GapMind for catabolism of small carbon sources

 

Protein CCNA_03750 in Caulobacter crescentus NA1000

Annotation: FitnessBrowser__Caulo:CCNA_03750

Length: 400 amino acids

Source: Caulo in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-threonine catabolism tdcB hi threonine ammonia-lyase (EC 4.3.1.19) (characterized) 43% 98% 292 L-serine ammonia-lyase (EC 4.3.1.17) 39% 268.9
L-threonine catabolism tdcB hi ilvA: threonine ammonia-lyase (EC 4.3.1.19) (TIGR01127) 99% 417.2 L-serine ammonia-lyase (EC 4.3.1.17) 39% 268.9
L-serine catabolism sdaB hi threonine ammonia-lyase (EC 4.3.1.19) (characterized) 43% 98% 292 serine racemase (EC 5.1.1.18) 37% 267.3
D-serine catabolism dsdA lo serine racemase (EC 5.1.1.18) (characterized) 39% 93% 199.9 threonine ammonia-lyase (EC 4.3.1.19) 43% 292.0

Sequence Analysis Tools

View CCNA_03750 at FitnessBrowser

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

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Sequence

MTLDLAAIQAAAGRLQGQIERTPCRHSKTLSKITGAEVWVKFENLQFTAAYKERGALNKL
MLLSETEKQRGVIAASAGNHAQGLAYHGARLGVPVTIVMPKTTPFVKVQHTRDFGATVVI
EGETYDDANAHARKLRDEQGLTFVHPFDDYDIMAGQGTIALEMLEDAPDLEILPVPIGGG
GLISGVATAAKALKPDIRIIGCEPAMYPSFTAKMRGVAAHCGGQTIAEGVAVKQVGELTY
GVVRPLLDDVLLLEEPYLEQAVSLYCNVEKTIAEGAGAASLAALLAYPERFRGKKCGLIL
CGGNIDTRLLASVLTRELVRAQRLASLRIIGDDRPGLLSTVASVIGAMGANIIEVNHNRL
ALDVPAKGAEFDITIETRDAQHTQEVMEALRESGYPPRVV

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 paper from 2022 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