| VTE5 74-304 |
| ID: | 1486643780 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 231 (218) | ||
| Sequences: | 1280 (952.4) | ||
| Seq/Len: | 5.872 | ||
| Nf(neff/√len): | 64.5 |
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: 5.872).
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 |
| 161_F | 200_T | 3.829 | 1.00 |
| 142_G | 155_A | 3.044 | 1.00 |
| 157_S | 161_F | 2.943 | 1.00 |
| 157_S | 200_T | 2.896 | 1.00 |
| 129_G | 163_F | 2.719 | 1.00 |
| 144_T | 155_A | 2.675 | 1.00 |
| 202_V | 220_A | 2.498 | 1.00 |
| 143_S | 155_A | 2.454 | 1.00 |
| 133_I | 163_F | 2.200 | 1.00 |
| 65_N | 68_R | 2.127 | 1.00 |
| 31_K | 34_H | 1.999 | 1.00 |
| 38_G | 128_C | 1.940 | 1.00 |
| 137_M | 141_F | 1.926 | 1.00 |
| 105_A | 109_S | 1.882 | 1.00 |
| 214_N | 218_P | 1.861 | 1.00 |
| 137_M | 159_S | 1.839 | 1.00 |
| 38_G | 102_Y | 1.829 | 1.00 |
| 161_F | 197_M | 1.828 | 1.00 |
| 27_S | 88_R | 1.814 | 1.00 |
| 199_A | 221_T | 1.766 | 1.00 |
| 35_I | 132_G | 1.727 | 1.00 |
| 119_I | 123_S | 1.726 | 1.00 |
| 163_F | 167_I | 1.717 | 1.00 |
| 130_G | 160_M | 1.712 | 1.00 |
| 126_M | 164_G | 1.647 | 1.00 |
| 146_I | 204_S | 1.635 | 1.00 |
| 195_V | 225_A | 1.607 | 0.99 |
| 154_W | 158_I | 1.588 | 0.99 |
| 160_M | 164_G | 1.566 | 0.99 |
| 127_M | 217_V | 1.547 | 0.99 |
| 160_M | 200_T | 1.515 | 0.99 |
| 156_G | 203_E | 1.507 | 0.99 |
| 113_F | 222_I | 1.485 | 0.99 |
| 137_M | 140_K | 1.483 | 0.99 |
| 213_D | 218_P | 1.477 | 0.99 |
| 133_I | 159_S | 1.473 | 0.99 |
| 165_F | 193_A | 1.467 | 0.99 |
| 145_K | 153_S | 1.420 | 0.98 |
| 98_G | 127_M | 1.407 | 0.98 |
| 31_K | 132_G | 1.404 | 0.98 |
| 220_A | 224_A | 1.355 | 0.98 |
| 30_R | 34_H | 1.345 | 0.97 |
| 27_S | 98_G | 1.344 | 0.97 |
| 131_D | 138_G | 1.333 | 0.97 |
| 159_S | 163_F | 1.324 | 0.97 |
| 12_V | 15_F | 1.324 | 0.97 |
| 102_Y | 127_M | 1.321 | 0.97 |
| 137_M | 155_A | 1.320 | 0.97 |
| 101_F | 215_I | 1.303 | 0.97 |
| 87_T | 99_P | 1.274 | 0.96 |
| 12_V | 17_S | 1.251 | 0.96 |
| 88_R | 98_G | 1.250 | 0.96 |
| 129_G | 133_I | 1.250 | 0.96 |
| 39_L | 129_G | 1.246 | 0.95 |
| 160_M | 196_S | 1.238 | 0.95 |
| 129_G | 167_I | 1.230 | 0.95 |
| 126_M | 167_I | 1.223 | 0.95 |
| 38_G | 41_F | 1.223 | 0.95 |
| 102_Y | 132_G | 1.221 | 0.95 |
| 126_M | 221_T | 1.206 | 0.94 |
| 31_K | 135_D | 1.197 | 0.94 |
| 112_F | 169_I | 1.189 | 0.94 |
| 198_V | 224_A | 1.187 | 0.94 |
| 144_T | 154_W | 1.159 | 0.93 |
| 120_G | 124_L | 1.142 | 0.92 |
| 153_S | 156_G | 1.138 | 0.92 |
| 99_P | 102_Y | 1.130 | 0.91 |
| 144_T | 153_S | 1.129 | 0.91 |
| 117_S | 217_V | 1.118 | 0.91 |
| 138_G | 156_G | 1.116 | 0.91 |
| 126_M | 199_A | 1.111 | 0.90 |
| 134_A | 203_E | 1.109 | 0.90 |
| 102_Y | 128_C | 1.109 | 0.90 |
| 27_S | 139_R | 1.106 | 0.90 |
| 203_E | 213_D | 1.106 | 0.90 |
| 31_K | 134_A | 1.104 | 0.90 |
| 63_L | 67_L | 1.093 | 0.89 |
| 14_S | 17_S | 1.083 | 0.89 |
| 48_F | 65_N | 1.082 | 0.89 |
| 109_S | 123_S | 1.074 | 0.88 |
| 162_I | 173_Y | 1.074 | 0.88 |
| 127_M | 214_N | 1.062 | 0.88 |
| 79_N | 86_V | 1.058 | 0.87 |
| 38_G | 98_G | 1.055 | 0.87 |
| 194_M | 198_V | 1.041 | 0.86 |
| 130_G | 164_G | 1.039 | 0.86 |
| 182_H | 187_T | 1.034 | 0.86 |
| 91_R | 97_K | 1.023 | 0.85 |
| 63_L | 96_L | 1.020 | 0.85 |
| 107_L | 111_V | 1.019 | 0.84 |
| 165_F | 200_T | 1.019 | 0.84 |
| 33_V | 98_G | 1.012 | 0.84 |
| 198_V | 220_A | 1.007 | 0.84 |
| 81_M | 84_K | 1.003 | 0.83 |
| 180_Y | 183_M | 1.001 | 0.83 |
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 | |
| 4q2eA | 2 | 0.9177 | 98.2 | 0.809 | Contact Map |
| 2mofA | 1 | 0.0996 | 5.4 | 0.953 | Contact Map |
| 4ogqB | 1 | 0.2641 | 3 | 0.958 | Contact Map |
| 3w5aC | 1 | 0.1212 | 2.9 | 0.959 | Contact Map |
| 2micA | 2 | 0.1039 | 2.6 | 0.96 | Contact Map |
| 2h88D | 2 | 0.1515 | 2.4 | 0.96 | Contact Map |
| 2l2tA | 2 | 0.1212 | 1.9 | 0.962 | Contact Map |
| 3rkoJ | 2 | 0.329 | 1.8 | 0.963 | Contact Map |
| 4lz6A | 1 | 0.6407 | 1.7 | 0.963 | Contact Map |
| 4n7wA | 2 | 0.6104 | 1.7 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)