The SUPERFAMILY database in 2004: additions and improvements - PubMed (original) (raw)

A section of the domain combination network in E.coli K-12. Nodes represent superfamilies labelled according to their SCOP (3) classification (see below for legend), edges indicate superfamilies that occur next to each other in domain architectures, and arrows show the N-to-C order. Node size and edge thickness are proportional to the logarithm of the number of proteins. All edges between the selected superfamilies are shown. The presence of edges in only one of the two possible directions illustrates the tendency of adjacent domains to appear in one N-to-C order (10,11). This and other visualizations are available online from the webserver. The superfamilies shown in the figure are: a.4.1, homeodomain-like; a.4.2, Methylated DNA–protein cysteine methyltransferase, C-terminal domain; a.60.7, 5′–3′ exonuclease, C-terminal subdomain; b.82.4, regulatory protein AraC; c.35.1, phosphosugar isomerase; c.53.1, resolvase-like; c.55.3, ribonuclease H-like; c.55.7, methylated DNA–protein cysteine methyltransferase domain; d.58.40,

d

-ribose-5-phosphate isomerase (RpiA), lid domain; d.60.1, probable bacterial effector binding domain; d.144.1, protein kinase-like (PK-like); e.8.1, DNA/RNA polymerases; and g.48.1, Ada DNA repair protein, N-terminal domain (N-Ada 10).