GapMind for catabolism of small carbon sources

 

Protein WP_009141268.1 in Collinsella tanakaei YIT 12063

Annotation: NCBI__GCF_000225705.1:WP_009141268.1

Length: 477 amino acids

Source: GCF_000225705.1 in NCBI

Candidate for 4 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism ascB hi 6-P-β-glucosidase (Arb;AscB;SMU.1102) (EC 3.2.1.86) (characterized) 71% 99% 731.5 β-glucosidase (BglZ) (EC 3.2.1.21) 59% 577.8
D-cellobiose catabolism bgl med 6-P-β-glucosidase (AscB) (EC 3.2.1.21|3.2.1.86) (characterized) 60% 99% 619.4 6-P-β-glucosidase (Arb;AscB;SMU.1102) (EC 3.2.1.86) 71% 731.5
lactose catabolism lacZ med β-galactosidase (GKGal1A;GK2337) (Gal1A) (EC 3.2.1.23) (characterized) 48% 99% 442.2 6-P-β-glucosidase (Arb;AscB;SMU.1102) (EC 3.2.1.86) 71% 731.5
lactose catabolism pbgal med 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized) 41% 99% 363.2 6-P-β-glucosidase (Arb;AscB;SMU.1102) (EC 3.2.1.86) 71% 731.5

Sequence Analysis Tools

View WP_009141268.1 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

MEKVFPEGFLWGGATAANQCEGAYNVDGRGLANVDVMPHGKDRFPVGLGLRKMLDFEDGY
FYPAQTGIDFYHHYKEDIALFAEMGFKTFRMSLAWTRIFPNGDESEPNEAGLAFYEDVFR
ECQKHGIEPLVTITHFDCPIHLIKEYGGWRNRKLIDFYKNLARVLFTRYKGLVKYWLTFN
EINMILHLPFMGAGLVFEEDEDKEAVEYLAAHNELVASAWATKIAHEIDPDVKIGCMLAA
GSYYPYSCRPEDVRAAQLANQDNYFFVDVQSRGYYPAYALKKLERAGIDVGMTEEDKQVL
AENTVDFISFSYYSTRCSAGEGSDAPKTEGNAFQGAKNPYLKESQWGWAIDPLGFRITLN
DLYDRYQKPLFVVENGLGAKDVVEEDGSINDDYRIDYLRKHIETMRDAVVEDGVDLLGYT
TWGPIDLVSASTGEMSKRYGFIYVDRDDAGNGTLARSKKKSFDWYKKVIATNGADLS

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