GapMind for catabolism of small carbon sources

 

Protein WP_104914355.1 in Pontimonas salivibrio CL-TW6

Annotation: NCBI__GCF_002950575.1:WP_104914355.1

Length: 415 amino acids

Source: GCF_002950575.1 in NCBI

Candidate for 1 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2'-deoxyinosine catabolism nupC' lo Purine/cytidine ABC transporter permease protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 38% 98% 198.7 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 202.2

Sequence Analysis Tools

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MFSLAEQKASWRSTIVMGFFAILILVFFGLLGRQEPVEYKISAEDAAISLPAFVGISSTV
NIVVGIMLLAMTAVAAWWVSKNTPVPLWWITLYGAVGLFGLLGWLAAGDTVPLAFLLANA
LILAVPIIFGGLSGVMSERVGVVNISIEAQLLAGAFVGAVVGSLTGNLYVALAAAMVAGM
LLGMVLAVFAVKYLADQIIVGVVLNVLVIGITNFLFSQWLSSDADRANFPGTLDIFAIPL
LSDLPVIGPVLFDNRVTVFAAFLAVPLLWWVLFRSRLGLRARSVGEYPLAADTVGINVGR
TRFWWVSLGGLLAGLGGAALTIGNTGAFGKEMTAGQGFIALAVVILGRWHPFYMSAAALL
FGFSIILRVWANQVSPGIPTDFILMVPYLVTLIAVVGFVGRVRPPASVGKPYVKE

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