| tato1a200 |
| ID: | 1485449879 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (191) | ||
| Sequences: | 1001 (734.6) | ||
| Seq/Len: | 5.241 | ||
| Nf(neff/√len): | 53.2 |
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: 5.241).
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 |
| 133_G | 137_S | 3.686 | 1.00 |
| 84_L | 140_V | 3.016 | 1.00 |
| 81_I | 141_A | 2.735 | 1.00 |
| 81_I | 137_S | 2.634 | 1.00 |
| 105_M | 108_N | 2.527 | 1.00 |
| 89_V | 129_I | 2.428 | 1.00 |
| 63_L | 164_S | 2.387 | 1.00 |
| 26_L | 66_T | 2.064 | 1.00 |
| 63_L | 160_L | 1.983 | 1.00 |
| 60_G | 167_L | 1.978 | 1.00 |
| 18_L | 140_V | 1.971 | 1.00 |
| 94_T | 101_Y | 1.889 | 1.00 |
| 93_F | 120_L | 1.875 | 1.00 |
| 190_R | 200_Y | 1.874 | 1.00 |
| 25_F | 30_A | 1.828 | 1.00 |
| 153_G | 157_R | 1.750 | 1.00 |
| 64_L | 161_I | 1.748 | 1.00 |
| 60_G | 171_P | 1.695 | 1.00 |
| 25_F | 29_T | 1.679 | 1.00 |
| 130_I | 134_V | 1.672 | 0.99 |
| 24_V | 59_F | 1.661 | 0.99 |
| 69_L | 79_V | 1.641 | 0.99 |
| 180_A | 184_R | 1.634 | 0.99 |
| 107_Q | 111_Q | 1.598 | 0.99 |
| 102_D | 105_M | 1.581 | 0.99 |
| 64_L | 168_I | 1.564 | 0.99 |
| 93_F | 101_Y | 1.528 | 0.99 |
| 22_V | 80_L | 1.478 | 0.98 |
| 147_Y | 153_G | 1.473 | 0.98 |
| 81_I | 140_V | 1.468 | 0.98 |
| 53_T | 179_Y | 1.458 | 0.98 |
| 113_D | 190_R | 1.420 | 0.98 |
| 82_L | 86_M | 1.394 | 0.98 |
| 90_T | 198_P | 1.385 | 0.97 |
| 175_F | 179_Y | 1.379 | 0.97 |
| 100_V | 192_Y | 1.371 | 0.97 |
| 23_A | 27_T | 1.358 | 0.97 |
| 90_T | 101_Y | 1.341 | 0.97 |
| 50_F | 179_Y | 1.332 | 0.97 |
| 80_L | 84_L | 1.322 | 0.96 |
| 130_I | 135_L | 1.315 | 0.96 |
| 138_L | 142_F | 1.303 | 0.96 |
| 193_V | 196_I | 1.283 | 0.95 |
| 176_S | 180_A | 1.256 | 0.95 |
| 34_F | 200_Y | 1.253 | 0.95 |
| 73_R | 77_K | 1.248 | 0.94 |
| 33_T | 95_D | 1.238 | 0.94 |
| 34_F | 194_N | 1.218 | 0.93 |
| 179_Y | 183_F | 1.201 | 0.93 |
| 114_Q | 117_T | 1.200 | 0.93 |
| 128_R | 132_L | 1.186 | 0.92 |
| 134_V | 138_L | 1.173 | 0.92 |
| 26_L | 83_L | 1.163 | 0.91 |
| 86_M | 152_K | 1.148 | 0.91 |
| 34_F | 187_K | 1.146 | 0.90 |
| 121_L | 156_R | 1.146 | 0.90 |
| 77_K | 136_P | 1.135 | 0.90 |
| 13_V | 17_V | 1.133 | 0.90 |
| 182_F | 189_L | 1.125 | 0.89 |
| 157_R | 196_I | 1.124 | 0.89 |
| 192_Y | 197_M | 1.115 | 0.89 |
| 88_A | 133_G | 1.113 | 0.89 |
| 88_A | 132_L | 1.109 | 0.88 |
| 14_S | 17_V | 1.104 | 0.88 |
| 74_Y | 78_P | 1.094 | 0.88 |
| 85_I | 133_G | 1.094 | 0.88 |
| 64_L | 157_R | 1.091 | 0.87 |
| 93_F | 125_F | 1.088 | 0.87 |
| 84_L | 137_S | 1.086 | 0.87 |
| 89_V | 109_A | 1.075 | 0.86 |
| 13_V | 21_S | 1.073 | 0.86 |
| 87_G | 198_P | 1.061 | 0.85 |
| 194_N | 197_M | 1.054 | 0.85 |
| 167_L | 170_L | 1.050 | 0.84 |
| 99_T | 104_T | 1.040 | 0.84 |
| 87_G | 194_N | 1.026 | 0.83 |
| 81_I | 85_I | 1.024 | 0.82 |
| 125_F | 129_I | 1.021 | 0.82 |
| 176_S | 183_F | 1.019 | 0.82 |
| 94_T | 194_N | 1.017 | 0.82 |
| 52_L | 79_V | 1.006 | 0.81 |
| 95_D | 128_R | 1.004 | 0.81 |
| 96_T | 124_A | 1.001 | 0.80 |
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 | |
| 4b4aA | 1 | 0.68 | 1.5 | 0.956 | Contact Map |
| 1q90M | 1 | 0.17 | 1.5 | 0.957 | Contact Map |
| 4i0uA | 10 | 0.325 | 1.2 | 0.959 | Contact Map |
| 4ev6A | 5 | 0.335 | 1.2 | 0.959 | Contact Map |
| 4httA | 2 | 0.69 | 1.1 | 0.96 | Contact Map |
| 3zilB | 1 | 0.055 | 1.1 | 0.96 | Contact Map |
| 3buaE | 4 | 0.08 | 1.1 | 0.96 | Contact Map |
| 4or5E | 2 | 0.15 | 0.9 | 0.962 | Contact Map |
| 2mv6A | 1 | 0.245 | 0.8 | 0.963 | Contact Map |
| 4tr2A | 2 | 0.04 | 0.8 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)