| SLF |
| ID: | 1509075316 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 389 (364) | ||
| Sequences: | 8052 (7228.2) | ||
| Seq/Len: | 22.121 | ||
| Nf(neff/√len): | 378.9 |
Jackhmmer Results: (2016_04)
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: 22.121).
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 |
| 229_H | 304_Y | 3.709 | 1.00 |
| 32_I | 36_W | 3.503 | 1.00 |
| 16_L | 20_T | 3.181 | 1.00 |
| 173_R | 194_D | 2.950 | 1.00 |
| 170_K | 248_E | 2.764 | 1.00 |
| 204_R | 248_E | 2.508 | 1.00 |
| 30_K | 41_Q | 2.489 | 1.00 |
| 60_F | 64_K | 2.443 | 1.00 |
| 74_F | 77_I | 2.439 | 1.00 |
| 270_L | 273_L | 2.413 | 1.00 |
| 77_I | 80_F | 2.361 | 1.00 |
| 59_E | 62_L | 2.330 | 1.00 |
| 140_L | 171_V | 2.309 | 1.00 |
| 61_I | 64_K | 2.254 | 1.00 |
| 95_M | 98_S | 2.238 | 1.00 |
| 33_S | 36_W | 2.229 | 1.00 |
| 60_F | 63_F | 2.196 | 1.00 |
| 120_A | 127_T | 2.185 | 1.00 |
| 79_S | 82_S | 2.165 | 1.00 |
| 244_D | 247_T | 2.158 | 1.00 |
| 297_H | 312_M | 2.123 | 1.00 |
| 143_S | 194_D | 2.092 | 1.00 |
| 75_I | 78_L | 2.085 | 1.00 |
| 25_S | 29_F | 2.078 | 1.00 |
| 346_D | 349_S | 2.072 | 1.00 |
| 138_R | 201_D | 2.002 | 1.00 |
| 118_L | 129_V | 1.997 | 1.00 |
| 243_F | 248_E | 1.918 | 1.00 |
| 61_I | 65_R | 1.917 | 1.00 |
| 227_M | 242_C | 1.906 | 1.00 |
| 78_L | 81_F | 1.904 | 1.00 |
| 276_S | 302_M | 1.890 | 1.00 |
| 242_C | 251_H | 1.806 | 1.00 |
| 131_N | 134_T | 1.803 | 1.00 |
| 62_L | 65_R | 1.759 | 1.00 |
| 18_L | 32_I | 1.758 | 1.00 |
| 76_N | 79_S | 1.756 | 1.00 |
| 271_V | 278_T | 1.753 | 1.00 |
| 22_P | 25_S | 1.752 | 1.00 |
| 168_Y | 199_S | 1.724 | 1.00 |
| 59_E | 64_K | 1.710 | 1.00 |
| 80_F | 83_G | 1.690 | 1.00 |
| 77_I | 81_F | 1.688 | 1.00 |
| 223_L | 228_V | 1.666 | 1.00 |
| 273_L | 278_T | 1.636 | 1.00 |
| 162_L | 167_N | 1.563 | 1.00 |
| 47_N | 51_N | 1.559 | 1.00 |
| 93_P | 96_D | 1.557 | 1.00 |
| 59_E | 63_F | 1.547 | 1.00 |
| 312_M | 315_T | 1.545 | 1.00 |
| 78_L | 82_S | 1.543 | 1.00 |
| 19_L | 52_R | 1.534 | 1.00 |
| 74_F | 78_L | 1.518 | 1.00 |
| 14_V | 18_L | 1.500 | 1.00 |
| 325_L | 328_W | 1.493 | 1.00 |
| 270_L | 274_C | 1.491 | 1.00 |
| 30_K | 40_I | 1.460 | 1.00 |
| 242_C | 253_M | 1.457 | 1.00 |
| 19_L | 48_R | 1.442 | 1.00 |
| 46_I | 49_H | 1.442 | 1.00 |
| 45_F | 49_H | 1.442 | 1.00 |
| 60_F | 65_R | 1.429 | 1.00 |
| 97_V | 100_M | 1.423 | 1.00 |
| 295_K | 315_T | 1.418 | 1.00 |
| 196_C | 203_W | 1.409 | 1.00 |
| 28_R | 31_C | 1.407 | 0.99 |
| 74_F | 80_F | 1.407 | 0.99 |
| 243_F | 250_F | 1.404 | 0.99 |
| 48_R | 52_R | 1.393 | 0.99 |
| 302_M | 311_I | 1.388 | 0.99 |
| 159_G | 228_V | 1.386 | 0.99 |
| 11_E | 35_A | 1.381 | 0.99 |
| 49_H | 53_K | 1.379 | 0.99 |
| 161_G | 245_M | 1.378 | 0.99 |
| 168_Y | 197_D | 1.375 | 0.99 |
| 331_H | 334_L | 1.372 | 0.99 |
| 332_I | 346_D | 1.371 | 0.99 |
| 272_I | 275_E | 1.369 | 0.99 |
| 228_V | 245_M | 1.364 | 0.99 |
| 81_F | 84_H | 1.361 | 0.99 |
| 23_V | 49_H | 1.355 | 0.99 |
| 116_D | 162_L | 1.344 | 0.99 |
| 27_M | 30_K | 1.335 | 0.99 |
| 96_D | 99_Y | 1.325 | 0.99 |
| 30_K | 37_S | 1.320 | 0.99 |
| 129_V | 198_L | 1.320 | 0.99 |
| 114_P | 119_I | 1.319 | 0.99 |
| 12_D | 15_F | 1.318 | 0.99 |
| 15_F | 44_T | 1.309 | 0.99 |
| 120_A | 171_V | 1.306 | 0.99 |
| 26_L | 40_I | 1.306 | 0.99 |
| 77_I | 83_G | 1.304 | 0.99 |
| 72_E | 78_L | 1.294 | 0.99 |
| 223_L | 226_E | 1.287 | 0.99 |
| 230_W | 250_F | 1.281 | 0.99 |
| 59_E | 65_R | 1.278 | 0.99 |
| 324_P | 328_W | 1.276 | 0.99 |
| 15_F | 19_L | 1.269 | 0.99 |
| 256_P | 310_W | 1.267 | 0.99 |
| 94_D | 98_S | 1.262 | 0.99 |
| 206_L | 243_F | 1.258 | 0.99 |
| 197_D | 200_T | 1.256 | 0.99 |
| 47_N | 167_N | 1.253 | 0.99 |
| 302_M | 313_K | 1.252 | 0.99 |
| 239_V | 252_D | 1.243 | 0.98 |
| 20_T | 52_R | 1.232 | 0.98 |
| 170_K | 195_V | 1.232 | 0.98 |
| 224_Y | 272_I | 1.225 | 0.98 |
| 58_D | 61_I | 1.223 | 0.98 |
| 232_A | 239_V | 1.203 | 0.98 |
| 15_F | 48_R | 1.201 | 0.98 |
| 159_G | 162_L | 1.199 | 0.98 |
| 76_N | 80_F | 1.197 | 0.98 |
| 95_M | 100_M | 1.192 | 0.98 |
| 37_S | 41_Q | 1.190 | 0.98 |
| 332_I | 335_L | 1.187 | 0.98 |
| 299_W | 312_M | 1.187 | 0.98 |
| 276_S | 300_V | 1.184 | 0.98 |
| 332_I | 353_K | 1.182 | 0.98 |
| 256_P | 299_W | 1.177 | 0.98 |
| 73_E | 76_N | 1.170 | 0.97 |
| 329_K | 332_I | 1.165 | 0.97 |
| 197_D | 204_R | 1.161 | 0.97 |
| 130_L | 137_F | 1.160 | 0.97 |
| 29_F | 33_S | 1.160 | 0.97 |
| 74_F | 79_S | 1.159 | 0.97 |
| 193_I | 250_F | 1.158 | 0.97 |
| 172_V | 243_F | 1.157 | 0.97 |
| 225_K | 229_H | 1.147 | 0.97 |
| 161_G | 164_T | 1.144 | 0.97 |
| 50_I | 53_K | 1.143 | 0.97 |
| 96_D | 100_M | 1.139 | 0.97 |
| 40_I | 45_F | 1.139 | 0.97 |
| 18_L | 26_L | 1.137 | 0.97 |
| 368_V | 371_E | 1.131 | 0.97 |
| 332_I | 348_N | 1.130 | 0.97 |
| 159_G | 230_W | 1.130 | 0.97 |
| 163_D | 223_L | 1.129 | 0.97 |
| 192_K | 205_E | 1.128 | 0.97 |
| 174_I | 193_I | 1.127 | 0.97 |
| 9_L | 14_V | 1.115 | 0.96 |
| 196_C | 201_D | 1.115 | 0.96 |
| 73_E | 79_S | 1.111 | 0.96 |
| 15_F | 39_L | 1.109 | 0.96 |
| 117_G | 132_P | 1.106 | 0.96 |
| 281_G | 297_H | 1.106 | 0.96 |
| 94_D | 100_M | 1.103 | 0.96 |
| 194_D | 205_E | 1.098 | 0.96 |
| 95_M | 99_Y | 1.094 | 0.96 |
| 128_I | 139_V | 1.091 | 0.96 |
| 87_V | 91_L | 1.088 | 0.96 |
| 333_L | 336_Q | 1.088 | 0.96 |
| 90_P | 93_P | 1.084 | 0.96 |
| 324_P | 327_V | 1.081 | 0.95 |
| 301_M | 304_Y | 1.077 | 0.95 |
| 92_F | 97_V | 1.077 | 0.95 |
| 341_L | 354_E | 1.076 | 0.95 |
| 133_A | 371_E | 1.075 | 0.95 |
| 13_L | 16_L | 1.074 | 0.95 |
| 89_N | 92_F | 1.071 | 0.95 |
| 79_S | 83_G | 1.071 | 0.95 |
| 165_I | 168_Y | 1.069 | 0.95 |
| 331_H | 346_D | 1.063 | 0.95 |
| 92_F | 95_M | 1.057 | 0.95 |
| 278_T | 300_V | 1.054 | 0.95 |
| 83_G | 86_D | 1.053 | 0.95 |
| 221_G | 228_V | 1.051 | 0.94 |
| 343_I | 354_E | 1.051 | 0.94 |
| 367_K | 370_K | 1.046 | 0.94 |
| 179_C | 186_P | 1.042 | 0.94 |
| 271_V | 274_C | 1.040 | 0.94 |
| 304_Y | 308_E | 1.039 | 0.94 |
| 344_S | 355_L | 1.039 | 0.94 |
| 73_E | 77_I | 1.031 | 0.94 |
| 336_Q | 339_S | 1.028 | 0.94 |
| 198_L | 203_W | 1.027 | 0.94 |
| 169_Y | 198_L | 1.018 | 0.93 |
| 77_I | 82_S | 1.016 | 0.93 |
| 269_G | 273_L | 1.015 | 0.93 |
| 297_H | 315_T | 1.013 | 0.93 |
| 46_I | 50_I | 1.010 | 0.93 |
| 328_W | 334_L | 1.009 | 0.93 |
| 328_W | 332_I | 1.007 | 0.93 |
| 112_I | 120_A | 1.005 | 0.93 |
| 94_D | 97_V | 1.002 | 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 | |
| 4yy8A | 2 | 0.8252 | 99.5 | 0.793 | Contact Map |
| 3ii7A | 1 | 0.6915 | 99.2 | 0.824 | Contact Map |
| 4chbA | 2 | 0.6864 | 99.2 | 0.827 | Contact Map |
| 1zgkA | 1 | 0.6889 | 99.1 | 0.829 | Contact Map |
| 2wozA | 1 | 0.7352 | 99.1 | 0.831 | Contact Map |
| 2vpjA | 1 | 0.6889 | 99 | 0.84 | Contact Map |
| 2uvkA | 2 | 0.6838 | 99 | 0.841 | Contact Map |
| 2ovrB | 1 | 0.838 | 98.8 | 0.848 | Contact Map |
| 3v7dB | 2 | 0.8509 | 98.8 | 0.849 | Contact Map |
| 3wsoA | 1 | 0.4936 | 98.8 | 0.85 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)