| GH8b_250 |
| ID: | 1444679792 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 350 (331) | ||
| Sequences: | 702 (491.1) | ||
| Seq/Len: | 2.121 | ||
| Nf(neff/√len): | 27.0 |
HHblits Results: (2015_06)
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: 2.121).
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 |
| 33_F | 342_S | 3.625 | 1.00 |
| 135_G | 144_L | 3.544 | 1.00 |
| 38_I | 44_V | 2.959 | 1.00 |
| 79_L | 146_L | 2.958 | 1.00 |
| 72_R | 76_E | 2.434 | 1.00 |
| 151_L | 197_F | 2.403 | 1.00 |
| 63_L | 79_L | 2.332 | 1.00 |
| 63_L | 78_L | 2.249 | 1.00 |
| 125_V | 194_L | 2.238 | 1.00 |
| 83_E | 146_L | 2.223 | 1.00 |
| 72_R | 140_S | 2.217 | 1.00 |
| 119_S | 158_E | 2.112 | 0.99 |
| 71_D | 74_M | 2.055 | 0.99 |
| 62_G | 78_L | 1.870 | 0.98 |
| 185_N | 227_W | 1.795 | 0.98 |
| 138_W | 204_W | 1.742 | 0.97 |
| 128_A | 197_F | 1.696 | 0.97 |
| 60_S | 123_A | 1.655 | 0.96 |
| 186_P | 228_V | 1.654 | 0.96 |
| 132_L | 200_L | 1.649 | 0.96 |
| 96_P | 127_I | 1.635 | 0.95 |
| 133_E | 196_R | 1.635 | 0.95 |
| 185_N | 188_Y | 1.603 | 0.95 |
| 245_I | 249_D | 1.584 | 0.94 |
| 60_S | 127_I | 1.578 | 0.94 |
| 155_A | 203_P | 1.513 | 0.92 |
| 193_L | 197_F | 1.510 | 0.92 |
| 154_I | 158_E | 1.509 | 0.92 |
| 135_G | 140_S | 1.470 | 0.91 |
| 126_W | 190_P | 1.457 | 0.90 |
| 72_R | 217_E | 1.411 | 0.88 |
| 62_G | 147_G | 1.406 | 0.88 |
| 153_R | 157_E | 1.403 | 0.88 |
| 189_Q | 211_N | 1.398 | 0.88 |
| 70_N | 137_L | 1.371 | 0.86 |
| 61_Y | 122_D | 1.361 | 0.86 |
| 303_S | 340_S | 1.353 | 0.85 |
| 323_V | 326_Q | 1.352 | 0.85 |
| 16_G | 20_A | 1.337 | 0.84 |
| 17_H | 20_A | 1.333 | 0.84 |
| 122_D | 252_R | 1.332 | 0.84 |
| 64_F | 68_V | 1.331 | 0.84 |
| 19_V | 23_G | 1.330 | 0.84 |
| 43_R | 184_L | 1.330 | 0.84 |
| 218_S | 224_S | 1.323 | 0.84 |
| 223_F | 280_L | 1.322 | 0.84 |
| 103_K | 113_G | 1.321 | 0.83 |
| 292_N | 295_T | 1.315 | 0.83 |
| 246_G | 306_F | 1.312 | 0.83 |
| 56_S | 100_W | 1.311 | 0.83 |
| 188_Y | 227_W | 1.308 | 0.83 |
| 222_G | 225_P | 1.295 | 0.82 |
| 79_L | 96_P | 1.294 | 0.82 |
| 207_M | 210_V | 1.290 | 0.81 |
| 262_Q | 267_R | 1.282 | 0.81 |
| 144_L | 148_T | 1.280 | 0.81 |
| 64_F | 346_F | 1.276 | 0.80 |
| 63_L | 67_L | 1.266 | 0.80 |
| 195_A | 208_R | 1.264 | 0.80 |
| 38_I | 74_M | 1.259 | 0.79 |
| 307_S | 324_Q | 1.251 | 0.79 |
| 18_A | 23_G | 1.249 | 0.78 |
| 64_F | 126_W | 1.241 | 0.78 |
| 63_L | 146_L | 1.240 | 0.78 |
| 225_P | 228_V | 1.240 | 0.78 |
| 122_D | 226_D | 1.238 | 0.78 |
| 97_A | 114_V | 1.233 | 0.77 |
| 337_A | 340_S | 1.227 | 0.77 |
| 17_H | 21_A | 1.226 | 0.77 |
| 79_L | 83_E | 1.225 | 0.77 |
| 98_W | 188_Y | 1.225 | 0.77 |
| 263_E | 268_A | 1.223 | 0.76 |
| 67_L | 70_N | 1.221 | 0.76 |
| 24_V | 83_E | 1.218 | 0.76 |
| 16_G | 19_V | 1.215 | 0.76 |
| 76_E | 143_F | 1.204 | 0.75 |
| 245_I | 290_Q | 1.197 | 0.74 |
| 85_N | 100_W | 1.196 | 0.74 |
| 55_T | 123_A | 1.195 | 0.74 |
| 287_P | 307_S | 1.193 | 0.74 |
| 126_W | 255_L | 1.186 | 0.73 |
| 246_G | 305_G | 1.184 | 0.73 |
| 75_F | 130_N | 1.182 | 0.73 |
| 159_V | 169_L | 1.181 | 0.73 |
| 307_S | 327_R | 1.175 | 0.72 |
| 119_S | 154_I | 1.169 | 0.72 |
| 171_P | 227_W | 1.165 | 0.71 |
| 98_W | 122_D | 1.165 | 0.71 |
| 155_A | 158_E | 1.164 | 0.71 |
| 126_W | 256_W | 1.164 | 0.71 |
| 126_W | 346_F | 1.160 | 0.71 |
| 63_L | 127_I | 1.160 | 0.71 |
| 63_L | 82_T | 1.155 | 0.70 |
| 119_S | 130_N | 1.149 | 0.70 |
| 38_I | 78_L | 1.145 | 0.69 |
| 78_L | 172_G | 1.141 | 0.69 |
| 218_S | 225_P | 1.138 | 0.69 |
| 18_A | 21_A | 1.125 | 0.67 |
| 43_R | 227_W | 1.116 | 0.67 |
| 150_L | 154_I | 1.114 | 0.66 |
| 59_Q | 95_L | 1.112 | 0.66 |
| 160_A | 177_V | 1.112 | 0.66 |
| 192_Q | 260_L | 1.109 | 0.66 |
| 103_K | 111_P | 1.105 | 0.65 |
| 67_L | 138_W | 1.099 | 0.65 |
| 23_G | 350_W | 1.095 | 0.64 |
| 339_F | 342_S | 1.092 | 0.64 |
| 56_S | 169_L | 1.092 | 0.64 |
| 67_L | 133_E | 1.091 | 0.64 |
| 29_A | 33_F | 1.090 | 0.64 |
| 197_F | 204_W | 1.087 | 0.64 |
| 155_A | 159_V | 1.083 | 0.63 |
| 120_A | 188_Y | 1.082 | 0.63 |
| 59_Q | 82_T | 1.081 | 0.63 |
| 17_H | 22_T | 1.081 | 0.63 |
| 59_Q | 78_L | 1.079 | 0.63 |
| 164_G | 296_G | 1.075 | 0.62 |
| 189_Q | 249_D | 1.073 | 0.62 |
| 28_P | 31_E | 1.071 | 0.62 |
| 46_D | 55_T | 1.062 | 0.61 |
| 282_A | 291_V | 1.060 | 0.61 |
| 132_L | 144_L | 1.060 | 0.61 |
| 101_G | 303_S | 1.059 | 0.61 |
| 18_A | 22_T | 1.057 | 0.60 |
| 33_F | 37_Y | 1.056 | 0.60 |
| 226_D | 248_Y | 1.055 | 0.60 |
| 31_E | 35_R | 1.045 | 0.59 |
| 28_P | 35_R | 1.040 | 0.59 |
| 80_Q | 335_N | 1.037 | 0.58 |
| 318_P | 321_R | 1.034 | 0.58 |
| 19_V | 22_T | 1.032 | 0.58 |
| 54_T | 58_G | 1.030 | 0.57 |
| 86_L | 227_W | 1.029 | 0.57 |
| 159_V | 207_M | 1.024 | 0.57 |
| 86_L | 188_Y | 1.022 | 0.57 |
| 152_Q | 214_L | 1.022 | 0.57 |
| 151_L | 201_K | 1.019 | 0.56 |
| 62_G | 252_R | 1.019 | 0.56 |
| 218_S | 228_V | 1.019 | 0.56 |
| 20_A | 108_D | 1.016 | 0.56 |
| 74_M | 78_L | 1.013 | 0.56 |
| 58_G | 291_V | 1.012 | 0.55 |
| 121_S | 159_V | 1.012 | 0.55 |
| 122_D | 338_Y | 1.012 | 0.55 |
| 101_G | 112_W | 1.012 | 0.55 |
| 319_T | 322_D | 1.012 | 0.55 |
| 55_T | 126_W | 1.012 | 0.55 |
| 69_A | 249_D | 1.007 | 0.55 |
| 118_N | 176_F | 1.007 | 0.55 |
| 170_L | 175_G | 1.003 | 0.54 |
| 253_V | 289_E | 1.002 | 0.54 |
| 48_S | 337_A | 1.000 | 0.54 |
| 16_G | 22_T | 1.000 | 0.54 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4q2bA | 6 | 0.92 | 100 | 0.154 | Contact Map |
| 3qxfA | 4 | 0.9143 | 100 | 0.165 | Contact Map |
| 5cd2A | 1 | 0 | 100 | 0.167 | Contact Map |
| 1wzzA | 1 | 0.8629 | 100 | 0.227 | Contact Map |
| 1v5dA | 2 | 0.9257 | 100 | 0.31 | Contact Map |
| 1wu4A | 1 | 0.9486 | 100 | 0.314 | Contact Map |
| 1kwfA | 1 | 0.9029 | 100 | 0.32 | Contact Map |
| 1h12A | 1 | 0.92 | 100 | 0.338 | Contact Map |
| 3renA | 2 | 0.8457 | 100 | 0.369 | Contact Map |
| 4v1sA | 2 | 0.8114 | 92.1 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)