| 5pp1ag_2 |
| ID: | 1516100265 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 314 (286) | ||
| Sequences: | 3936 (2304.4) | ||
| Seq/Len: | 13.762 | ||
| Nf(neff/√len): | 136.3 |
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: 13.762).
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 |
| 149_R | 205_E | 5.363 | 1.00 |
| 29_R | 306_D | 4.320 | 1.00 |
| 25_G | 299_D | 3.280 | 1.00 |
| 168_D | 182_K | 3.223 | 1.00 |
| 7_S | 32_E | 3.034 | 1.00 |
| 9_V | 66_P | 2.819 | 1.00 |
| 26_L | 305_C | 2.709 | 1.00 |
| 25_G | 302_G | 2.620 | 1.00 |
| 220_Q | 303_P | 2.618 | 1.00 |
| 145_L | 280_V | 2.554 | 1.00 |
| 25_G | 28_A | 2.471 | 1.00 |
| 252_D | 256_R | 2.434 | 1.00 |
| 31_H | 309_I | 2.380 | 1.00 |
| 218_D | 307_A | 2.317 | 1.00 |
| 34_Y | 66_P | 2.293 | 1.00 |
| 263_L | 266_T | 2.271 | 1.00 |
| 214_V | 246_I | 2.263 | 1.00 |
| 247_S | 250_V | 2.257 | 1.00 |
| 271_K | 281_L | 2.209 | 1.00 |
| 303_P | 306_D | 2.149 | 1.00 |
| 248_D | 251_K | 2.133 | 1.00 |
| 299_D | 302_G | 2.116 | 1.00 |
| 214_V | 270_I | 2.080 | 1.00 |
| 221_V | 255_V | 2.075 | 1.00 |
| 115_E | 124_S | 2.059 | 1.00 |
| 18_H | 289_F | 1.996 | 1.00 |
| 219_D | 259_K | 1.964 | 1.00 |
| 115_E | 125_P | 1.939 | 1.00 |
| 9_V | 36_F | 1.897 | 1.00 |
| 26_L | 33_P | 1.882 | 1.00 |
| 217_I | 222_I | 1.863 | 1.00 |
| 249_E | 252_D | 1.858 | 1.00 |
| 220_Q | 255_V | 1.854 | 1.00 |
| 273_G | 277_N | 1.845 | 1.00 |
| 273_G | 279_R | 1.803 | 1.00 |
| 31_H | 305_C | 1.802 | 1.00 |
| 29_R | 302_G | 1.779 | 1.00 |
| 207_L | 279_R | 1.729 | 1.00 |
| 216_V | 255_V | 1.674 | 1.00 |
| 155_D | 158_A | 1.661 | 1.00 |
| 229_T | 242_E | 1.649 | 1.00 |
| 29_R | 309_I | 1.633 | 1.00 |
| 210_D | 227_I | 1.590 | 1.00 |
| 68_A | 308_L | 1.572 | 1.00 |
| 163_H | 169_C | 1.570 | 1.00 |
| 158_A | 161_R | 1.561 | 1.00 |
| 120_A | 311_Q | 1.555 | 1.00 |
| 211_D | 228_V | 1.555 | 1.00 |
| 216_V | 258_A | 1.553 | 1.00 |
| 208_T | 274_A | 1.537 | 1.00 |
| 257_A | 268_M | 1.535 | 1.00 |
| 248_D | 252_D | 1.524 | 1.00 |
| 21_S | 293_E | 1.515 | 1.00 |
| 25_G | 29_R | 1.514 | 1.00 |
| 148_P | 205_E | 1.510 | 1.00 |
| 140_L | 280_V | 1.491 | 1.00 |
| 168_D | 184_E | 1.482 | 1.00 |
| 151_L | 162_F | 1.480 | 1.00 |
| 251_K | 255_V | 1.471 | 1.00 |
| 258_A | 266_T | 1.468 | 1.00 |
| 216_V | 221_V | 1.468 | 1.00 |
| 269_D | 282_E | 1.442 | 1.00 |
| 113_R | 138_A | 1.434 | 1.00 |
| 212_V | 244_I | 1.434 | 1.00 |
| 159_V | 203_F | 1.431 | 1.00 |
| 146_P | 277_N | 1.427 | 1.00 |
| 222_I | 303_P | 1.425 | 1.00 |
| 214_V | 221_V | 1.409 | 1.00 |
| 23_T | 35_V | 1.385 | 0.99 |
| 7_S | 67_A | 1.368 | 0.99 |
| 8_I | 31_H | 1.367 | 0.99 |
| 293_E | 299_D | 1.362 | 0.99 |
| 137_L | 147_V | 1.362 | 0.99 |
| 150_S | 204_Q | 1.361 | 0.99 |
| 153_T | 159_V | 1.357 | 0.99 |
| 62_Q | 65_R | 1.352 | 0.99 |
| 7_S | 34_Y | 1.351 | 0.99 |
| 264_R | 307_A | 1.330 | 0.99 |
| 302_G | 306_D | 1.323 | 0.99 |
| 217_I | 304_L | 1.317 | 0.99 |
| 293_E | 296_A | 1.296 | 0.99 |
| 216_V | 254_C | 1.293 | 0.99 |
| 12_G | 19_V | 1.292 | 0.99 |
| 257_A | 280_V | 1.288 | 0.99 |
| 218_D | 310_A | 1.285 | 0.99 |
| 253_Q | 280_V | 1.270 | 0.99 |
| 184_E | 188_L | 1.258 | 0.99 |
| 180_T | 235_R | 1.257 | 0.99 |
| 256_R | 260_L | 1.255 | 0.99 |
| 130_N | 285_A | 1.240 | 0.98 |
| 25_G | 305_C | 1.237 | 0.98 |
| 224_A | 292_F | 1.236 | 0.98 |
| 219_D | 255_V | 1.226 | 0.98 |
| 10_V | 23_T | 1.210 | 0.98 |
| 9_V | 69_V | 1.207 | 0.98 |
| 307_A | 311_Q | 1.201 | 0.98 |
| 145_L | 257_A | 1.185 | 0.98 |
| 211_D | 239_E | 1.182 | 0.98 |
| 8_I | 305_C | 1.178 | 0.98 |
| 228_V | 238_E | 1.178 | 0.98 |
| 170_I | 182_K | 1.174 | 0.98 |
| 6_T | 31_H | 1.172 | 0.98 |
| 161_R | 165_E | 1.169 | 0.97 |
| 28_A | 302_G | 1.164 | 0.97 |
| 8_I | 26_L | 1.161 | 0.97 |
| 37_D | 40_R | 1.159 | 0.97 |
| 54_A | 110_V | 1.151 | 0.97 |
| 250_V | 270_I | 1.149 | 0.97 |
| 246_I | 251_K | 1.144 | 0.97 |
| 250_V | 278_Y | 1.138 | 0.97 |
| 293_E | 301_C | 1.133 | 0.97 |
| 146_P | 256_R | 1.124 | 0.97 |
| 48_S | 51_E | 1.123 | 0.97 |
| 221_V | 258_A | 1.123 | 0.97 |
| 115_E | 118_G | 1.121 | 0.97 |
| 140_L | 257_A | 1.111 | 0.96 |
| 120_A | 308_L | 1.110 | 0.96 |
| 24_E | 28_A | 1.107 | 0.96 |
| 182_K | 206_L | 1.103 | 0.96 |
| 32_E | 67_A | 1.099 | 0.96 |
| 168_D | 185_A | 1.096 | 0.96 |
| 220_Q | 251_K | 1.093 | 0.96 |
| 145_L | 253_Q | 1.091 | 0.96 |
| 22_V | 304_L | 1.079 | 0.95 |
| 69_V | 114_W | 1.076 | 0.95 |
| 270_I | 278_Y | 1.075 | 0.95 |
| 253_Q | 270_I | 1.071 | 0.95 |
| 265_Y | 304_L | 1.069 | 0.95 |
| 257_A | 261_V | 1.062 | 0.95 |
| 169_C | 183_L | 1.056 | 0.95 |
| 10_V | 19_V | 1.052 | 0.95 |
| 71_L | 127_A | 1.052 | 0.95 |
| 137_L | 202_C | 1.042 | 0.94 |
| 209_G | 271_K | 1.033 | 0.94 |
| 255_V | 259_K | 1.026 | 0.94 |
| 27_R | 33_P | 1.021 | 0.93 |
| 307_A | 310_A | 1.019 | 0.93 |
| 227_I | 242_E | 1.017 | 0.93 |
| 23_T | 27_R | 1.015 | 0.93 |
| 122_Y | 304_L | 1.015 | 0.93 |
| 171_Y | 203_F | 1.005 | 0.93 |
| 149_R | 166_V | 1.002 | 0.92 |
| 218_D | 311_Q | 1.001 | 0.92 |
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 | |
| 3vpbA | 4 | 0.8471 | 100 | 0.47 | Contact Map |
| 4iwxA | 1 | 0.8885 | 100 | 0.475 | Contact Map |
| 1gsaA | 1 | 0.879 | 100 | 0.507 | Contact Map |
| 3vpdA | 2 | 0.8471 | 100 | 0.514 | Contact Map |
| 2p0aA | 2 | 0.8503 | 100 | 0.541 | Contact Map |
| 1pk8A | 8 | 0.8854 | 100 | 0.56 | Contact Map |
| 2q7dA | 2 | 0.8567 | 100 | 0.564 | Contact Map |
| 3t7aA | 1 | 0.8471 | 100 | 0.567 | Contact Map |
| 1i7nA | 2 | 0.8822 | 100 | 0.568 | Contact Map |
| 3r5xA | 4 | 0.8535 | 100 | 0.576 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)