% 583.6
D-fructose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 47% 98% 456.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 59% 583.6
sucrose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 47% 98% 456.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 59% 583.6
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 42% 98% 370.9 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 59% 583.6
xylitol catabolism PS417_12065 lo D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 95% 322.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 59% 583.6

Sequence Analysis Tools

View WP_106712778.1 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

MTDPTVLLAARGICKSFIGFRALDAVDLTIRRGEIHALLGENGAGKSTLIKVLTGVHQPD
LGVMELDGQPIHVRDTLQAQQLGIGTVYQEVNLLPNMSVADNLFVGRQPMRFGFIDRRRM
EKRARELLSQYDLHIDVSSDLSRYSVAVQQLVAIARAVDMSGRILILDEPTASLDRHETE
ILFATLRRLKERGLGIVFITHFLDQVYEICDRVTVLRNGKVAGSELTSQLPKMQLVSLML
GRALAAVTHNVRRDRQEPETKQFSFKGMGRSRSVAPFDLDIGEGEVIGMAGLLGSGRTET
ARLLFGIDSADTGQAAVDGVPVRIRSPQDAVALGFGLCPEDRKTDGIIGDLSVRENIVLA
LQAQRGWFKRLPRRQQVALADKFVKALDIRTTDIEKPIKFLSGGNQQKVILARWLATNPR
FLILDEPTRGIDVGAHAEIIALINQLCDDGMALLVISSEIEEIVAYSTRVVVLRDRVQRG
ELAGDDITTTKIMQKIAAEPGEVHG

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