| mad2 |
| ID: | 1417716929 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 205 (200) | ||
| Sequences: | 653 (501.4) | ||
| Seq/Len: | 3.265 | ||
| Nf(neff/√len): | 35.5 |
Jackhmmer Results: (2014_04_16)
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: 3.265).
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 |
| 76_L | 104_I | 2.485 | 1.00 |
| 35_R | 98_E | 2.255 | 1.00 |
| 35_R | 142_L | 2.245 | 1.00 |
| 32_L | 43_F | 1.930 | 1.00 |
| 29_N | 56_T | 1.791 | 0.99 |
| 56_T | 62_I | 1.768 | 0.99 |
| 74_D | 78_K | 1.759 | 0.99 |
| 52_T | 170_S | 1.717 | 0.99 |
| 61_L | 64_Y | 1.691 | 0.99 |
| 72_L | 81_V | 1.665 | 0.98 |
| 32_L | 38_Y | 1.613 | 0.98 |
| 167_W | 170_S | 1.612 | 0.98 |
| 128_I | 134_Q | 1.602 | 0.98 |
| 107_D | 110_A | 1.576 | 0.97 |
| 38_Y | 153_L | 1.545 | 0.97 |
| 98_E | 102_F | 1.545 | 0.97 |
| 59_L | 64_Y | 1.515 | 0.97 |
| 31_I | 88_I | 1.465 | 0.96 |
| 124_I | 131_V | 1.444 | 0.95 |
| 72_L | 194_N | 1.439 | 0.95 |
| 111_K | 117_R | 1.433 | 0.95 |
| 145_L | 164_P | 1.432 | 0.95 |
| 68_V | 81_V | 1.431 | 0.95 |
| 5_L | 8_E | 1.372 | 0.93 |
| 28_I | 86_V | 1.369 | 0.93 |
| 27_G | 102_F | 1.360 | 0.93 |
| 100_W | 139_V | 1.340 | 0.92 |
| 119_K | 127_E | 1.333 | 0.92 |
| 56_T | 155_I | 1.302 | 0.91 |
| 75_W | 157_T | 1.298 | 0.90 |
| 29_N | 38_Y | 1.295 | 0.90 |
| 100_W | 138_T | 1.292 | 0.90 |
| 38_Y | 43_F | 1.287 | 0.90 |
| 38_Y | 151_F | 1.284 | 0.90 |
| 158_D | 162_V | 1.278 | 0.89 |
| 22_E | 49_Y | 1.260 | 0.89 |
| 35_R | 102_F | 1.260 | 0.89 |
| 38_Y | 64_Y | 1.238 | 0.87 |
| 33_Y | 78_K | 1.235 | 0.87 |
| 4_Q | 7_R | 1.233 | 0.87 |
| 96_V | 100_W | 1.227 | 0.87 |
| 37_I | 132_I | 1.224 | 0.87 |
| 131_V | 139_V | 1.207 | 0.85 |
| 20_V | 155_I | 1.204 | 0.85 |
| 68_V | 153_L | 1.201 | 0.85 |
| 17_A | 155_I | 1.198 | 0.85 |
| 37_I | 149_C | 1.198 | 0.85 |
| 81_V | 86_V | 1.196 | 0.85 |
| 23_F | 181_V | 1.193 | 0.85 |
| 22_E | 29_N | 1.175 | 0.83 |
| 47_Q | 50_G | 1.173 | 0.83 |
| 38_Y | 56_T | 1.170 | 0.83 |
| 143_P | 199_Y | 1.161 | 0.82 |
| 15_G | 34_Q | 1.160 | 0.82 |
| 16_S | 191_H | 1.157 | 0.82 |
| 98_E | 142_L | 1.157 | 0.82 |
| 134_Q | 138_T | 1.153 | 0.82 |
| 108_K | 113_D | 1.147 | 0.81 |
| 97_L | 145_L | 1.129 | 0.80 |
| 106_C | 164_P | 1.128 | 0.80 |
| 63_K | 67_N | 1.115 | 0.79 |
| 71_Q | 75_W | 1.115 | 0.79 |
| 27_G | 131_V | 1.111 | 0.78 |
| 174_F | 177_N | 1.108 | 0.78 |
| 136_T | 184_R | 1.108 | 0.78 |
| 21_A | 73_K | 1.104 | 0.78 |
| 30_S | 40_S | 1.098 | 0.77 |
| 120_S | 123_A | 1.098 | 0.77 |
| 5_L | 9_Q | 1.096 | 0.77 |
| 111_K | 114_S | 1.093 | 0.77 |
| 21_A | 153_L | 1.093 | 0.77 |
| 75_W | 191_H | 1.083 | 0.76 |
| 20_V | 191_H | 1.081 | 0.76 |
| 15_G | 71_Q | 1.077 | 0.75 |
| 110_A | 114_S | 1.073 | 0.75 |
| 27_G | 147_V | 1.073 | 0.75 |
| 183_L | 186_F | 1.070 | 0.75 |
| 199_Y | 203_V | 1.069 | 0.74 |
| 45_R | 54_L | 1.069 | 0.74 |
| 19_I | 22_E | 1.062 | 0.74 |
| 137_A | 141_F | 1.053 | 0.73 |
| 160_D | 163_V | 1.052 | 0.73 |
| 134_Q | 139_V | 1.044 | 0.72 |
| 76_L | 157_T | 1.042 | 0.72 |
| 88_I | 142_L | 1.042 | 0.72 |
| 4_Q | 9_Q | 1.038 | 0.71 |
| 98_E | 145_L | 1.025 | 0.70 |
| 16_S | 133_R | 1.021 | 0.70 |
| 111_K | 159_K | 1.021 | 0.70 |
| 61_L | 65_L | 1.020 | 0.69 |
| 32_L | 37_I | 1.020 | 0.69 |
| 12_T | 74_D | 1.018 | 0.69 |
| 22_E | 48_K | 1.010 | 0.68 |
| 187_T | 199_Y | 1.006 | 0.68 |
| 26_F | 128_I | 1.003 | 0.68 |
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 | |
| 2vfxA | 12 | 1 | 100 | 0.105 | Contact Map |
| 4aezB | 3 | 0.9268 | 100 | 0.131 | Contact Map |
| 3abdA | 2 | 0.9073 | 100 | 0.188 | Contact Map |
| 4j2gA | 2 | 0.7463 | 92.1 | 0.893 | Contact Map |
| 2qyfB | 2 | 0.7756 | 66.7 | 0.92 | Contact Map |
| 3rpjA | 2 | 0.5951 | 7.7 | 0.952 | Contact Map |
| 2jp7A | 1 | 0.2244 | 6.5 | 0.953 | Contact Map |
| 3kh1A | 2 | 0.3902 | 5 | 0.956 | Contact Map |
| 1wloA | 1 | 0.4293 | 4.5 | 0.957 | Contact Map |
| 2lxlA | 1 | 0.7024 | 3.6 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)