Domain Combinations in Archaeal, Eubacterial and Eukaryotic Proteomes

Gordana Apic¹, Julian Gough¹and Sarah A. Teichmann²

¹MR C Laboratory of Molecular Biol,ogy, Hills Road, Cambridge CB2 2QH,UK.
²Depatment of Biochemistry & Molecular Biology, Univerity College London, Darwin BldgGower Street, London WC1E 6BT, UK.

DATA

Structural Classification of Proteins

SCOP version 1.53

Genome Abbreviations and Summary of Structural Assignment Statistics

Archaea

Bacteria

Eukaryotes

Fasta Files of Protein Sequences for each of the forty Genomes

(and database sources and dates)

Structural Assignments are available from the SUPERFAMILY database.

To obtain Domainmap format parse the .clu files from the SUPERFAMILY with this perl script. The script requires also .leng files for each genome.

Example how to run the script:
extract_genes_from_clu.pl xx.clu xx.leng > xx.domainmap

Example of domainmap format for E.coli genome : ec.domainmap

DOMAIN COMBINATIONS IN GENOMES COMPARED TO PDB

Domain combinations present in genomes but not in PDB with gene names, descriptions and domainmap
information.

Domain combinations present in PDB only.

INVERTED DOMAIN PAIRS

PDB structures containing inverted domain pairs

Two-domain proteins from the genomes that have inverted domain pairs