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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.