| ItkFL 340-620 |
| ID: | 1379134853 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 281 (260) | ||
| Sequences: | 44325 (30781.1) | ||
| Seq/Len: | 170.481 | ||
| Nf(neff/√len): | 1909.0 |
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: 170.481).
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 |
| 257_K | 262_D | 3.633 | 1.00 |
| 124_C | 209_M | 3.229 | 1.00 |
| 40_L | 48_K | 3.184 | 1.00 |
| 150_L | 160_S | 3.052 | 1.00 |
| 28_Q | 40_L | 2.963 | 1.00 |
| 29_E | 37_L | 2.855 | 1.00 |
| 202_V | 255_C | 2.483 | 1.00 |
| 75_S | 81_Q | 2.406 | 1.00 |
| 132_A | 267_S | 2.405 | 1.00 |
| 41_G | 49_V | 2.371 | 1.00 |
| 41_G | 51_I | 2.370 | 1.00 |
| 29_E | 32_S | 2.363 | 1.00 |
| 132_A | 136_E | 2.328 | 1.00 |
| 105_S | 147_R | 2.242 | 1.00 |
| 100_E | 153_E | 2.207 | 1.00 |
| 97_E | 158_K | 2.180 | 1.00 |
| 126_D | 157_I | 2.163 | 1.00 |
| 254_H | 272_Q | 2.156 | 1.00 |
| 126_D | 156_V | 2.139 | 1.00 |
| 259_R | 262_D | 2.091 | 1.00 |
| 152_G | 156_V | 2.090 | 1.00 |
| 254_H | 264_P | 2.085 | 1.00 |
| 76_H | 133_Y | 2.055 | 1.00 |
| 128_C | 205_F | 2.026 | 1.00 |
| 127_V | 149_C | 1.992 | 1.00 |
| 25_T | 42_Y | 1.992 | 1.00 |
| 255_C | 269_L | 1.991 | 1.00 |
| 40_L | 98_F | 1.985 | 1.00 |
| 149_C | 157_I | 1.963 | 1.00 |
| 116_A | 119_T | 1.916 | 1.00 |
| 83_Y | 97_E | 1.860 | 1.00 |
| 144_L | 208_L | 1.852 | 1.00 |
| 131_M | 205_F | 1.807 | 1.00 |
| 187_S | 200_S | 1.765 | 1.00 |
| 103_C | 106_D | 1.763 | 1.00 |
| 42_Y | 48_K | 1.761 | 1.00 |
| 206_G | 255_C | 1.709 | 1.00 |
| 27_V | 42_Y | 1.690 | 1.00 |
| 117_A | 245_S | 1.682 | 1.00 |
| 128_C | 269_L | 1.672 | 1.00 |
| 130_G | 159_V | 1.654 | 1.00 |
| 202_V | 266_F | 1.642 | 1.00 |
| 131_M | 144_L | 1.612 | 1.00 |
| 51_I | 95_V | 1.601 | 1.00 |
| 29_E | 39_H | 1.593 | 1.00 |
| 81_Q | 97_E | 1.587 | 1.00 |
| 152_G | 158_K | 1.581 | 1.00 |
| 124_C | 212_V | 1.571 | 1.00 |
| 185_W | 211_E | 1.523 | 1.00 |
| 25_T | 44_L | 1.522 | 1.00 |
| 240_K | 243_L | 1.516 | 1.00 |
| 123_M | 157_I | 1.510 | 1.00 |
| 78_K | 129_E | 1.509 | 1.00 |
| 131_M | 266_F | 1.499 | 1.00 |
| 146_A | 185_W | 1.469 | 1.00 |
| 136_E | 267_S | 1.464 | 1.00 |
| 146_A | 208_L | 1.399 | 0.99 |
| 132_A | 270_L | 1.395 | 0.99 |
| 124_C | 205_F | 1.392 | 0.99 |
| 23_E | 43_W | 1.383 | 0.99 |
| 125_L | 129_E | 1.376 | 0.99 |
| 149_C | 208_L | 1.373 | 0.99 |
| 32_S | 37_L | 1.371 | 0.99 |
| 78_K | 130_G | 1.370 | 0.99 |
| 179_T | 182_P | 1.366 | 0.99 |
| 105_S | 109_R | 1.363 | 0.99 |
| 99_M | 158_K | 1.361 | 0.99 |
| 122_G | 126_D | 1.356 | 0.99 |
| 265_A | 268_R | 1.355 | 0.99 |
| 125_L | 274_A | 1.347 | 0.99 |
| 99_M | 152_G | 1.344 | 0.99 |
| 38_V | 50_A | 1.342 | 0.99 |
| 53_T | 91_P | 1.332 | 0.99 |
| 49_V | 95_V | 1.318 | 0.99 |
| 252_M | 256_W | 1.317 | 0.99 |
| 142_R | 196_Y | 1.313 | 0.99 |
| 127_V | 157_I | 1.296 | 0.99 |
| 139_V | 165_T | 1.296 | 0.99 |
| 27_V | 40_L | 1.292 | 0.99 |
| 251_I | 272_Q | 1.289 | 0.99 |
| 129_E | 270_L | 1.285 | 0.99 |
| 266_F | 269_L | 1.280 | 0.99 |
| 209_M | 251_I | 1.263 | 0.99 |
| 143_D | 148_N | 1.253 | 0.99 |
| 80_V | 96_F | 1.247 | 0.99 |
| 80_V | 99_M | 1.242 | 0.98 |
| 53_T | 93_C | 1.236 | 0.98 |
| 187_S | 190_V | 1.231 | 0.98 |
| 128_C | 266_F | 1.226 | 0.98 |
| 47_D | 83_Y | 1.224 | 0.98 |
| 117_A | 120_L | 1.224 | 0.98 |
| 80_V | 160_S | 1.214 | 0.98 |
| 145_A | 182_P | 1.204 | 0.98 |
| 249_Y | 253_N | 1.197 | 0.98 |
| 251_I | 269_L | 1.189 | 0.98 |
| 39_H | 53_T | 1.184 | 0.98 |
| 120_L | 212_V | 1.182 | 0.98 |
| 148_N | 161_D | 1.182 | 0.98 |
| 99_M | 150_L | 1.179 | 0.98 |
| 250_Q | 254_H | 1.171 | 0.98 |
| 251_I | 255_C | 1.157 | 0.97 |
| 133_Y | 137_A | 1.152 | 0.97 |
| 205_F | 255_C | 1.150 | 0.97 |
| 141_H | 144_L | 1.145 | 0.97 |
| 254_H | 257_K | 1.145 | 0.97 |
| 146_A | 211_E | 1.135 | 0.97 |
| 135_E | 266_F | 1.134 | 0.97 |
| 120_L | 213_F | 1.133 | 0.97 |
| 129_E | 274_A | 1.128 | 0.97 |
| 264_P | 269_L | 1.125 | 0.97 |
| 48_K | 98_F | 1.123 | 0.97 |
| 33_G | 36_G | 1.122 | 0.97 |
| 42_Y | 46_K | 1.119 | 0.96 |
| 138_C | 198_S | 1.110 | 0.96 |
| 105_S | 211_E | 1.107 | 0.96 |
| 70_V | 165_T | 1.106 | 0.96 |
| 199_K | 265_A | 1.102 | 0.96 |
| 101_H | 155_Q | 1.098 | 0.96 |
| 213_F | 248_V | 1.096 | 0.96 |
| 205_F | 209_M | 1.087 | 0.96 |
| 196_Y | 200_S | 1.084 | 0.96 |
| 48_K | 100_E | 1.074 | 0.95 |
| 129_E | 132_A | 1.073 | 0.95 |
| 190_V | 200_S | 1.069 | 0.95 |
| 128_C | 270_L | 1.066 | 0.95 |
| 43_W | 47_D | 1.064 | 0.95 |
| 151_V | 157_I | 1.059 | 0.95 |
| 119_T | 122_G | 1.047 | 0.94 |
| 125_L | 270_L | 1.047 | 0.94 |
| 82_L | 85_V | 1.042 | 0.94 |
| 30_I | 98_F | 1.032 | 0.94 |
| 122_G | 156_V | 1.031 | 0.94 |
| 26_F | 39_H | 1.022 | 0.93 |
| 127_V | 208_L | 1.021 | 0.93 |
| 131_M | 135_E | 1.017 | 0.93 |
| 254_H | 268_R | 1.015 | 0.93 |
| 73_K | 137_A | 1.012 | 0.93 |
| 144_L | 159_V | 1.005 | 0.93 |
| 145_A | 148_N | 1.000 | 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 | |
| 4hcuA | 1 | 0.9359 | 100 | 0.117 | Contact Map |
| 3genA | 1 | 0.9395 | 100 | 0.124 | Contact Map |
| 2h8hA | 1 | 0.9964 | 100 | 0.131 | Contact Map |
| 1opkA | 1 | 1 | 100 | 0.132 | Contact Map |
| 1fmkA | 1 | 0.9466 | 100 | 0.133 | Contact Map |
| 1qcfA | 1 | 0.9964 | 100 | 0.148 | Contact Map |
| 3sxsA | 1 | 0.9395 | 100 | 0.15 | Contact Map |
| 3cblA | 1 | 0.9964 | 100 | 0.155 | Contact Map |
| 3tt0A | 2 | 0.9858 | 100 | 0.159 | Contact Map |
| 1k9aA | 6 | 0.968 | 100 | 0.16 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)