Skip to main content

Table 1 Comparison of PSI-BLAST-ISS and the Consensus server performance

From: PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

Target

Template

Align length

Rmsd, Å

Seq id, %

Consensus server

PSI-BLAST-ISS (consensus, 0.8)

PSI-BLAST-ISS (consensus, 0.9)

     

discrepancies

d-len/cons-len

discrepancies

d-len/cons-len

discrepancies

d-len/cons-len

T0196

1jny

80

1.6

33

68–77

       10/62       

68–74, 77

       8/56       

69–72

       4/50       

T0200

1ush

210

2.7

16

71

1/45

-

0/58

-

0/50

T0202

1u0r

245

2.0

26

59–62, 94

5/146

59, 108

2/186

-

0/144

T0204

1gup

280

2.0

25

164

1/173

139, 141

2/17

-

0/14

T0208

1i60

254

3.1

11

258–262

5/102

292

1/90

-

0/85

T0211

1eut

126

1.7

22

-

0/13

-

0/65

-

0/55

T0216

1vpb

417

2.5

25

-

0/177

38–39, 71

3/238

-

0/107

T0222

1rzm

239

2.7

14

154

1/96

154, 246, 281–285

7/143

154, 246, 281–285

7/116

T0223

1vfr

123

2.5

11

-

0/22

113–119, 121–124, 128–132

16/39

113–116

4/24

T0228

1qpn

145

3.1

11

-

0/21

170–172, 174–181

11/57

-

0/39

T0229

1ml8

125

1.9

35

120–127

8/61

82–83, 120–127

10/114

120–127

8/84

T0231

1v6f

136

1.4

79

-

0/133

-

0/130

-

0/125

T0232

11gs

199

2.1

19

-

0/32

5–6, 40, 42–43, 66, 158

7/114

6, 40, 42–43, 66, 158

6/97

T0233

1kgz

319

1.8

36

136, 325–326

3/276

136, 245, 325–327

5/306

136, 245

2/279

T0234

1g76

118

2.8

14

16

1/59

11, 13–14, 16

4/67

11, 13–14, 16

4/58

T0235

1nb8

276

2.4

26

442–443, 478

3/44

207–208, 443, 478–479

5/104

207–208, 443

3/93

T0240

1lr0

70

2.5

17

25,33

2/39

10–11, 20–22, 24–26, 28–30, 65–66

13/51

20–22, 24–26

6/43

T0244

1iim

242

2.6

24

206, 229–234

7/157

231–234

4/153

-

0/115

T0246

1cnz

353

1.4

57

-

0/315

-

0/313

-

0/276

T0247

1pj5

338

2.1

25

76, 115–126, 128–129, 162–165, 261, 302

21/227

76, 162, 305

3/227

76

1/150

T0264

1vhv

244

2.1

34

60

1/120

17–19

3/92

17–19

3/81

T0265

1sfx

87

3.0

25

-

0/50

-

0/50

-

0/42

T0266

1dbu

145

1.8

25

60–65, 77

7/91

28, 77

2/132

-

0/95

T0267

1tiq

165

2.1

16

80–83

4/77

68, 80–81

3/102

68, 80–81

3/91

T0268

1m6y

277

1.6

49

121, 153–154

3/216

44, 126, 249

3/258

126

1/216

T0269

1qmv

182

2.1

35

89–92, 95, 119–120

7/125

119–120

2/128

-

0/99

T0274

1i0r

144

1.7

24

43,102–103

3/86

8, 43, 73

3/107

43

1/87

T0275

1mjh

125

2.0

30

26–30, 41–45

10/75

26–30, 41–42

7/107

29–30, 41

3/92

T0276

1sbq

153

1.7

26

92–94

3/56

18, 39, 150–151

4/122

-

0/84

T0279

1jr2

240

5.9

16

-

0/31

144–145, 202–204, 258

6/68

-

0/6

T0280

1o5o

144

3.0

19

170–175

6/55

119

1/51

-

0/46

T0282

1gq6

275

2.4

21

245

1/129

41–42, 208–210

5/202

42

1/138

     

Total:

113/3311

Total:

140/3947

Total:

57/3081

     

Average per target:

3.5/103.5

Average per target:

4.4/123.3

Average per target:

1.8/96.3

     

Fraction

3.4%

Fraction

3.5%

Fraction

1.9%

  1. Target-template structure-based alignments that were used as reference are characterized by the number of superimposed residues (column Align length), root-mean-square deviation of their Cα atoms (Rmsd), and the sequence identity (Seq id). Differences between each structure-based alignment and alignments obtained either by the Consensus server or PSI-BLAST-ISS are reported in corresponding discrepancies columns. The discrepancies are reported as segments, and their begin-end positions are given with respect to the target sequence. Only consensus segments of at least 3 residues were considered. Columns d-len/cons-len provide ratios between the length of discrepancies (d-len) and the total length of the alignment considered to be reliable (cons-len) by the corresponding method.