| T0831 -force run |
| ID: | 1403741859 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 419 (419) | ||
| Sequences: | 67 (58.1) | ||
| Seq/Len: | 0.160 | ||
| Nf(neff/√len): | 2.8 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 0.160).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 242_C | 245_C | 1.997 | 0.54 |
| 22_R | 30_G | 1.858 | 0.46 |
| 49_R | 90_T | 1.756 | 0.41 |
| 414_L | 417_L | 1.735 | 0.39 |
| 12_K | 18_E | 1.691 | 0.37 |
| 70_L | 103_L | 1.687 | 0.37 |
| 70_L | 93_D | 1.674 | 0.36 |
| 49_R | 68_Q | 1.664 | 0.36 |
| 63_K | 348_N | 1.663 | 0.36 |
| 6_L | 16_E | 1.645 | 0.35 |
| 230_C | 242_C | 1.636 | 0.34 |
| 230_C | 245_C | 1.636 | 0.34 |
| 322_G | 333_K | 1.611 | 0.33 |
| 244_F | 350_V | 1.606 | 0.33 |
| 32_A | 48_Y | 1.590 | 0.32 |
| 71_H | 354_D | 1.577 | 0.31 |
| 48_Y | 71_H | 1.574 | 0.31 |
| 18_E | 33_G | 1.556 | 0.30 |
| 22_R | 358_M | 1.556 | 0.30 |
| 32_A | 414_L | 1.551 | 0.30 |
| 65_D | 362_R | 1.545 | 0.30 |
| 96_L | 404_L | 1.540 | 0.29 |
| 108_M | 381_I | 1.529 | 0.29 |
| 224_I | 305_I | 1.527 | 0.29 |
| 21_H | 370_E | 1.525 | 0.29 |
| 305_I | 325_S | 1.515 | 0.28 |
| 412_L | 416_N | 1.512 | 0.28 |
| 22_R | 355_E | 1.510 | 0.28 |
| 70_L | 360_T | 1.508 | 0.28 |
| 261_N | 326_M | 1.500 | 0.28 |
| 143_W | 335_E | 1.485 | 0.27 |
| 194_L | 400_A | 1.474 | 0.26 |
| 65_D | 355_E | 1.464 | 0.26 |
| 189_G | 279_G | 1.460 | 0.26 |
| 364_R | 370_E | 1.459 | 0.26 |
| 22_R | 65_D | 1.457 | 0.26 |
| 205_Q | 335_E | 1.445 | 0.25 |
| 21_H | 58_H | 1.433 | 0.25 |
| 32_A | 413_Y | 1.399 | 0.23 |
| 13_C | 21_H | 1.386 | 0.23 |
| 75_N | 107_Y | 1.377 | 0.22 |
| 167_I | 224_I | 1.375 | 0.22 |
| 259_F | 362_R | 1.372 | 0.22 |
| 309_A | 363_L | 1.369 | 0.22 |
| 29_N | 354_D | 1.364 | 0.22 |
| 33_G | 330_E | 1.363 | 0.22 |
| 33_G | 71_H | 1.357 | 0.22 |
| 13_C | 70_L | 1.339 | 0.21 |
| 167_I | 194_L | 1.317 | 0.20 |
| 68_Q | 370_E | 1.316 | 0.20 |
| 142_W | 230_C | 1.313 | 0.20 |
| 223_V | 410_Q | 1.301 | 0.20 |
| 22_R | 71_H | 1.300 | 0.19 |
| 13_C | 104_R | 1.296 | 0.19 |
| 6_L | 31_L | 1.289 | 0.19 |
| 29_N | 75_N | 1.285 | 0.19 |
| 258_L | 396_D | 1.282 | 0.19 |
| 70_L | 410_Q | 1.278 | 0.19 |
| 5_L | 343_W | 1.276 | 0.19 |
| 5_L | 416_N | 1.274 | 0.19 |
| 12_K | 19_E | 1.274 | 0.19 |
| 21_H | 244_F | 1.267 | 0.18 |
| 70_L | 104_R | 1.265 | 0.18 |
| 146_V | 163_V | 1.264 | 0.18 |
| 4_E | 162_R | 1.260 | 0.18 |
| 259_F | 358_M | 1.257 | 0.18 |
| 89_P | 92_R | 1.251 | 0.18 |
| 12_K | 33_G | 1.250 | 0.18 |
| 104_R | 360_T | 1.250 | 0.18 |
| 107_Y | 355_E | 1.250 | 0.18 |
| 104_R | 301_S | 1.249 | 0.18 |
| 355_E | 362_R | 1.247 | 0.18 |
| 21_H | 70_L | 1.242 | 0.18 |
| 29_N | 259_F | 1.240 | 0.17 |
| 71_H | 355_E | 1.238 | 0.17 |
| 25_V | 79_L | 1.238 | 0.17 |
| 149_R | 225_E | 1.237 | 0.17 |
| 72_A | 350_V | 1.233 | 0.17 |
| 355_E | 358_M | 1.230 | 0.17 |
| 70_L | 370_E | 1.228 | 0.17 |
| 50_E | 342_Y | 1.226 | 0.17 |
| 22_R | 362_R | 1.224 | 0.17 |
| 30_G | 358_M | 1.219 | 0.17 |
| 9_L | 37_I | 1.213 | 0.17 |
| 186_D | 396_D | 1.207 | 0.16 |
| 258_L | 360_T | 1.204 | 0.16 |
| 22_R | 33_G | 1.195 | 0.16 |
| 33_G | 381_I | 1.195 | 0.16 |
| 90_T | 93_D | 1.193 | 0.16 |
| 94_G | 167_I | 1.190 | 0.16 |
| 97_E | 303_K | 1.176 | 0.15 |
| 70_L | 364_R | 1.175 | 0.15 |
| 74_H | 159_L | 1.174 | 0.15 |
| 31_L | 102_Q | 1.168 | 0.15 |
| 44_A | 48_Y | 1.165 | 0.15 |
| 7_T | 134_R | 1.164 | 0.15 |
| 213_K | 264_K | 1.163 | 0.15 |
| 76_L | 96_L | 1.163 | 0.15 |
| 44_A | 71_H | 1.159 | 0.15 |
| 33_G | 255_E | 1.155 | 0.15 |
| 165_N | 170_N | 1.152 | 0.15 |
| 21_H | 34_I | 1.148 | 0.15 |
| 249_E | 409_G | 1.148 | 0.15 |
| 13_C | 62_L | 1.147 | 0.15 |
| 68_Q | 107_Y | 1.145 | 0.15 |
| 132_L | 350_V | 1.145 | 0.15 |
| 142_W | 242_C | 1.144 | 0.15 |
| 142_W | 245_C | 1.144 | 0.15 |
| 14_G | 363_L | 1.142 | 0.14 |
| 51_V | 96_L | 1.141 | 0.14 |
| 206_K | 303_K | 1.138 | 0.14 |
| 29_N | 76_L | 1.134 | 0.14 |
| 143_W | 254_Y | 1.133 | 0.14 |
| 101_K | 296_S | 1.133 | 0.14 |
| 65_D | 71_H | 1.130 | 0.14 |
| 122_L | 322_G | 1.128 | 0.14 |
| 57_E | 215_L | 1.126 | 0.14 |
| 198_M | 205_Q | 1.123 | 0.14 |
| 34_I | 387_E | 1.122 | 0.14 |
| 131_E | 271_E | 1.120 | 0.14 |
| 30_G | 355_E | 1.119 | 0.14 |
| 63_K | 412_L | 1.119 | 0.14 |
| 254_Y | 363_L | 1.118 | 0.14 |
| 370_E | 386_V | 1.117 | 0.14 |
| 354_D | 358_M | 1.116 | 0.14 |
| 18_E | 63_K | 1.115 | 0.14 |
| 48_Y | 414_L | 1.115 | 0.14 |
| 292_L | 350_V | 1.114 | 0.14 |
| 9_L | 355_E | 1.113 | 0.14 |
| 299_E | 322_G | 1.112 | 0.14 |
| 34_I | 58_H | 1.111 | 0.14 |
| 336_Y | 395_N | 1.108 | 0.14 |
| 52_L | 362_R | 1.104 | 0.13 |
| 299_E | 335_E | 1.098 | 0.13 |
| 75_N | 96_L | 1.096 | 0.13 |
| 92_R | 180_M | 1.095 | 0.13 |
| 32_A | 296_S | 1.095 | 0.13 |
| 37_I | 78_E | 1.093 | 0.13 |
| 194_L | 254_Y | 1.092 | 0.13 |
| 43_L | 381_I | 1.092 | 0.13 |
| 227_A | 352_A | 1.089 | 0.13 |
| 29_N | 358_M | 1.088 | 0.13 |
| 337_K | 343_W | 1.083 | 0.13 |
| 29_N | 413_Y | 1.082 | 0.13 |
| 240_N | 244_F | 1.079 | 0.13 |
| 212_V | 345_A | 1.075 | 0.13 |
| 96_L | 212_V | 1.075 | 0.13 |
| 71_H | 76_L | 1.075 | 0.13 |
| 59_K | 91_L | 1.074 | 0.13 |
| 2_M | 404_L | 1.071 | 0.13 |
| 70_L | 329_F | 1.071 | 0.13 |
| 14_G | 33_G | 1.071 | 0.13 |
| 5_L | 35_H | 1.069 | 0.13 |
| 122_L | 321_E | 1.068 | 0.12 |
| 244_F | 339_L | 1.066 | 0.12 |
| 244_F | 360_T | 1.065 | 0.12 |
| 160_V | 363_L | 1.064 | 0.12 |
| 156_D | 163_V | 1.064 | 0.12 |
| 143_W | 194_L | 1.063 | 0.12 |
| 2_M | 96_L | 1.061 | 0.12 |
| 159_L | 415_T | 1.061 | 0.12 |
| 234_P | 363_L | 1.058 | 0.12 |
| 205_Q | 305_I | 1.058 | 0.12 |
| 12_K | 363_L | 1.056 | 0.12 |
| 18_E | 22_R | 1.054 | 0.12 |
| 36_I | 360_T | 1.051 | 0.12 |
| 66_S | 343_W | 1.051 | 0.12 |
| 32_A | 299_E | 1.051 | 0.12 |
| 33_G | 379_H | 1.051 | 0.12 |
| 29_N | 48_Y | 1.048 | 0.12 |
| 143_W | 159_L | 1.047 | 0.12 |
| 92_R | 364_R | 1.046 | 0.12 |
| 29_N | 71_H | 1.046 | 0.12 |
| 27_A | 104_R | 1.044 | 0.12 |
| 4_E | 25_V | 1.044 | 0.12 |
| 115_V | 415_T | 1.043 | 0.12 |
| 299_E | 333_K | 1.042 | 0.12 |
| 197_Q | 231_H | 1.041 | 0.12 |
| 32_A | 71_H | 1.040 | 0.12 |
| 5_L | 231_H | 1.039 | 0.12 |
| 369_R | 380_I | 1.039 | 0.12 |
| 227_A | 410_Q | 1.039 | 0.12 |
| 104_R | 197_Q | 1.035 | 0.12 |
| 291_G | 358_M | 1.033 | 0.12 |
| 49_R | 224_I | 1.032 | 0.12 |
| 150_A | 185_R | 1.031 | 0.12 |
| 115_V | 330_E | 1.030 | 0.12 |
| 103_L | 232_L | 1.030 | 0.12 |
| 143_W | 205_Q | 1.028 | 0.12 |
| 242_C | 258_L | 1.027 | 0.12 |
| 245_C | 258_L | 1.027 | 0.12 |
| 29_N | 44_A | 1.026 | 0.11 |
| 17_C | 21_H | 1.026 | 0.11 |
| 270_F | 274_I | 1.024 | 0.11 |
| 1_T | 315_D | 1.022 | 0.11 |
| 22_R | 255_E | 1.018 | 0.11 |
| 76_L | 355_E | 1.016 | 0.11 |
| 2_M | 29_N | 1.016 | 0.11 |
| 340_H | 365_V | 1.016 | 0.11 |
| 74_H | 199_E | 1.016 | 0.11 |
| 5_L | 232_L | 1.016 | 0.11 |
| 5_L | 191_Q | 1.016 | 0.11 |
| 5_L | 17_C | 1.015 | 0.11 |
| 9_L | 71_H | 1.014 | 0.11 |
| 233_R | 345_A | 1.014 | 0.11 |
| 49_R | 93_D | 1.013 | 0.11 |
| 147_I | 384_H | 1.013 | 0.11 |
| 6_L | 30_G | 1.013 | 0.11 |
| 32_A | 417_L | 1.012 | 0.11 |
| 10_Q | 299_E | 1.009 | 0.11 |
| 22_R | 48_Y | 1.009 | 0.11 |
| 76_L | 107_Y | 1.009 | 0.11 |
| 310_K | 359_A | 1.008 | 0.11 |
| 142_W | 205_Q | 1.007 | 0.11 |
| 9_L | 78_E | 1.004 | 0.11 |
| 21_H | 103_L | 1.003 | 0.11 |
| 63_K | 236_R | 1.003 | 0.11 |
| 19_E | 74_H | 1.003 | 0.11 |
| 143_W | 242_C | 1.003 | 0.11 |
| 143_W | 245_C | 1.003 | 0.11 |
| 65_D | 358_M | 1.003 | 0.11 |
| 20_A | 76_L | 1.002 | 0.11 |
| 163_V | 199_E | 1.002 | 0.11 |
| 75_N | 259_F | 1.001 | 0.11 |
| 202_N | 318_F | 1.001 | 0.11 |
| 9_L | 22_R | 1.000 | 0.11 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4qn1A | 1 | 0.8854 | 100 | 0.063 | Contact Map |
| 3qwpA | 1 | 0.2959 | 94.4 | 0.955 | Contact Map |
| 3n71A | 1 | 0.3294 | 87.4 | 0.962 | Contact Map |
| 4wuyA | 1 | 0.2768 | 86.9 | 0.963 | Contact Map |
| 4yvqC | 1 | 0 | 83.6 | 0.964 | Contact Map |
| 4yvoA | 1 | 0 | 80 | 0.966 | Contact Map |
| 4ui9O | 1 | 0 | 79 | 0.966 | Contact Map |
| 3u3wA | 2 | 0.3532 | 76.9 | 0.967 | Contact Map |
| 4gpkA | 12 | 0.2983 | 76.5 | 0.967 | Contact Map |
| 4jhrA | 2 | 0.4105 | 76.3 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)