| Kox_competence |
| ID: | 1485868578 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 314 (298) | ||
| Sequences: | 2249 (1686.9) | ||
| Seq/Len: | 7.547 | ||
| Nf(neff/√len): | 97.7 |
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: 7.547).
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 |
| 132_I | 152_A | 3.767 | 1.00 |
| 93_A | 106_C | 2.873 | 1.00 |
| 47_A | 101_P | 2.871 | 1.00 |
| 60_G | 88_S | 2.728 | 1.00 |
| 158_L | 185_L | 2.653 | 1.00 |
| 86_L | 110_A | 2.496 | 1.00 |
| 37_M | 253_L | 2.466 | 1.00 |
| 18_M | 249_A | 2.413 | 1.00 |
| 149_W | 200_L | 2.370 | 1.00 |
| 103_L | 135_I | 2.322 | 1.00 |
| 35_S | 39_E | 2.312 | 1.00 |
| 90_I | 110_A | 2.261 | 1.00 |
| 14_W | 250_D | 2.257 | 1.00 |
| 135_I | 142_A | 2.188 | 1.00 |
| 93_A | 102_A | 2.105 | 1.00 |
| 40_T | 259_L | 2.059 | 1.00 |
| 131_C | 152_A | 2.036 | 1.00 |
| 146_E | 200_L | 2.034 | 1.00 |
| 136_L | 142_A | 2.027 | 1.00 |
| 37_M | 46_M | 2.004 | 1.00 |
| 99_Q | 102_A | 2.003 | 1.00 |
| 101_P | 147_S | 1.989 | 1.00 |
| 218_L | 251_R | 1.985 | 1.00 |
| 64_L | 84_M | 1.900 | 1.00 |
| 124_P | 159_I | 1.895 | 1.00 |
| 89_A | 106_C | 1.868 | 1.00 |
| 36_L | 257_F | 1.854 | 1.00 |
| 128_W | 156_A | 1.810 | 1.00 |
| 48_I | 102_A | 1.742 | 1.00 |
| 51_L | 54_A | 1.733 | 1.00 |
| 13_P | 30_P | 1.709 | 1.00 |
| 254_A | 258_W | 1.688 | 1.00 |
| 132_I | 148_L | 1.674 | 1.00 |
| 250_D | 254_A | 1.673 | 1.00 |
| 125_W | 160_F | 1.663 | 1.00 |
| 43_S | 47_A | 1.660 | 1.00 |
| 11_A | 15_Q | 1.648 | 1.00 |
| 251_R | 255_I | 1.629 | 1.00 |
| 34_K | 43_S | 1.614 | 1.00 |
| 90_I | 106_C | 1.591 | 1.00 |
| 157_A | 192_L | 1.573 | 1.00 |
| 93_A | 98_M | 1.565 | 1.00 |
| 42_I | 215_A | 1.559 | 1.00 |
| 26_R | 47_A | 1.556 | 1.00 |
| 91_F | 95_L | 1.541 | 1.00 |
| 127_L | 131_C | 1.528 | 1.00 |
| 107_V | 131_C | 1.498 | 0.99 |
| 153_F | 196_L | 1.479 | 0.99 |
| 39_E | 260_L | 1.470 | 0.99 |
| 108_A | 131_C | 1.460 | 0.99 |
| 34_K | 38_Q | 1.442 | 0.99 |
| 42_I | 256_L | 1.433 | 0.99 |
| 149_W | 196_L | 1.426 | 0.99 |
| 211_A | 259_L | 1.407 | 0.99 |
| 258_W | 262_Q | 1.405 | 0.99 |
| 94_G | 98_M | 1.402 | 0.99 |
| 53_I | 89_A | 1.402 | 0.99 |
| 166_P | 181_A | 1.375 | 0.99 |
| 13_P | 33_I | 1.368 | 0.99 |
| 214_I | 217_P | 1.360 | 0.99 |
| 14_W | 246_W | 1.350 | 0.99 |
| 47_A | 105_T | 1.341 | 0.98 |
| 21_L | 219_V | 1.337 | 0.98 |
| 52_H | 220_T | 1.337 | 0.98 |
| 240_I | 244_A | 1.332 | 0.98 |
| 92_Y | 201_F | 1.320 | 0.98 |
| 166_P | 177_R | 1.318 | 0.98 |
| 51_L | 216_V | 1.317 | 0.98 |
| 30_P | 33_I | 1.308 | 0.98 |
| 47_A | 99_Q | 1.303 | 0.98 |
| 58_S | 61_W | 1.295 | 0.98 |
| 100_P | 145_S | 1.294 | 0.98 |
| 189_L | 193_L | 1.292 | 0.98 |
| 157_A | 189_L | 1.285 | 0.98 |
| 156_A | 160_F | 1.281 | 0.98 |
| 45_L | 215_A | 1.252 | 0.97 |
| 48_I | 53_I | 1.247 | 0.97 |
| 207_T | 262_Q | 1.246 | 0.97 |
| 41_G | 208_S | 1.240 | 0.97 |
| 33_I | 253_L | 1.235 | 0.97 |
| 162_Y | 185_L | 1.208 | 0.97 |
| 218_L | 248_S | 1.204 | 0.96 |
| 221_F | 225_P | 1.203 | 0.96 |
| 33_I | 37_M | 1.197 | 0.96 |
| 56_G | 60_G | 1.196 | 0.96 |
| 4_S | 8_T | 1.195 | 0.96 |
| 154_A | 193_L | 1.187 | 0.96 |
| 13_P | 16_S | 1.187 | 0.96 |
| 286_I | 295_T | 1.186 | 0.96 |
| 52_H | 223_V | 1.181 | 0.96 |
| 275_L | 278_S | 1.178 | 0.96 |
| 126_Q | 130_C | 1.169 | 0.96 |
| 153_F | 200_L | 1.164 | 0.95 |
| 62_L | 66_G | 1.164 | 0.95 |
| 26_R | 48_I | 1.164 | 0.95 |
| 52_H | 99_Q | 1.154 | 0.95 |
| 165_A | 184_H | 1.151 | 0.95 |
| 216_V | 220_T | 1.146 | 0.95 |
| 162_Y | 184_H | 1.144 | 0.95 |
| 182_L | 216_V | 1.142 | 0.95 |
| 35_S | 38_Q | 1.137 | 0.95 |
| 31_R | 35_S | 1.137 | 0.95 |
| 4_S | 7_H | 1.130 | 0.94 |
| 194_A | 198_I | 1.128 | 0.94 |
| 48_I | 96_T | 1.121 | 0.94 |
| 260_L | 263_L | 1.112 | 0.94 |
| 96_T | 102_A | 1.111 | 0.94 |
| 179_S | 183_C | 1.107 | 0.94 |
| 193_L | 197_Q | 1.105 | 0.93 |
| 182_L | 213_F | 1.101 | 0.93 |
| 96_T | 99_Q | 1.097 | 0.93 |
| 161_W | 188_G | 1.094 | 0.93 |
| 58_S | 62_L | 1.093 | 0.93 |
| 219_V | 252_I | 1.089 | 0.93 |
| 207_T | 263_L | 1.085 | 0.93 |
| 45_L | 219_V | 1.083 | 0.93 |
| 32_E | 36_L | 1.081 | 0.92 |
| 161_W | 192_L | 1.079 | 0.92 |
| 244_A | 247_Q | 1.066 | 0.92 |
| 79_R | 119_G | 1.064 | 0.92 |
| 45_L | 216_V | 1.062 | 0.92 |
| 278_S | 286_I | 1.060 | 0.92 |
| 26_R | 105_T | 1.059 | 0.91 |
| 125_W | 156_A | 1.056 | 0.91 |
| 65_R | 81_P | 1.049 | 0.91 |
| 114_A | 118_S | 1.043 | 0.91 |
| 207_T | 264_P | 1.040 | 0.90 |
| 53_I | 198_I | 1.038 | 0.90 |
| 222_V | 248_S | 1.037 | 0.90 |
| 122_W | 127_L | 1.037 | 0.90 |
| 23_M | 96_T | 1.029 | 0.90 |
| 34_K | 47_A | 1.024 | 0.90 |
| 251_R | 254_A | 1.012 | 0.89 |
| 129_V | 133_G | 1.012 | 0.89 |
| 184_H | 188_G | 1.008 | 0.89 |
| 17_V | 52_H | 1.004 | 0.88 |
| 59_L | 155_V | 1.003 | 0.88 |
| 115_L | 118_S | 1.003 | 0.88 |
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 | |
| 4u2pA | 4 | 0.2038 | 4.9 | 0.966 | Contact Map |
| 3r1xA | 4 | 0.2102 | 3.8 | 0.968 | Contact Map |
| 2ra6A | 4 | 0.1911 | 3.6 | 0.969 | Contact Map |
| 4orrA | 1 | 0.1975 | 2.4 | 0.971 | Contact Map |
| 1ow1A | 1 | 0.2229 | 2.4 | 0.971 | Contact Map |
| 1fadA | 1 | 0.1242 | 2.3 | 0.971 | Contact Map |
| 1t3oA | 1 | 0.1019 | 1.9 | 0.973 | Contact Map |
| 3oq9A | 5 | 0.1242 | 1.7 | 0.973 | Contact Map |
| 1hw1A | 2 | 0.1624 | 1.7 | 0.973 | Contact Map |
| 1httA | 4 | 0.1911 | 1.7 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)