Data Dictionary

Data dictionary

Every field carried on a record page, the spreadsheet column it comes from, and how completely it is populated across the 2874 records in the source dataset.

Field	Source column	Record section	Records populated	Coverage	Notes
CAZy family	`CaZy family`	Identification and annotation	2874	100%	CAZy sequence-based glycosyltransferase family assignment.
Gene symbol	`Gene Symbol`	Identification and annotation	2806	98%	Approved or commonly used gene symbol; blank where none is assigned.
Synonyms / alternate names	`Synonym`	Identification and annotation	2129	74%	Semicolon-delimited alternate gene and protein names.
UniProt accession	`Uniprot`	Identification and annotation	2874	100%	UniProtKB accession; primary key for each record.
NCBI Gene ID	`Gene_ID`	Identification and annotation	1548	54%	NCBI Gene identifier.
Source species	`Species`	Identification and annotation	2874	100%	Source organism binomial.
Taxonomic domain	`Domain`	Identification and annotation	2874	100%	Eukaryota, Bacteria, Archaea or Viruses.
UniProt annotation level	`Annotation level`	Identification and annotation	2874	100%	UniProt annotation score, 1-5.
Enzyme function	`Enzyme function`	Function and localisation	2874	100%	Curated activity description with EC number where assigned.
Subcellular location	`Subcellular Location`	Function and localisation	1564	54%	Semicolon-delimited compartment assignments.
Fold type	`Fold type`	Structure and mechanism	2874	100%	GT-A, GT-B or GT-C catalytic fold class.
Catalytic mechanism	`Mechanism`	Structure and mechanism	2856	99%	Inverting or retaining stereochemical outcome.
Cation dependence	`Cation`	Structure and mechanism	2851	99%	Divalent cation requirement.
Oligomeric state	`Oligomer`	Structure and mechanism	608	21%	Quaternary structure / partner subunits.
PDB structures	`PDB`	Structure and mechanism	232	8%	Semicolon-delimited PDB entry IDs, linked to RCSB.
Sugar nucleotide donor	`Sugar nucleotide donor`	Donor and acceptor specificity	1511	53%	Activated sugar donor substrate(s).
Donor CCD code(s)	`Donor CCD`	Donor and acceptor specificity	1454	51%	PDB Chemical Component Dictionary code(s) for the donor.
Acceptor substrate(s)	`Acceptor`	Donor and acceptor specificity	2484	86%	Acceptor substrate(s); often a long semicolon-delimited list.
Acceptor CCD / GlycoCT	`Acceptor GlycoCT`	Donor and acceptor specificity	108	4%	Acceptor CCD code or userCCD modelling identifier.
Full protein sequence	`Full protein sequence`	sequence	2873	100%	Full-length protein sequence, one-letter amino-acid code.
Catalytic domain sequence	`Catalytic domain sequence`	sequence	2800	97%	Sequence span assigned to the catalytic domain.
Curation note	`Student`	Curation	0	0%	Free-text curation provenance note; populated for few records.

Record category colour key

Row and badge colours are carried over from the fill colours of the source workbook, and encode how well characterised an entry is.

Model organism, annotation ≥ 4. Entry from an established model organism with a UniProt annotation score of 4 or 5.

Non-model organism, annotation 4–5. Well-annotated entry from an organism outside the model set.

Lower annotation. UniProt annotation level 1–3, or no level assigned.

Annotation level below 4. Flagged on the record page and in the family table; treat curated enzymology for these entries as provisional.

Verified PDB CCD code. The acceptor identifier corresponds to a chemical component defined in the PDB Chemical Component Dictionary.

userCCD modelling identifier. A locally defined identifier used for modelling where no PDB component exists.

Controlled vocabularies

Fold type

GT-A and GT-B denote the two Rossmann-like nucleotide-binding fold classes that account for most soluble glycosyltransferases; GT-C denotes the integral-membrane, polyprenyl-phosphate dependent fold. Entries with no structural assignment are left unpopulated.

Mechanism

Inverting and retaining describe the stereochemical outcome at the anomeric carbon of the transferred sugar relative to the donor.

Annotation level

The UniProt annotation score, 1 (least) to 5 (most annotated). Some entries carry the literal values None (no UniProt) or Correct this entry, preserved verbatim from curation.