| rcl2 |
| ID: | 1484036012 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 269 (258) | ||
| Sequences: | 1710 (1221.7) | ||
| Seq/Len: | 6.628 | ||
| Nf(neff/√len): | 76.1 |
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: 6.628).
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 |
| 148_G | 174_T | 3.690 | 1.00 |
| 235_C | 244_C | 3.543 | 1.00 |
| 155_G | 172_I | 3.184 | 1.00 |
| 152_L | 177_C | 2.913 | 1.00 |
| 149_A | 180_V | 2.824 | 1.00 |
| 103_V | 106_A | 2.628 | 1.00 |
| 71_D | 137_Y | 2.585 | 1.00 |
| 116_Y | 157_D | 2.574 | 1.00 |
| 152_L | 185_F | 2.558 | 1.00 |
| 89_A | 92_D | 2.512 | 1.00 |
| 80_F | 154_A | 2.392 | 1.00 |
| 183_N | 187_Y | 2.224 | 1.00 |
| 181_G | 185_F | 2.218 | 1.00 |
| 177_C | 219_P | 2.143 | 1.00 |
| 141_V | 158_L | 2.113 | 1.00 |
| 112_F | 178_P | 2.083 | 1.00 |
| 74_K | 137_Y | 2.080 | 1.00 |
| 108_V | 153_L | 1.919 | 1.00 |
| 24_A | 142_T | 1.891 | 1.00 |
| 83_T | 92_D | 1.845 | 1.00 |
| 66_F | 79_T | 1.842 | 1.00 |
| 189_V | 196_F | 1.760 | 1.00 |
| 67_I | 126_V | 1.744 | 1.00 |
| 205_I | 253_S | 1.727 | 1.00 |
| 254_I | 258_L | 1.726 | 1.00 |
| 67_I | 78_V | 1.704 | 1.00 |
| 224_W | 247_S | 1.701 | 1.00 |
| 28_Y | 82_G | 1.694 | 1.00 |
| 74_K | 136_D | 1.694 | 1.00 |
| 98_T | 110_A | 1.672 | 1.00 |
| 148_G | 177_C | 1.664 | 1.00 |
| 112_F | 149_A | 1.637 | 1.00 |
| 83_T | 89_A | 1.628 | 1.00 |
| 27_A | 79_T | 1.628 | 1.00 |
| 106_A | 182_N | 1.619 | 1.00 |
| 20_Y | 175_V | 1.599 | 1.00 |
| 69_R | 137_Y | 1.566 | 0.99 |
| 179_R | 210_P | 1.523 | 0.99 |
| 211_P | 214_F | 1.522 | 0.99 |
| 152_L | 189_V | 1.490 | 0.99 |
| 190_D | 220_G | 1.482 | 0.99 |
| 49_D | 70_S | 1.481 | 0.99 |
| 24_A | 27_A | 1.472 | 0.99 |
| 81_R | 88_S | 1.468 | 0.99 |
| 89_A | 93_M | 1.461 | 0.99 |
| 99_D | 107_K | 1.453 | 0.99 |
| 120_V | 157_D | 1.436 | 0.99 |
| 20_Y | 140_I | 1.398 | 0.99 |
| 203_R | 256_D | 1.389 | 0.98 |
| 94_V | 110_A | 1.386 | 0.98 |
| 80_F | 119_V | 1.383 | 0.98 |
| 67_I | 127_V | 1.382 | 0.98 |
| 76_I | 131_L | 1.362 | 0.98 |
| 149_A | 178_P | 1.361 | 0.98 |
| 75_T | 140_I | 1.343 | 0.98 |
| 56_F | 65_G | 1.341 | 0.98 |
| 139_V | 170_L | 1.341 | 0.98 |
| 116_Y | 120_V | 1.330 | 0.98 |
| 172_I | 196_F | 1.327 | 0.98 |
| 53_I | 130_Q | 1.324 | 0.98 |
| 120_V | 124_F | 1.304 | 0.97 |
| 75_T | 138_K | 1.297 | 0.97 |
| 183_N | 217_L | 1.295 | 0.97 |
| 174_T | 198_R | 1.294 | 0.97 |
| 116_Y | 150_Q | 1.293 | 0.97 |
| 12_A | 17_L | 1.291 | 0.97 |
| 152_L | 219_P | 1.271 | 0.97 |
| 109_H | 112_F | 1.266 | 0.97 |
| 198_R | 218_H | 1.253 | 0.97 |
| 129_D | 133_A | 1.247 | 0.96 |
| 138_K | 171_S | 1.240 | 0.96 |
| 141_V | 151_A | 1.237 | 0.96 |
| 108_V | 113_L | 1.235 | 0.96 |
| 198_R | 219_P | 1.234 | 0.96 |
| 54_K | 126_V | 1.232 | 0.96 |
| 159_Y | 170_L | 1.230 | 0.96 |
| 128_Q | 132_T | 1.225 | 0.96 |
| 202_K | 256_D | 1.225 | 0.96 |
| 126_V | 130_Q | 1.214 | 0.96 |
| 29_C | 40_C | 1.213 | 0.96 |
| 27_A | 66_F | 1.211 | 0.96 |
| 17_L | 199_T | 1.209 | 0.96 |
| 257_H | 260_Y | 1.204 | 0.95 |
| 94_V | 216_Y | 1.203 | 0.95 |
| 97_F | 107_K | 1.192 | 0.95 |
| 78_V | 141_V | 1.187 | 0.95 |
| 255_A | 258_L | 1.172 | 0.94 |
| 155_G | 170_L | 1.171 | 0.94 |
| 123_Y | 126_V | 1.171 | 0.94 |
| 52_L | 55_T | 1.162 | 0.94 |
| 128_Q | 133_A | 1.161 | 0.94 |
| 151_A | 174_T | 1.160 | 0.94 |
| 174_T | 177_C | 1.157 | 0.94 |
| 92_D | 111_G | 1.154 | 0.94 |
| 255_A | 267_S | 1.150 | 0.94 |
| 88_S | 111_G | 1.135 | 0.93 |
| 190_D | 196_F | 1.120 | 0.93 |
| 20_Y | 75_T | 1.117 | 0.92 |
| 116_Y | 154_A | 1.109 | 0.92 |
| 128_Q | 138_K | 1.102 | 0.92 |
| 106_A | 188_Y | 1.101 | 0.92 |
| 119_V | 123_Y | 1.095 | 0.91 |
| 179_R | 218_H | 1.093 | 0.91 |
| 149_A | 206_V | 1.092 | 0.91 |
| 253_S | 256_D | 1.088 | 0.91 |
| 88_S | 92_D | 1.087 | 0.91 |
| 208_H | 246_N | 1.083 | 0.91 |
| 141_V | 154_A | 1.075 | 0.90 |
| 225_I | 232_V | 1.074 | 0.90 |
| 83_T | 146_L | 1.073 | 0.90 |
| 108_V | 185_F | 1.072 | 0.90 |
| 113_L | 117_N | 1.070 | 0.90 |
| 180_V | 185_F | 1.060 | 0.90 |
| 126_V | 129_D | 1.058 | 0.89 |
| 236_T | 239_I | 1.056 | 0.89 |
| 24_A | 28_Y | 1.054 | 0.89 |
| 70_S | 73_Q | 1.050 | 0.89 |
| 242_K | 245_S | 1.042 | 0.88 |
| 83_T | 178_P | 1.032 | 0.88 |
| 176_G | 181_G | 1.027 | 0.87 |
| 16_E | 171_S | 1.022 | 0.87 |
| 83_T | 112_F | 1.016 | 0.87 |
| 175_V | 199_T | 1.014 | 0.87 |
| 172_I | 189_V | 1.014 | 0.87 |
| 92_D | 146_L | 1.008 | 0.86 |
| 242_K | 246_N | 1.000 | 0.86 |
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 | |
| 4l3wA | 1 | 0.9851 | 100 | 0.181 | Contact Map |
| 3o0dA | 7 | 0.9665 | 100 | 0.242 | Contact Map |
| 3ngmA | 4 | 0.9517 | 100 | 0.249 | Contact Map |
| 3g7nA | 2 | 0.9182 | 100 | 0.255 | Contact Map |
| 1tiaA | 1 | 0.9442 | 100 | 0.262 | Contact Map |
| 1tglA | 1 | 0.9814 | 100 | 0.276 | Contact Map |
| 1tibA | 1 | 0.9442 | 100 | 0.279 | Contact Map |
| 1uwcA | 2 | 0.9071 | 100 | 0.287 | Contact Map |
| 3uueA | 1 | 0.9405 | 100 | 0.289 | Contact Map |
| 2yijA | 2 | 0.9517 | 100 | 0.403 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)