| HDAC1 |
| ID: | 1494877484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (435) | ||
| Sequences: | 612 (304.7) | ||
| Seq/Len: | 1.407 | ||
| Nf(neff/√len): | 14.6 |
HHblits Results: (2016_02)
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: 1.407).
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 |
| 300_M | 322_A | 3.955 | 1.00 |
| 247_I | 291_V | 3.458 | 1.00 |
| 198_V | 247_I | 3.302 | 1.00 |
| 244_K | 286_K | 3.281 | 1.00 |
| 186_E | 215_D | 3.203 | 1.00 |
| 175_I | 291_V | 3.084 | 1.00 |
| 251_M | 296_L | 3.025 | 1.00 |
| 202_K | 232_D | 2.859 | 1.00 |
| 235_D | 355_N | 2.810 | 1.00 |
| 251_M | 259_V | 2.787 | 1.00 |
| 12_C | 131_T | 2.778 | 1.00 |
| 198_V | 250_V | 2.678 | 1.00 |
| 248_S | 252_E | 2.651 | 1.00 |
| 371_E | 374_R | 2.547 | 1.00 |
| 38_T | 42_L | 2.501 | 1.00 |
| 114_T | 155_V | 2.491 | 1.00 |
| 126_L | 299_L | 2.431 | 1.00 |
| 175_I | 247_I | 2.341 | 0.99 |
| 320_A | 327_I | 2.313 | 0.99 |
| 235_D | 238_S | 2.197 | 0.99 |
| 286_K | 289_E | 2.191 | 0.99 |
| 170_Q | 257_S | 2.173 | 0.99 |
| 226_V | 369_L | 2.154 | 0.99 |
| 248_S | 290_F | 2.138 | 0.99 |
| 173_L | 250_V | 2.102 | 0.98 |
| 249_K | 252_E | 2.076 | 0.98 |
| 292_K | 324_D | 2.048 | 0.98 |
| 251_M | 294_F | 1.911 | 0.97 |
| 240_E | 244_K | 1.831 | 0.96 |
| 426_S | 429_E | 1.747 | 0.94 |
| 193_D | 377_P | 1.745 | 0.94 |
| 263_C | 288_V | 1.713 | 0.93 |
| 50_K | 325_T | 1.672 | 0.92 |
| 65_T | 73_I | 1.656 | 0.91 |
| 363_E | 366_K | 1.632 | 0.91 |
| 72_Y | 76_L | 1.618 | 0.90 |
| 198_V | 340_F | 1.580 | 0.89 |
| 231_R | 361_Y | 1.576 | 0.88 |
| 240_E | 286_K | 1.572 | 0.88 |
| 269_S | 351_S | 1.551 | 0.87 |
| 314_C | 347_H | 1.546 | 0.87 |
| 20_G | 33_H | 1.522 | 0.86 |
| 249_K | 253_M | 1.506 | 0.85 |
| 122_S | 299_L | 1.506 | 0.85 |
| 269_S | 348_I | 1.500 | 0.85 |
| 292_K | 322_A | 1.478 | 0.84 |
| 177_I | 263_C | 1.468 | 0.83 |
| 206_Y | 275_C | 1.466 | 0.83 |
| 133_I | 292_K | 1.453 | 0.82 |
| 57_H | 63_E | 1.449 | 0.82 |
| 280_I | 314_C | 1.427 | 0.81 |
| 309_R | 339_Y | 1.417 | 0.80 |
| 10_K | 13_Y | 1.415 | 0.80 |
| 30_M | 34_R | 1.411 | 0.80 |
| 72_Y | 75_F | 1.410 | 0.80 |
| 64_M | 146_K | 1.406 | 0.79 |
| 113_S | 138_A | 1.401 | 0.79 |
| 226_V | 250_V | 1.400 | 0.79 |
| 169_H | 257_S | 1.393 | 0.78 |
| 175_I | 280_I | 1.385 | 0.78 |
| 13_Y | 16_D | 1.378 | 0.77 |
| 127_N | 167_K | 1.378 | 0.77 |
| 127_N | 169_H | 1.376 | 0.77 |
| 246_V | 370_F | 1.376 | 0.77 |
| 65_T | 70_D | 1.375 | 0.77 |
| 193_D | 220_K | 1.373 | 0.77 |
| 12_C | 246_V | 1.371 | 0.77 |
| 106_L | 110_C | 1.369 | 0.77 |
| 260_V | 301_L | 1.362 | 0.76 |
| 424_S | 427_D | 1.355 | 0.76 |
| 261_L | 298_M | 1.346 | 0.75 |
| 114_T | 160_L | 1.344 | 0.75 |
| 76_L | 81_P | 1.338 | 0.74 |
| 206_Y | 312_A | 1.324 | 0.73 |
| 228_Y | 242_I | 1.321 | 0.73 |
| 164_E | 167_K | 1.309 | 0.72 |
| 95_N | 272_R | 1.298 | 0.71 |
| 403_D | 407_R | 1.289 | 0.70 |
| 61_A | 107_F | 1.281 | 0.70 |
| 23_Y | 42_L | 1.274 | 0.69 |
| 128_K | 254_F | 1.267 | 0.69 |
| 107_F | 324_D | 1.266 | 0.68 |
| 168_Y | 390_D | 1.262 | 0.68 |
| 33_H | 336_Y | 1.259 | 0.68 |
| 158_I | 308_I | 1.243 | 0.66 |
| 422_E | 425_D | 1.242 | 0.66 |
| 13_Y | 24_Y | 1.242 | 0.66 |
| 110_C | 113_S | 1.242 | 0.66 |
| 427_D | 430_G | 1.234 | 0.66 |
| 113_S | 116_G | 1.232 | 0.65 |
| 223_Y | 375_M | 1.232 | 0.65 |
| 249_K | 370_F | 1.227 | 0.65 |
| 240_E | 245_P | 1.226 | 0.65 |
| 28_H | 34_R | 1.225 | 0.65 |
| 106_L | 365_I | 1.222 | 0.64 |
| 404_P | 407_R | 1.213 | 0.64 |
| 116_G | 138_A | 1.212 | 0.63 |
| 158_I | 301_L | 1.210 | 0.63 |
| 291_V | 298_M | 1.208 | 0.63 |
| 111_Q | 314_C | 1.201 | 0.62 |
| 108_E | 111_Q | 1.200 | 0.62 |
| 21_N | 36_R | 1.194 | 0.62 |
| 366_K | 370_F | 1.189 | 0.61 |
| 15_Y | 127_N | 1.182 | 0.61 |
| 298_M | 340_F | 1.182 | 0.61 |
| 95_N | 102_V | 1.181 | 0.61 |
| 47_L | 51_M | 1.177 | 0.60 |
| 257_S | 387_I | 1.177 | 0.60 |
| 23_Y | 348_I | 1.169 | 0.59 |
| 241_A | 245_P | 1.166 | 0.59 |
| 253_M | 374_R | 1.165 | 0.59 |
| 59_A | 115_G | 1.163 | 0.59 |
| 226_V | 372_N | 1.162 | 0.59 |
| 280_I | 347_H | 1.158 | 0.58 |
| 118_V | 121_A | 1.155 | 0.58 |
| 161_A | 299_L | 1.154 | 0.58 |
| 162_I | 165_L | 1.154 | 0.58 |
| 202_K | 275_C | 1.153 | 0.58 |
| 254_F | 347_H | 1.151 | 0.58 |
| 275_C | 354_T | 1.147 | 0.57 |
| 75_F | 81_P | 1.144 | 0.57 |
| 234_I | 239_Y | 1.143 | 0.57 |
| 21_N | 33_H | 1.137 | 0.56 |
| 70_D | 352_N | 1.137 | 0.56 |
| 148_E | 163_L | 1.136 | 0.56 |
| 179_I | 276_F | 1.134 | 0.56 |
| 285_A | 348_I | 1.126 | 0.55 |
| 424_S | 428_E | 1.123 | 0.55 |
| 259_V | 296_L | 1.119 | 0.54 |
| 45_Y | 51_M | 1.119 | 0.54 |
| 108_E | 321_V | 1.118 | 0.54 |
| 28_H | 31_K | 1.116 | 0.54 |
| 173_L | 196_M | 1.116 | 0.54 |
| 83_N | 87_Y | 1.115 | 0.54 |
| 54_Y | 324_D | 1.114 | 0.54 |
| 254_F | 391_A | 1.113 | 0.54 |
| 261_L | 288_V | 1.107 | 0.53 |
| 56_P | 265_S | 1.103 | 0.53 |
| 279_T | 350_P | 1.100 | 0.52 |
| 39_H | 282_E | 1.099 | 0.52 |
| 255_Q | 379_A | 1.098 | 0.52 |
| 72_Y | 81_P | 1.096 | 0.52 |
| 173_L | 373_L | 1.093 | 0.52 |
| 196_M | 204_G | 1.092 | 0.52 |
| 63_E | 288_V | 1.090 | 0.51 |
| 16_D | 21_N | 1.088 | 0.51 |
| 114_T | 161_A | 1.086 | 0.51 |
| 28_H | 32_P | 1.085 | 0.51 |
| 35_I | 109_F | 1.081 | 0.51 |
| 363_E | 367_Q | 1.076 | 0.50 |
| 9_R | 66_K | 1.076 | 0.50 |
| 316_T | 340_F | 1.075 | 0.50 |
| 238_S | 362_L | 1.074 | 0.50 |
| 75_F | 79_I | 1.071 | 0.49 |
| 276_F | 355_N | 1.069 | 0.49 |
| 73_I | 155_V | 1.068 | 0.49 |
| 40_N | 335_D | 1.064 | 0.49 |
| 122_S | 309_R | 1.064 | 0.49 |
| 290_F | 294_F | 1.062 | 0.49 |
| 80_R | 83_N | 1.060 | 0.48 |
| 64_M | 321_V | 1.059 | 0.48 |
| 173_L | 259_V | 1.058 | 0.48 |
| 64_M | 107_F | 1.058 | 0.48 |
| 23_Y | 314_C | 1.056 | 0.48 |
| 59_A | 134_A | 1.052 | 0.48 |
| 417_I | 422_E | 1.051 | 0.47 |
| 112_L | 138_A | 1.050 | 0.47 |
| 187_E | 190_Y | 1.050 | 0.47 |
| 72_Y | 117_S | 1.050 | 0.47 |
| 21_N | 27_G | 1.045 | 0.47 |
| 334_N | 342_P | 1.045 | 0.47 |
| 24_Y | 28_H | 1.042 | 0.47 |
| 9_R | 292_K | 1.035 | 0.46 |
| 124_V | 167_K | 1.028 | 0.45 |
| 285_A | 317_Y | 1.027 | 0.45 |
| 109_F | 338_E | 1.022 | 0.45 |
| 43_L | 54_Y | 1.022 | 0.45 |
| 14_Y | 20_G | 1.018 | 0.44 |
| 76_L | 79_I | 1.017 | 0.44 |
| 235_D | 276_F | 1.015 | 0.44 |
| 285_A | 402_E | 1.013 | 0.44 |
| 285_A | 321_V | 1.013 | 0.44 |
| 40_N | 334_N | 1.011 | 0.43 |
| 11_V | 259_V | 1.008 | 0.43 |
| 247_I | 290_F | 1.008 | 0.43 |
| 251_M | 291_V | 1.006 | 0.43 |
| 27_G | 36_R | 1.005 | 0.43 |
| 226_V | 360_E | 1.005 | 0.43 |
| 76_L | 117_S | 1.003 | 0.43 |
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 | |
| 4bkxB | 1 | 0.7608 | 100 | 0.351 | Contact Map |
| 4a69A | 2 | 0.7567 | 100 | 0.417 | Contact Map |
| 4ly1A | 3 | 0.7588 | 100 | 0.424 | Contact Map |
| 4qa5A | 2 | 0.7588 | 100 | 0.452 | Contact Map |
| 4bz7A | 4 | 0.7897 | 100 | 0.469 | Contact Map |
| 1c3pA | 1 | 0.7485 | 100 | 0.57 | Contact Map |
| 1zz1A | 4 | 0.7031 | 100 | 0.593 | Contact Map |
| 2vqmA | 1 | 0.7402 | 100 | 0.594 | Contact Map |
| 3menA | 4 | 0.6371 | 100 | 0.61 | Contact Map |
| 4zurA | 2 | 0 | 100 | 0.62 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)