| VIP Receptor Sequence Alignment |
| ID: | 1488226678 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 349 (349) | ||
| Sequences: | 1021 (598.6) | ||
| Seq/Len: | 2.926 | ||
| Nf(neff/√len): | 32.0 |
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: 2.926).
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 |
| 325_C | 330_E | 2.782 | 1.00 |
| 325_C | 328_N | 2.591 | 1.00 |
| 251_C | 254_R | 2.488 | 1.00 |
| 325_C | 331_V | 2.473 | 1.00 |
| 15_A | 21_V | 2.473 | 1.00 |
| 7_D | 11_C | 2.393 | 1.00 |
| 2_C | 7_D | 2.303 | 1.00 |
| 326_F | 330_E | 2.277 | 1.00 |
| 2_C | 11_C | 2.239 | 1.00 |
| 324_Y | 330_E | 2.194 | 1.00 |
| 4_R | 14_E | 2.149 | 1.00 |
| 47_G | 60_C | 2.103 | 1.00 |
| 10_T | 23_R | 2.032 | 1.00 |
| 324_Y | 328_N | 1.937 | 0.99 |
| 98_M | 116_M | 1.874 | 0.99 |
| 2_C | 12_W | 1.848 | 0.99 |
| 60_C | 65_N | 1.840 | 0.99 |
| 111_R | 115_H | 1.835 | 0.99 |
| 121_S | 166_N | 1.757 | 0.99 |
| 328_N | 331_V | 1.709 | 0.98 |
| 232_W | 236_T | 1.699 | 0.98 |
| 317_G | 325_C | 1.674 | 0.98 |
| 7_D | 12_W | 1.671 | 0.98 |
| 249_F | 276_L | 1.651 | 0.98 |
| 61_G | 65_N | 1.578 | 0.97 |
| 7_D | 26_P | 1.572 | 0.97 |
| 317_G | 320_V | 1.553 | 0.96 |
| 178_H | 251_C | 1.536 | 0.96 |
| 318_F | 322_V | 1.533 | 0.96 |
| 57_A | 60_C | 1.527 | 0.96 |
| 331_V | 334_E | 1.514 | 0.96 |
| 195_Y | 200_W | 1.511 | 0.96 |
| 59_A | 65_N | 1.509 | 0.96 |
| 321_A | 324_Y | 1.502 | 0.95 |
| 281_L | 285_P | 1.500 | 0.95 |
| 49_S | 60_C | 1.499 | 0.95 |
| 86_G | 90_S | 1.490 | 0.95 |
| 90_S | 94_L | 1.488 | 0.95 |
| 173_E | 176_Y | 1.475 | 0.95 |
| 283_L | 288_G | 1.469 | 0.95 |
| 107_L | 111_R | 1.459 | 0.94 |
| 321_A | 330_E | 1.456 | 0.94 |
| 56_Y | 60_C | 1.445 | 0.94 |
| 334_E | 337_R | 1.444 | 0.94 |
| 7_D | 25_C | 1.442 | 0.94 |
| 320_V | 330_E | 1.441 | 0.94 |
| 334_E | 339_W | 1.440 | 0.94 |
| 161_Y | 169_W | 1.417 | 0.93 |
| 2_C | 6_W | 1.408 | 0.93 |
| 327_L | 330_E | 1.396 | 0.93 |
| 178_H | 254_R | 1.395 | 0.93 |
| 115_H | 118_L | 1.394 | 0.93 |
| 169_W | 200_W | 1.392 | 0.92 |
| 278_K | 283_L | 1.389 | 0.92 |
| 94_L | 100_I | 1.387 | 0.92 |
| 6_W | 9_I | 1.383 | 0.92 |
| 127_I | 131_I | 1.374 | 0.92 |
| 12_W | 25_C | 1.373 | 0.92 |
| 62_Y | 65_N | 1.368 | 0.92 |
| 6_W | 11_C | 1.366 | 0.92 |
| 317_G | 330_E | 1.357 | 0.91 |
| 322_V | 327_L | 1.355 | 0.91 |
| 2_C | 25_C | 1.341 | 0.91 |
| 159_F | 287_F | 1.341 | 0.91 |
| 324_Y | 327_L | 1.335 | 0.90 |
| 276_L | 279_S | 1.333 | 0.90 |
| 11_C | 26_P | 1.330 | 0.90 |
| 321_A | 325_C | 1.318 | 0.89 |
| 86_G | 94_L | 1.306 | 0.89 |
| 152_C | 169_W | 1.305 | 0.89 |
| 110_T | 121_S | 1.294 | 0.88 |
| 161_Y | 173_E | 1.280 | 0.88 |
| 317_G | 328_N | 1.279 | 0.88 |
| 203_P | 210_W | 1.276 | 0.87 |
| 234_I | 238_I | 1.270 | 0.87 |
| 256_L | 260_L | 1.269 | 0.87 |
| 161_Y | 200_W | 1.261 | 0.87 |
| 44_T | 48_W | 1.261 | 0.87 |
| 326_F | 331_V | 1.259 | 0.86 |
| 173_E | 200_W | 1.256 | 0.86 |
| 174_G | 177_L | 1.256 | 0.86 |
| 248_L | 252_I | 1.249 | 0.86 |
| 317_G | 321_A | 1.238 | 0.85 |
| 173_E | 177_L | 1.231 | 0.85 |
| 11_C | 25_C | 1.231 | 0.85 |
| 174_G | 287_F | 1.221 | 0.84 |
| 43_C | 60_C | 1.221 | 0.84 |
| 107_L | 161_Y | 1.221 | 0.84 |
| 90_S | 104_F | 1.210 | 0.83 |
| 192_F | 198_I | 1.208 | 0.83 |
| 325_C | 329_G | 1.198 | 0.82 |
| 169_W | 173_E | 1.192 | 0.82 |
| 106_K | 249_F | 1.188 | 0.82 |
| 174_G | 195_Y | 1.184 | 0.81 |
| 332_Q | 339_W | 1.182 | 0.81 |
| 108_H | 112_N | 1.181 | 0.81 |
| 171_L | 177_L | 1.176 | 0.81 |
| 107_L | 115_H | 1.176 | 0.81 |
| 317_G | 324_Y | 1.164 | 0.80 |
| 320_V | 328_N | 1.160 | 0.80 |
| 170_L | 249_F | 1.150 | 0.79 |
| 40_T | 59_A | 1.146 | 0.78 |
| 6_W | 30_R | 1.133 | 0.77 |
| 90_S | 97_A | 1.126 | 0.77 |
| 275_R | 279_S | 1.125 | 0.77 |
| 291_Y | 309_E | 1.124 | 0.77 |
| 321_A | 328_N | 1.115 | 0.76 |
| 15_A | 19_E | 1.113 | 0.76 |
| 115_H | 173_E | 1.110 | 0.75 |
| 170_L | 279_S | 1.110 | 0.75 |
| 278_K | 285_P | 1.108 | 0.75 |
| 281_L | 284_I | 1.107 | 0.75 |
| 22_V | 38_N | 1.106 | 0.75 |
| 178_H | 183_I | 1.101 | 0.74 |
| 317_G | 331_V | 1.098 | 0.74 |
| 320_V | 325_C | 1.097 | 0.74 |
| 117_H | 188_E | 1.094 | 0.74 |
| 109_C | 122_F | 1.092 | 0.74 |
| 245_N | 288_G | 1.091 | 0.73 |
| 203_P | 207_I | 1.090 | 0.73 |
| 152_C | 173_E | 1.086 | 0.73 |
| 109_C | 125_R | 1.083 | 0.73 |
| 29_F | 32_L | 1.076 | 0.72 |
| 150_V | 154_A | 1.074 | 0.72 |
| 323_L | 326_F | 1.073 | 0.72 |
| 195_Y | 199_G | 1.071 | 0.72 |
| 115_H | 119_F | 1.069 | 0.71 |
| 122_F | 125_R | 1.069 | 0.71 |
| 175_L | 189_R | 1.068 | 0.71 |
| 20_V | 42_N | 1.064 | 0.71 |
| 2_C | 26_P | 1.059 | 0.70 |
| 213_V | 233_I | 1.059 | 0.70 |
| 166_N | 241_S | 1.059 | 0.70 |
| 318_F | 324_Y | 1.057 | 0.70 |
| 87_H | 97_A | 1.055 | 0.70 |
| 5_Q | 14_E | 1.052 | 0.70 |
| 94_L | 97_A | 1.052 | 0.70 |
| 277_A | 284_I | 1.047 | 0.69 |
| 109_C | 115_H | 1.046 | 0.69 |
| 245_N | 252_I | 1.044 | 0.69 |
| 28_Y | 32_L | 1.043 | 0.69 |
| 109_C | 112_N | 1.042 | 0.69 |
| 337_R | 340_R | 1.041 | 0.68 |
| 39_V | 49_S | 1.041 | 0.68 |
| 127_I | 336_K | 1.040 | 0.68 |
| 48_W | 59_A | 1.040 | 0.68 |
| 340_R | 343_H | 1.038 | 0.68 |
| 332_Q | 337_R | 1.038 | 0.68 |
| 180_L | 200_W | 1.035 | 0.68 |
| 11_C | 15_A | 1.035 | 0.68 |
| 265_V | 270_T | 1.032 | 0.67 |
| 90_S | 100_I | 1.028 | 0.67 |
| 305_K | 310_L | 1.028 | 0.67 |
| 47_G | 65_N | 1.023 | 0.66 |
| 108_H | 115_H | 1.018 | 0.66 |
| 305_K | 308_F | 1.016 | 0.66 |
| 212_V | 216_H | 1.015 | 0.66 |
| 160_Q | 165_A | 1.015 | 0.66 |
| 9_I | 30_R | 1.014 | 0.65 |
| 158_F | 185_F | 1.010 | 0.65 |
| 49_S | 105_R | 1.000 | 0.64 |
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 | |
| 4k5yA | 3 | 0.7135 | 100 | 0.41 | Contact Map |
| 4l6rA | 1 | 0.9628 | 100 | 0.513 | Contact Map |
| 4jkvA | 2 | 0.8481 | 100 | 0.707 | Contact Map |
| 4qinA | 1 | 0.8825 | 100 | 0.719 | Contact Map |
| 2qkhA | 1 | 0.1777 | 99.8 | 0.8 | Contact Map |
| 3n94A | 1 | 0.1862 | 99.7 | 0.802 | Contact Map |
| 4hj0A | 2 | 0.1748 | 99.7 | 0.803 | Contact Map |
| 3c5tA | 1 | 0.1862 | 99.7 | 0.805 | Contact Map |
| 4rwfA | 1 | 0 | 99.7 | 0.808 | Contact Map |
| 2xdgA | 2 | 0.1948 | 99.7 | 0.811 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)