Table 4a: Comparison of DIAL4 domain boundary definitions with those given by SCOP, 3Dee and CATH for the 55 protein dataset (Jones et al., 1998).


PDB CODE

DIAL4

SCOP

3DEE

CATH

No of domains

Boundary

Boundary

Overlap Score (%) #

Boundary

Overlap Score

(%)#

Boundary

Overlap Score

(%)#

1atnA

4

0-31;78-135;337-372

136-180;273-336

181-272

32-77

4-146

147-372

****

0-137;337-372

138-336

****

0-372

****

1ezm-

2

1-149

150-298

1-298

****

1-152

153-298

98.99

1-152

153-298

98.99

1fnr-

2

19-151

152-314

19-154

155-314

98.99

19-154

155-314

98.99

19-151

152-314

100

1gpb-

2

19-481;813-841

482-812

19-841

****

19-481;832-841

482-831

95.60

19-485;813-836

486-812

98.90

1lap-

2

1-166

167-484

1-161

162-484

98.96

1-165

166-484

99.79

1-165

166-484

99.79

1pfkA

2

0-138;258-319

139-255

0-319

****

0-138;252-304

139-251;303-319

97.81

0-141;256-302

142-255;303-319

93.12

1phh-

3

1-46;100-180;269-343

181-268;344-396

47-99

1-173;276-396

174-275

****

1-394

****

1-180;268-343

181-268;344-394

****

1rhd-

2

1-155

156-293

1-149

150-293

97.95

1-156

157-293

99.66

1-156

157-293

99.66

1vsgA

2

1-20;87-251

23-85;252-362

1-362

****

1-33;88-254

34-87;255-362

98.62

1-255

256-362

80.66

 

1wsyB

2

3-37;88-185

39-87;186-394

3-394

****

9-53;87-205

54-86;206-393

94.13

9-53;87-205

54-86;206-393

94.13

3cd4-

2

1-99

100-178

1-97

98-178

99.44

1-97

98-174

97.20

1-98

99-178

99.43

3gapA

2

7-126

127-206

7-137

138-206

94.50

1-136

137-208

91.35

9-137

138-205

96.79

3grs-

3

18-61;96-160;291-363

63-95;161-290

363-470

18165;291363

166-290

364-478

89.80

18-161;289-364

162-288

365-478

90.88

18-160;290-365

161-289

366-478

90.00

 

3pgk-

2

1-183

185-415

1-415

****

1-192;403-415

193-402

94.69

1-186

193-401

97.75

4gcr-

3

1-84

85-174

1-85

86-174

99.42

1-83

84-174

99.42

1-83

84-174

99.42

8acn-

2

2-527

528-754

2-528

529-754

99.73

2-201

202-319

320-511

532-754

****

2-202

203-315

316-490

534-753

****

8adh-

2

1-174;317-373

175-316

1-174;325-374

175-324

96.00

1-178;318-374

179-317

98.39

1-178;318-374

179-317

98.34

8atcB

2

8-100

101-153

8-100

101-153

100

8-98

99-153

98.63

8-100

101-153

100

2cyp-

2

2-146;270-294

147-252

2-294

****

2-144;263-294

145-262

93.51

4-144;266-274

145-265

92.83

5fbp-

2

6-110

121-335

6-335

****

6-199

200-335

77.74

6-199

200-335

77.44

8atcA

2

1-134

135-304

1-150

151-310

92.90

1-130;292-310

131-291

92.58

1-133;292-310

134-291

93.54

2pmgA

4

1-202

204-303;390-419

305-389

421-561

1-190

191-303

304-420

421-561

91.97

1-188

189-302

303-419

420-561

91.44

1-197

198-300

301-400

401-561

92.69

1bbhA

1

1-131

1-131

100

1-31

100

1-31

100

1gmpA

1

1-96

1-96

100

1-96

100

1-96

100

1gox-

1

0-359

0-359

100

0-359

100

0-359

100

1rcb-

1

1-129

1-129

100

1-129

100

1-129

100

1wsyA

1

1-267

1-267

100

1-267

100

1-267

100

2ccyA

1

2-128

2-128

100

2-128

100

2-128

100

2had-

1

1-310

1-310

100

1-310

100

1-310

100

2stv-

1

12-195

12-195

100

12-195

100

12-195

100

3chy-

1

2-129

2-129

100

2-129

100

2-129

100

3dfr-

1

1-162

1-162

100

1-162

100

1-162

100

1rbb-

1

1-175

1-175

100

1-175

100

1-175

100

1brd-

1

8-226

8-226

100

8-226

100

Not present

Not present

1tlk-

1

33-135

33-135

100

33-135

100

33-135

100

1fxiA

1

1-96

1-96

100

1-96

100

1-96

100

1ofv-

1

1-169

1-169

100

1-169

100

1-169

100

1ppn-

1

1-212

1-212

100

1-18;112-207

19-111;208-212

****

1-212

100

2azaA

1

1-129

1-129

100

1-129

100

1-129

100

1tie-

1

1-170

1-170

100

1-170

100

1-170

100

1snc-

1

7-141

7-141

100

7-141

100

7-141

100

1aak-

1

2-178

2-178

100

2-178

100

2-178

100

1bbpA

1

31-291

31-291

100

31-291

100

31-291

100

4blmA

1

1-166

1-166

100

31-70;217-291

71-216

****

1-166

100

1sgt-

1

16-245

16-245

100

16-23;122-233

24-121;234-245

****

16-27;121-232

28-120;233-245

****

5p2l-

1

1-166

1-166

100

1-166

100

1-166

100

3cla-

1

6-219

6-219

100

6-219

100

6-219

100

1ula-

1

1-289

1-289

100

1-289

100

1-289

100

1gmfA

1

4-124

4-124

100

4-124

100

4-124

100

1ace-

1

4-535

4-535

100

4-535

100

4-535

100

1gky-

1

0-186

0-186

100

1-32;83-186

33-82

****

1-32;93-186

33-92

****

1pyp-

1

1-281

1-281

100

1-281

100

1-281

100

2rn2-

1

1-155

1-155

100

1-155

100

1-155

100

1rveA

1

2-245

2-245

100

2-245

100

2-245

100

2tmvP

1

1-154

1-154

100

1-154

100

1-154

100

Average Overlap Score

99.1

98.11

98.03

# Where the number of domains were different from that suggested by DIAL. Domain boundaries for such cases are provided in italics. Exact boundary comparisons were not possible and scores are marked as ‘****’.



Overlap Score Calculation:

Residue no  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17
A           1   1   1   1   1   1   1   1   1   1   2   2   2   2   2   2   2
B           1   1   1   1   1   1   1   1   2   2   2   2   2   2   2   2   2


   A1*    A2* 
B1*  8     0
B2*  2     7

A1*, A2*, B1* and B2* are the two domains of chain A and B respectively.

Overlap score=((8+7)/17)*100=88.23