| 1PHP |
| ID: | 1429464220 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 394 (394) | ||
| Sequences: | 1913 (1132.6) | ||
| Seq/Len: | 4.855 | ||
| Nf(neff/√len): | 57.1 |
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: 4.855).
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 |
| 190_T | 310_S | 4.488 | 1.00 |
| 17_F | 57_A | 3.693 | 1.00 |
| 34_D | 38_R | 3.545 | 1.00 |
| 384_Q | 389_V | 3.511 | 1.00 |
| 232_D | 288_A | 3.409 | 1.00 |
| 27_E | 30_A | 2.912 | 1.00 |
| 298_K | 301_E | 2.873 | 1.00 |
| 130_L | 134_F | 2.744 | 1.00 |
| 47_L | 52_A | 2.732 | 1.00 |
| 264_V | 302_L | 2.723 | 1.00 |
| 235_K | 289_D | 2.714 | 1.00 |
| 79_R | 82_E | 2.656 | 1.00 |
| 325_D | 359_K | 2.636 | 1.00 |
| 106_L | 110_D | 2.596 | 1.00 |
| 18_C | 47_L | 2.589 | 1.00 |
| 17_F | 159_I | 2.520 | 1.00 |
| 172_E | 176_E | 2.472 | 1.00 |
| 46_Y | 169_F | 2.452 | 1.00 |
| 223_Y | 292_A | 2.438 | 1.00 |
| 261_Y | 306_V | 2.206 | 1.00 |
| 94_A | 120_Y | 2.204 | 1.00 |
| 22_F | 40_A | 2.200 | 1.00 |
| 53_K | 108_E | 2.189 | 1.00 |
| 106_L | 112_L | 2.161 | 1.00 |
| 34_D | 79_R | 2.132 | 1.00 |
| 9_V | 166_V | 2.122 | 1.00 |
| 89_A | 110_D | 2.114 | 1.00 |
| 282_P | 298_K | 2.112 | 1.00 |
| 269_A | 276_A | 2.056 | 1.00 |
| 45_R | 49_E | 2.040 | 1.00 |
| 338_L | 346_S | 2.011 | 1.00 |
| 332_K | 336_E | 1.993 | 1.00 |
| 272_F | 324_M | 1.991 | 1.00 |
| 300_R | 304_R | 1.985 | 1.00 |
| 270_D | 277_N | 1.980 | 1.00 |
| 57_A | 138_A | 1.980 | 1.00 |
| 212_V | 215_L | 1.969 | 1.00 |
| 186_D | 311_K | 1.961 | 1.00 |
| 301_E | 305_D | 1.956 | 1.00 |
| 181_A | 347_V | 1.908 | 1.00 |
| 331_T | 356_A | 1.906 | 1.00 |
| 218_G | 319_M | 1.887 | 1.00 |
| 227_K | 240_E | 1.883 | 1.00 |
| 157_E | 161_H | 1.876 | 1.00 |
| 250_M | 260_F | 1.870 | 1.00 |
| 100_K | 136_E | 1.864 | 1.00 |
| 264_V | 298_K | 1.861 | 1.00 |
| 97_D | 100_K | 1.856 | 1.00 |
| 190_T | 307_I | 1.847 | 1.00 |
| 175_L | 388_V | 1.845 | 1.00 |
| 251_E | 255_E | 1.830 | 1.00 |
| 332_K | 360_F | 1.803 | 1.00 |
| 107_N | 110_D | 1.784 | 1.00 |
| 148_A | 156_T | 1.770 | 1.00 |
| 11_V | 47_L | 1.746 | 1.00 |
| 46_Y | 50_H | 1.746 | 1.00 |
| 300_R | 333_A | 1.735 | 1.00 |
| 206_D | 248_S | 1.713 | 1.00 |
| 167_A | 391_L | 1.704 | 0.99 |
| 79_R | 83_L | 1.692 | 0.99 |
| 7_R | 169_F | 1.667 | 0.99 |
| 279_K | 290_W | 1.663 | 0.99 |
| 243_I | 247_K | 1.651 | 0.99 |
| 15_R | 55_I | 1.649 | 0.99 |
| 190_T | 214_N | 1.644 | 0.99 |
| 68_V | 71_L | 1.624 | 0.99 |
| 81_G | 87_P | 1.618 | 0.99 |
| 329_H | 332_K | 1.595 | 0.99 |
| 92_N | 98_E | 1.593 | 0.99 |
| 210_E | 252_K | 1.586 | 0.99 |
| 227_K | 243_I | 1.582 | 0.99 |
| 128_P | 161_H | 1.574 | 0.99 |
| 299_T | 303_Y | 1.574 | 0.99 |
| 72_R | 90_K | 1.567 | 0.99 |
| 193_I | 205_I | 1.561 | 0.99 |
| 251_E | 254_K | 1.557 | 0.99 |
| 74_D | 78_K | 1.555 | 0.99 |
| 15_R | 53_K | 1.518 | 0.99 |
| 314_V | 380_M | 1.509 | 0.98 |
| 270_D | 290_W | 1.503 | 0.98 |
| 20_V | 56_L | 1.498 | 0.98 |
| 280_V | 297_P | 1.496 | 0.98 |
| 93_E | 96_G | 1.488 | 0.98 |
| 44_I | 56_L | 1.487 | 0.98 |
| 55_I | 138_A | 1.480 | 0.98 |
| 259_R | 306_V | 1.480 | 0.98 |
| 336_E | 340_E | 1.473 | 0.98 |
| 199_K | 239_E | 1.463 | 0.98 |
| 160_A | 390_A | 1.463 | 0.98 |
| 206_D | 252_K | 1.462 | 0.98 |
| 132_K | 162_Y | 1.435 | 0.98 |
| 101_A | 105_R | 1.428 | 0.98 |
| 57_A | 117_V | 1.427 | 0.98 |
| 270_D | 289_D | 1.424 | 0.98 |
| 48_I | 53_K | 1.424 | 0.98 |
| 214_N | 261_Y | 1.422 | 0.98 |
| 216_I | 303_Y | 1.415 | 0.97 |
| 202_I | 242_K | 1.411 | 0.97 |
| 7_R | 46_Y | 1.399 | 0.97 |
| 18_C | 56_L | 1.394 | 0.97 |
| 244_E | 247_K | 1.392 | 0.97 |
| 41_L | 83_L | 1.387 | 0.97 |
| 17_F | 138_A | 1.386 | 0.97 |
| 242_K | 245_L | 1.370 | 0.97 |
| 266_V | 283_I | 1.363 | 0.97 |
| 274_N | 326_A | 1.363 | 0.97 |
| 345_Y | 367_D | 1.361 | 0.97 |
| 45_R | 86_R | 1.358 | 0.96 |
| 13_G | 108_E | 1.358 | 0.96 |
| 223_Y | 266_V | 1.356 | 0.96 |
| 304_R | 337_A | 1.350 | 0.96 |
| 152_A | 157_E | 1.337 | 0.96 |
| 177_V | 345_Y | 1.330 | 0.96 |
| 307_I | 337_A | 1.326 | 0.96 |
| 358_E | 363_A | 1.316 | 0.96 |
| 179_G | 379_F | 1.311 | 0.95 |
| 269_A | 293_L | 1.302 | 0.95 |
| 142_V | 166_V | 1.289 | 0.95 |
| 57_A | 159_I | 1.283 | 0.95 |
| 268_V | 281_V | 1.279 | 0.95 |
| 304_R | 308_R | 1.278 | 0.95 |
| 308_R | 340_E | 1.272 | 0.94 |
| 122_G | 130_L | 1.270 | 0.94 |
| 171_M | 388_V | 1.268 | 0.94 |
| 86_R | 110_D | 1.266 | 0.94 |
| 149_A | 171_M | 1.265 | 0.94 |
| 214_N | 259_R | 1.259 | 0.94 |
| 210_E | 256_K | 1.253 | 0.94 |
| 286_I | 292_A | 1.250 | 0.94 |
| 181_A | 314_V | 1.241 | 0.93 |
| 229_L | 250_M | 1.237 | 0.93 |
| 214_N | 310_S | 1.231 | 0.93 |
| 7_R | 172_E | 1.226 | 0.93 |
| 275_D | 324_M | 1.222 | 0.93 |
| 26_M | 60_L | 1.218 | 0.93 |
| 74_D | 90_K | 1.213 | 0.92 |
| 95_V | 120_Y | 1.212 | 0.92 |
| 132_K | 136_E | 1.212 | 0.92 |
| 91_T | 102_A | 1.208 | 0.92 |
| 38_R | 83_L | 1.206 | 0.92 |
| 44_I | 111_V | 1.205 | 0.92 |
| 120_Y | 133_A | 1.204 | 0.92 |
| 302_L | 306_V | 1.200 | 0.92 |
| 287_P | 290_W | 1.192 | 0.91 |
| 117_V | 130_L | 1.192 | 0.91 |
| 229_L | 254_K | 1.177 | 0.91 |
| 214_N | 306_V | 1.175 | 0.91 |
| 149_A | 156_T | 1.175 | 0.91 |
| 73_L | 90_K | 1.172 | 0.91 |
| 131_A | 158_G | 1.171 | 0.91 |
| 81_G | 113_L | 1.169 | 0.90 |
| 282_P | 285_A | 1.166 | 0.90 |
| 47_L | 54_V | 1.166 | 0.90 |
| 12_R | 108_E | 1.163 | 0.90 |
| 120_Y | 130_L | 1.162 | 0.90 |
| 41_L | 84_L | 1.159 | 0.90 |
| 216_I | 299_T | 1.156 | 0.90 |
| 91_T | 99_V | 1.146 | 0.89 |
| 126_N | 158_G | 1.144 | 0.89 |
| 103_V | 112_L | 1.142 | 0.89 |
| 41_L | 77_A | 1.139 | 0.89 |
| 319_M | 334_I | 1.131 | 0.88 |
| 91_T | 112_L | 1.130 | 0.88 |
| 18_C | 43_T | 1.128 | 0.88 |
| 354_A | 358_E | 1.125 | 0.88 |
| 178_L | 379_F | 1.116 | 0.87 |
| 248_S | 252_K | 1.113 | 0.87 |
| 368_H | 376_S | 1.106 | 0.87 |
| 278_T | 326_A | 1.104 | 0.87 |
| 20_V | 40_A | 1.104 | 0.87 |
| 6_I | 47_L | 1.102 | 0.87 |
| 325_D | 328_A | 1.098 | 0.86 |
| 103_V | 106_L | 1.086 | 0.85 |
| 18_C | 44_I | 1.082 | 0.85 |
| 300_R | 329_H | 1.077 | 0.85 |
| 177_V | 367_D | 1.071 | 0.84 |
| 233_V | 238_L | 1.070 | 0.84 |
| 48_I | 110_D | 1.059 | 0.83 |
| 77_A | 81_G | 1.057 | 0.83 |
| 22_F | 56_L | 1.056 | 0.83 |
| 313_V | 338_L | 1.056 | 0.83 |
| 270_D | 276_A | 1.052 | 0.83 |
| 14_K | 139_D | 1.051 | 0.83 |
| 56_L | 113_L | 1.050 | 0.83 |
| 214_N | 309_E | 1.049 | 0.83 |
| 58_S | 148_A | 1.047 | 0.83 |
| 341_A | 344_T | 1.044 | 0.82 |
| 226_V | 262_M | 1.042 | 0.82 |
| 180_K | 186_D | 1.039 | 0.82 |
| 354_A | 357_V | 1.039 | 0.82 |
| 307_I | 341_A | 1.036 | 0.82 |
| 270_D | 287_P | 1.033 | 0.81 |
| 140_L | 166_V | 1.033 | 0.81 |
| 126_N | 157_E | 1.028 | 0.81 |
| 58_S | 73_L | 1.016 | 0.80 |
| 266_V | 292_A | 1.015 | 0.80 |
| 305_D | 308_R | 1.014 | 0.80 |
| 179_G | 183_S | 1.013 | 0.80 |
| 305_D | 309_E | 1.006 | 0.79 |
| 35_T | 358_E | 1.006 | 0.79 |
| 9_V | 140_L | 1.004 | 0.79 |
| 220_G | 237_L | 1.003 | 0.79 |
| 78_K | 81_G | 1.001 | 0.78 |
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 | |
| 1phpA | 1 | 1 | 100 | -0.024 | Contact Map |
| 1vpeA | 1 | 0.9975 | 100 | -0.016 | Contact Map |
| 3q3vA | 2 | 0.9873 | 100 | -0.01 | Contact Map |
| 1v6sA | 2 | 0.9873 | 100 | -0.009 | Contact Map |
| 3zlbA | 1 | 0.9924 | 100 | -0.007 | Contact Map |
| 1qpgA | 1 | 0.9975 | 100 | -0.006 | Contact Map |
| 4feyA | 1 | 0.9822 | 100 | -0.004 | Contact Map |
| 4dg5A | 1 | 0.9898 | 100 | -0.003 | Contact Map |
| 3oz7A | 2 | 0.9949 | 100 | -0.002 | Contact Map |
| 16pkA | 1 | 0.9924 | 100 | -0.002 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)