| T0812 |
| ID: | 1402433122 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (199) | ||
| Sequences: | 549 (318.9) | ||
| Seq/Len: | 2.759 | ||
| Nf(neff/√len): | 22.6 |
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: 2.759).
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 |
| 199_A | 202_I | 2.266 | 1.00 |
| 80_Y | 98_Q | 2.102 | 1.00 |
| 62_L | 164_I | 1.996 | 1.00 |
| 4_K | 7_I | 1.996 | 1.00 |
| 101_I | 161_I | 1.952 | 0.99 |
| 20_L | 62_L | 1.932 | 0.99 |
| 101_I | 129_I | 1.916 | 0.99 |
| 152_E | 156_D | 1.849 | 0.99 |
| 62_L | 66_F | 1.785 | 0.99 |
| 73_A | 186_V | 1.750 | 0.98 |
| 77_K | 130_E | 1.713 | 0.98 |
| 94_T | 167_K | 1.709 | 0.98 |
| 4_K | 11_V | 1.680 | 0.98 |
| 62_L | 136_W | 1.680 | 0.98 |
| 79_K | 128_E | 1.658 | 0.98 |
| 179_I | 182_I | 1.650 | 0.97 |
| 4_K | 20_L | 1.597 | 0.97 |
| 104_G | 154_F | 1.595 | 0.97 |
| 43_V | 46_M | 1.537 | 0.96 |
| 93_S | 167_K | 1.535 | 0.96 |
| 4_K | 62_L | 1.529 | 0.96 |
| 76_G | 80_Y | 1.527 | 0.96 |
| 78_L | 184_M | 1.523 | 0.95 |
| 76_G | 185_E | 1.520 | 0.95 |
| 167_K | 181_E | 1.498 | 0.95 |
| 150_T | 153_D | 1.459 | 0.94 |
| 131_M | 184_M | 1.456 | 0.94 |
| 196_T | 199_A | 1.443 | 0.93 |
| 71_L | 178_R | 1.431 | 0.93 |
| 129_I | 193_T | 1.401 | 0.92 |
| 99_V | 182_I | 1.397 | 0.92 |
| 159_Y | 201_L | 1.372 | 0.91 |
| 111_I | 149_V | 1.366 | 0.91 |
| 24_D | 28_Q | 1.361 | 0.90 |
| 4_K | 9_T | 1.351 | 0.90 |
| 166_I | 170_Y | 1.335 | 0.89 |
| 104_G | 159_Y | 1.332 | 0.89 |
| 22_L | 169_T | 1.309 | 0.88 |
| 79_K | 150_T | 1.307 | 0.88 |
| 118_A | 125_T | 1.305 | 0.88 |
| 136_W | 176_Q | 1.281 | 0.87 |
| 169_T | 177_S | 1.260 | 0.85 |
| 78_L | 99_V | 1.259 | 0.85 |
| 138_Y | 153_D | 1.253 | 0.85 |
| 17_Q | 20_L | 1.245 | 0.84 |
| 111_I | 154_F | 1.232 | 0.84 |
| 23_V | 165_L | 1.232 | 0.84 |
| 26_A | 161_I | 1.208 | 0.82 |
| 114_R | 157_I | 1.205 | 0.82 |
| 157_I | 185_E | 1.197 | 0.81 |
| 155_L | 175_R | 1.197 | 0.81 |
| 58_F | 105_T | 1.196 | 0.81 |
| 4_K | 14_K | 1.190 | 0.80 |
| 44_A | 97_P | 1.190 | 0.80 |
| 80_Y | 166_I | 1.189 | 0.80 |
| 168_A | 186_V | 1.182 | 0.80 |
| 61_K | 82_I | 1.182 | 0.80 |
| 154_F | 164_I | 1.179 | 0.80 |
| 56_E | 165_L | 1.177 | 0.79 |
| 149_V | 154_F | 1.175 | 0.79 |
| 20_L | 66_F | 1.165 | 0.79 |
| 127_H | 169_T | 1.159 | 0.78 |
| 17_Q | 66_F | 1.150 | 0.77 |
| 70_K | 120_L | 1.149 | 0.77 |
| 101_I | 162_H | 1.149 | 0.77 |
| 67_E | 184_M | 1.147 | 0.77 |
| 101_I | 193_T | 1.145 | 0.77 |
| 104_G | 164_I | 1.142 | 0.77 |
| 81_A | 124_L | 1.129 | 0.75 |
| 82_I | 89_E | 1.118 | 0.74 |
| 89_E | 149_V | 1.112 | 0.74 |
| 85_E | 175_R | 1.110 | 0.74 |
| 138_Y | 149_V | 1.108 | 0.73 |
| 196_T | 200_D | 1.105 | 0.73 |
| 38_Q | 45_H | 1.103 | 0.73 |
| 60_W | 155_L | 1.103 | 0.73 |
| 103_G | 108_H | 1.097 | 0.72 |
| 76_G | 84_F | 1.088 | 0.72 |
| 71_L | 176_Q | 1.087 | 0.71 |
| 4_K | 17_Q | 1.085 | 0.71 |
| 97_P | 110_R | 1.085 | 0.71 |
| 132_T | 136_W | 1.084 | 0.71 |
| 111_I | 157_I | 1.081 | 0.71 |
| 153_D | 201_L | 1.071 | 0.70 |
| 60_W | 136_W | 1.069 | 0.70 |
| 154_F | 161_I | 1.067 | 0.69 |
| 103_G | 150_T | 1.059 | 0.69 |
| 99_V | 129_I | 1.054 | 0.68 |
| 85_E | 177_S | 1.054 | 0.68 |
| 86_A | 185_E | 1.051 | 0.68 |
| 71_L | 200_D | 1.050 | 0.68 |
| 5_G | 8_R | 1.045 | 0.67 |
| 3_A | 6_L | 1.044 | 0.67 |
| 17_Q | 62_L | 1.040 | 0.67 |
| 100_I | 128_E | 1.030 | 0.65 |
| 60_W | 182_I | 1.029 | 0.65 |
| 42_I | 102_R | 1.028 | 0.65 |
| 66_F | 161_I | 1.026 | 0.65 |
| 16_E | 30_T | 1.025 | 0.65 |
| 14_K | 20_L | 1.024 | 0.65 |
| 125_T | 136_W | 1.021 | 0.64 |
| 69_K | 84_F | 1.015 | 0.64 |
| 77_K | 204_K | 1.001 | 0.62 |
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 | |
| 1wfxA | 1 | 0.4461 | 8 | 0.957 | Contact Map |
| 2d7nA | 1 | 0.3578 | 3.1 | 0.965 | Contact Map |
| 1cjcA | 1 | 0.4755 | 2.5 | 0.967 | Contact Map |
| 2llzA | 1 | 0.4167 | 2.4 | 0.967 | Contact Map |
| 2jovA | 1 | 0.3725 | 2.2 | 0.968 | Contact Map |
| 2fo3A | 1 | 0.5196 | 2.2 | 0.968 | Contact Map |
| 4a0tA | 3 | 0.4265 | 2.1 | 0.968 | Contact Map |
| 2qa1A | 1 | 0.4951 | 2.1 | 0.968 | Contact Map |
| 3zxuB | 2 | 0.451 | 2 | 0.968 | Contact Map |
| 3achA | 1 | 0.6127 | 1.9 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)