Results of running MAP using secondary structure assignments (I) and PHD secondary structure predictions (II) shown beside THREADER results (III) for eleven protein structures having type B and C similarities (Russell &Barton 1994) within the domain database. The first column for each method shows the top ten scoring domains, which are denoted by a PDB four letter code (Bernstein et al., 1977), a chain identifier as the fifth character (if any), followed by an underscore and a Roman numeral denoting the domain (if any). Bold inverted text denotes a correct match using the strict classification, grey backgrounds show loose classifications (see text). The second column shows the score for each domain, the third the protein structure class, and the fourth the name of the fold/structure. Upper case denotes fold families under the strict definitions. Upper case names in parentheses (if present) denote the name of the loose family classification. The globins 1HBG, 1MYGA and 1ECA and the cupredoxin 1PAZ are sequence similar to the query so are not shown inverted and are not included in the evaluation statistics (see text).
Strict fold classifications:
4HB-1= Up-down-up-down four helix bundle (4HB); 4HB-2= up-up-down-down (interleukin-4
type) 4HB; GLOBIN= globin-type folds; W-HTH= winged helix-turn-helix (HTH) folds;
EF-HAND= calcium binding EF hands; CYTOC= cytochromes C; THIO= thioredoxin-like folds;
FLAVO= flavodoxin-like folds; ROSS= Rossman folds; PBL= periplasmic binding
protein-like folds; ACTIN-ATPASE= actin/HSC-70/hexokinse like folds; G-PROT=
G-protein (ras) like folds; FAD-BIND= FAD/NAD binding protein-like folds;
-BARREL=
(TIM) barrels;
-GRASP=
-grasp (ferredoxin) like
folds; IG= Immunoglobulin superfamily; CUP= Cuppredoxins (plastocyanin-like);
-TREFOIL=
-trefoils (interleukin-1-
-like); OB-FOLD=
oligonucleotide/oligosaccharride binding folds.
Loose fold classifications:
4HB= 4HB-1, 4HB-2, ferritin; HTH= W-HTH, -rep., trp-rep.; DWAB
(doubly-wound-
)= ROSS, FLAVO, THIO, PBL, G-PROT, sugar phosphatase,
pfk, pgk, dhfr; GKBS (greek key
sandwich)= IG, CUP,
-amylase inhibitor,
sod, macromycin, prealbumin.
Other abbreviations: sod: superoxide dismutase; pfk= phosphrofuctokinase; pgk= phosphoglcerate kinase; dhfr= dihdrofolate reducatse; ldh= lactate dehydrogenase; ser-prot= serine proteinase; asp-prot= aspartic proteinase; inh.= inhibitor; rep.=repressor; glut.=glutathione; red.=reductase; thym. phosph.=thymidine phosphorylase; ribo.=ribonuclease; glyc.=glycoprotein; P-glucomutase= phosphoglucomutase; glyc. ribo trans.= glycinamide ribotransferase.