| MC1T |
| ID: | 1481096325 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 358 (347) | ||
| Sequences: | 350 (216.5) | ||
| Seq/Len: | 1.009 | ||
| Nf(neff/√len): | 11.6 |
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: 1.009).
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 |
| 271_F | 276_S | 2.067 | 0.96 |
| 68_E | 74_R | 1.497 | 0.77 |
| 23_E | 38_L | 1.445 | 0.73 |
| 25_E | 35_R | 1.438 | 0.73 |
| 31_K | 35_R | 1.434 | 0.72 |
| 34_R | 37_S | 1.432 | 0.72 |
| 25_E | 30_D | 1.413 | 0.71 |
| 25_E | 28_V | 1.401 | 0.70 |
| 250_A | 273_L | 1.397 | 0.69 |
| 32_L | 37_S | 1.393 | 0.69 |
| 26_E | 37_S | 1.385 | 0.69 |
| 30_D | 33_P | 1.373 | 0.68 |
| 25_E | 37_S | 1.362 | 0.67 |
| 72_R | 78_G | 1.347 | 0.65 |
| 25_E | 31_K | 1.343 | 0.65 |
| 27_E | 30_D | 1.343 | 0.65 |
| 14_E | 17_T | 1.337 | 0.65 |
| 22_S | 25_E | 1.333 | 0.64 |
| 23_E | 26_E | 1.329 | 0.64 |
| 22_S | 36_E | 1.316 | 0.63 |
| 38_L | 42_R | 1.305 | 0.62 |
| 23_E | 27_E | 1.298 | 0.61 |
| 30_D | 37_S | 1.291 | 0.61 |
| 34_R | 39_R | 1.275 | 0.59 |
| 16_E | 20_S | 1.275 | 0.59 |
| 32_L | 35_R | 1.269 | 0.59 |
| 41_K | 46_R | 1.263 | 0.58 |
| 23_E | 31_K | 1.260 | 0.58 |
| 250_A | 256_F | 1.257 | 0.57 |
| 30_D | 35_R | 1.256 | 0.57 |
| 39_R | 42_R | 1.249 | 0.57 |
| 24_E | 33_P | 1.249 | 0.57 |
| 31_K | 37_S | 1.248 | 0.57 |
| 116_K | 177_I | 1.247 | 0.57 |
| 35_R | 38_L | 1.247 | 0.57 |
| 15_D | 18_E | 1.245 | 0.56 |
| 26_E | 29_E | 1.244 | 0.56 |
| 22_S | 33_P | 1.241 | 0.56 |
| 23_E | 37_S | 1.230 | 0.55 |
| 51_E | 56_P | 1.226 | 0.55 |
| 30_D | 34_R | 1.224 | 0.54 |
| 28_V | 37_S | 1.222 | 0.54 |
| 21_S | 25_E | 1.222 | 0.54 |
| 28_V | 31_K | 1.221 | 0.54 |
| 25_E | 33_P | 1.221 | 0.54 |
| 27_E | 34_R | 1.208 | 0.53 |
| 49_I | 52_D | 1.205 | 0.53 |
| 24_E | 27_E | 1.202 | 0.52 |
| 23_E | 28_V | 1.194 | 0.52 |
| 30_D | 40_P | 1.192 | 0.51 |
| 63_T | 66_A | 1.189 | 0.51 |
| 19_E | 22_S | 1.188 | 0.51 |
| 24_E | 28_V | 1.188 | 0.51 |
| 17_T | 22_S | 1.185 | 0.51 |
| 13_K | 26_E | 1.180 | 0.50 |
| 24_E | 30_D | 1.176 | 0.50 |
| 28_V | 33_P | 1.174 | 0.50 |
| 52_D | 55_E | 1.172 | 0.50 |
| 28_V | 34_R | 1.172 | 0.50 |
| 206_T | 284_C | 1.171 | 0.50 |
| 59_E | 64_R | 1.164 | 0.49 |
| 33_P | 37_S | 1.164 | 0.49 |
| 21_S | 37_S | 1.158 | 0.48 |
| 20_S | 26_E | 1.155 | 0.48 |
| 34_R | 41_K | 1.155 | 0.48 |
| 28_V | 32_L | 1.154 | 0.48 |
| 24_E | 37_S | 1.154 | 0.48 |
| 40_P | 45_T | 1.152 | 0.48 |
| 51_E | 57_E | 1.152 | 0.48 |
| 25_E | 38_L | 1.147 | 0.47 |
| 40_P | 43_K | 1.146 | 0.47 |
| 51_E | 54_P | 1.142 | 0.47 |
| 15_D | 20_S | 1.142 | 0.47 |
| 44_R | 53_D | 1.137 | 0.46 |
| 70_E | 76_K | 1.134 | 0.46 |
| 48_V | 51_E | 1.133 | 0.46 |
| 28_V | 35_R | 1.131 | 0.46 |
| 25_E | 29_E | 1.131 | 0.46 |
| 45_T | 50_N | 1.129 | 0.46 |
| 211_M | 285_I | 1.129 | 0.46 |
| 26_E | 31_K | 1.125 | 0.45 |
| 24_E | 31_K | 1.124 | 0.45 |
| 48_V | 52_D | 1.124 | 0.45 |
| 26_E | 30_D | 1.122 | 0.45 |
| 61_E | 65_K | 1.121 | 0.45 |
| 27_E | 40_P | 1.121 | 0.45 |
| 69_K | 73_R | 1.118 | 0.45 |
| 35_R | 39_R | 1.117 | 0.45 |
| 34_R | 52_D | 1.116 | 0.44 |
| 187_S | 348_E | 1.115 | 0.44 |
| 203_F | 207_F | 1.115 | 0.44 |
| 21_S | 24_E | 1.115 | 0.44 |
| 69_K | 75_L | 1.113 | 0.44 |
| 24_E | 41_K | 1.113 | 0.44 |
| 13_K | 17_T | 1.112 | 0.44 |
| 30_D | 39_R | 1.111 | 0.44 |
| 24_E | 35_R | 1.110 | 0.44 |
| 32_L | 40_P | 1.108 | 0.44 |
| 42_R | 45_T | 1.106 | 0.44 |
| 22_S | 30_D | 1.106 | 0.44 |
| 14_E | 38_L | 1.104 | 0.43 |
| 27_E | 31_K | 1.104 | 0.43 |
| 22_S | 26_E | 1.103 | 0.43 |
| 37_S | 40_P | 1.102 | 0.43 |
| 116_K | 278_F | 1.099 | 0.43 |
| 16_E | 22_S | 1.098 | 0.43 |
| 20_S | 27_E | 1.097 | 0.43 |
| 42_R | 47_D | 1.093 | 0.42 |
| 13_K | 23_E | 1.092 | 0.42 |
| 29_E | 34_R | 1.091 | 0.42 |
| 14_E | 37_S | 1.091 | 0.42 |
| 17_T | 41_K | 1.087 | 0.42 |
| 17_T | 26_E | 1.084 | 0.42 |
| 40_P | 46_R | 1.084 | 0.42 |
| 71_R | 77_R | 1.081 | 0.41 |
| 17_T | 37_S | 1.081 | 0.41 |
| 54_P | 57_E | 1.078 | 0.41 |
| 25_E | 36_E | 1.075 | 0.41 |
| 21_S | 28_V | 1.074 | 0.41 |
| 28_V | 40_P | 1.073 | 0.41 |
| 13_K | 25_E | 1.071 | 0.40 |
| 26_E | 57_E | 1.070 | 0.40 |
| 20_S | 31_K | 1.069 | 0.40 |
| 30_D | 42_R | 1.067 | 0.40 |
| 18_E | 26_E | 1.067 | 0.40 |
| 29_E | 33_P | 1.063 | 0.40 |
| 23_E | 29_E | 1.061 | 0.39 |
| 20_S | 28_V | 1.060 | 0.39 |
| 41_K | 48_V | 1.060 | 0.39 |
| 40_P | 47_D | 1.059 | 0.39 |
| 21_S | 27_E | 1.058 | 0.39 |
| 16_E | 38_L | 1.057 | 0.39 |
| 27_E | 41_K | 1.055 | 0.39 |
| 22_S | 32_L | 1.053 | 0.39 |
| 24_E | 40_P | 1.052 | 0.39 |
| 21_S | 29_E | 1.051 | 0.39 |
| 35_R | 48_V | 1.050 | 0.38 |
| 26_E | 51_E | 1.049 | 0.38 |
| 56_P | 62_E | 1.049 | 0.38 |
| 25_E | 49_I | 1.048 | 0.38 |
| 20_S | 25_E | 1.048 | 0.38 |
| 14_E | 24_E | 1.046 | 0.38 |
| 16_E | 33_P | 1.045 | 0.38 |
| 18_E | 27_E | 1.044 | 0.38 |
| 57_E | 60_D | 1.041 | 0.38 |
| 19_E | 34_R | 1.041 | 0.38 |
| 40_P | 52_D | 1.041 | 0.38 |
| 156_F | 207_F | 1.041 | 0.38 |
| 34_R | 43_K | 1.040 | 0.38 |
| 18_E | 32_L | 1.040 | 0.38 |
| 38_L | 41_K | 1.037 | 0.37 |
| 47_D | 50_N | 1.036 | 0.37 |
| 29_E | 45_T | 1.034 | 0.37 |
| 24_E | 32_L | 1.032 | 0.37 |
| 31_K | 40_P | 1.032 | 0.37 |
| 33_P | 38_L | 1.032 | 0.37 |
| 39_R | 43_K | 1.031 | 0.37 |
| 18_E | 28_V | 1.030 | 0.37 |
| 29_E | 38_L | 1.030 | 0.37 |
| 30_D | 41_K | 1.030 | 0.37 |
| 52_D | 56_P | 1.029 | 0.37 |
| 30_D | 36_E | 1.028 | 0.37 |
| 25_E | 32_L | 1.028 | 0.37 |
| 46_R | 54_P | 1.025 | 0.36 |
| 22_S | 38_L | 1.024 | 0.36 |
| 26_E | 33_P | 1.024 | 0.36 |
| 22_S | 37_S | 1.024 | 0.36 |
| 30_D | 38_L | 1.022 | 0.36 |
| 37_S | 43_K | 1.021 | 0.36 |
| 19_E | 31_K | 1.021 | 0.36 |
| 43_K | 50_N | 1.020 | 0.36 |
| 42_R | 46_R | 1.020 | 0.36 |
| 17_T | 30_D | 1.019 | 0.36 |
| 20_S | 34_R | 1.019 | 0.36 |
| 26_E | 34_R | 1.018 | 0.36 |
| 14_E | 33_P | 1.016 | 0.36 |
| 206_T | 254_V | 1.016 | 0.36 |
| 22_S | 28_V | 1.015 | 0.35 |
| 25_E | 34_R | 1.015 | 0.35 |
| 17_T | 21_S | 1.015 | 0.35 |
| 44_R | 49_I | 1.014 | 0.35 |
| 20_S | 35_R | 1.012 | 0.35 |
| 36_E | 41_K | 1.012 | 0.35 |
| 23_E | 32_L | 1.011 | 0.35 |
| 15_D | 41_K | 1.010 | 0.35 |
| 13_K | 16_E | 1.009 | 0.35 |
| 53_D | 57_E | 1.009 | 0.35 |
| 297_T | 327_N | 1.008 | 0.35 |
| 17_T | 27_E | 1.008 | 0.35 |
| 37_S | 42_R | 1.007 | 0.35 |
| 41_K | 50_N | 1.006 | 0.35 |
| 20_S | 29_E | 1.006 | 0.35 |
| 34_R | 42_R | 1.006 | 0.35 |
| 19_E | 23_E | 1.005 | 0.35 |
| 28_V | 38_L | 1.005 | 0.35 |
| 14_E | 27_E | 1.003 | 0.34 |
| 15_D | 19_E | 1.003 | 0.34 |
| 200_M | 264_R | 1.001 | 0.34 |
| 27_E | 47_D | 1.001 | 0.34 |
| 23_E | 35_R | 1.000 | 0.34 |
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 | |
| 4cbcA | 4 | 0.2486 | 50.6 | 0.967 | Contact Map |
| 4ltoA | 4 | 0.3715 | 33.1 | 0.97 | Contact Map |
| 3wu2M | 2 | 0.0922 | 31.1 | 0.971 | Contact Map |
| 4uerb | 1 | 0.0112 | 16 | 0.975 | Contact Map |
| 4noxA | 1 | 0.0112 | 8.8 | 0.977 | Contact Map |
| 1lnqA | 8 | 0.3156 | 7 | 0.978 | Contact Map |
| 1so2A | 4 | 0.0838 | 6.3 | 0.979 | Contact Map |
| 4dkwA | 4 | 0.176 | 4.8 | 0.98 | Contact Map |
| 4gyiA | 1 | 0.0279 | 4.6 | 0.98 | Contact Map |
| 4x5mA | 3 | 0.2458 | 3.9 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)