| Vav1 |
| ID: | 1401900620 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 210 (202) | ||
| Sequences: | 920 (593.6) | ||
| Seq/Len: | 4.554 | ||
| Nf(neff/√len): | 41.8 |
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: 4.554).
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 |
| 107_A | 118_Q | 4.243 | 1.00 |
| 45_R | 197_T | 2.758 | 1.00 |
| 57_E | 105_K | 2.604 | 1.00 |
| 62_T | 178_V | 2.451 | 1.00 |
| 70_F | 167_N | 2.306 | 1.00 |
| 51_E | 181_Q | 2.188 | 1.00 |
| 78_L | 82_D | 2.079 | 1.00 |
| 60_T | 97_H | 2.070 | 1.00 |
| 51_E | 189_L | 1.883 | 1.00 |
| 70_F | 162_S | 1.862 | 1.00 |
| 55_T | 182_R | 1.821 | 1.00 |
| 59_Y | 130_Y | 1.813 | 1.00 |
| 52_I | 193_L | 1.762 | 1.00 |
| 134_C | 187_H | 1.745 | 1.00 |
| 184_L | 187_H | 1.744 | 1.00 |
| 182_R | 189_L | 1.659 | 0.99 |
| 199_E | 203_K | 1.618 | 0.99 |
| 134_C | 185_K | 1.605 | 0.99 |
| 48_C | 193_L | 1.544 | 0.99 |
| 171_T | 174_D | 1.543 | 0.99 |
| 144_L | 154_V | 1.498 | 0.98 |
| 103_E | 122_K | 1.485 | 0.98 |
| 134_C | 184_L | 1.447 | 0.98 |
| 45_R | 201_M | 1.441 | 0.97 |
| 177_M | 181_Q | 1.428 | 0.97 |
| 181_Q | 184_L | 1.406 | 0.97 |
| 101_L | 130_Y | 1.386 | 0.97 |
| 52_I | 97_H | 1.378 | 0.96 |
| 59_Y | 179_P | 1.378 | 0.96 |
| 197_T | 206_L | 1.368 | 0.96 |
| 23_I | 26_D | 1.352 | 0.96 |
| 144_L | 158_L | 1.351 | 0.96 |
| 197_T | 201_M | 1.350 | 0.96 |
| 10_Y | 13_V | 1.345 | 0.96 |
| 130_Y | 179_P | 1.341 | 0.96 |
| 51_E | 182_R | 1.336 | 0.96 |
| 137_V | 180_M | 1.318 | 0.95 |
| 45_R | 206_L | 1.318 | 0.95 |
| 134_C | 137_V | 1.312 | 0.95 |
| 117_Y | 202_E | 1.305 | 0.95 |
| 193_L | 197_T | 1.292 | 0.94 |
| 167_N | 170_F | 1.277 | 0.94 |
| 107_A | 154_V | 1.276 | 0.94 |
| 77_F | 83_I | 1.262 | 0.93 |
| 93_L | 129_V | 1.258 | 0.93 |
| 198_Q | 201_M | 1.253 | 0.93 |
| 26_D | 30_S | 1.250 | 0.93 |
| 49_L | 53_Q | 1.245 | 0.93 |
| 137_V | 184_L | 1.243 | 0.93 |
| 178_V | 185_K | 1.232 | 0.92 |
| 51_E | 186_Y | 1.227 | 0.92 |
| 55_T | 181_Q | 1.220 | 0.92 |
| 51_E | 188_L | 1.219 | 0.92 |
| 64_G | 98_T | 1.205 | 0.91 |
| 133_Y | 179_P | 1.196 | 0.91 |
| 107_A | 119_V | 1.181 | 0.90 |
| 147_V | 151_R | 1.176 | 0.90 |
| 96_V | 102_K | 1.176 | 0.90 |
| 63_L | 124_K | 1.145 | 0.88 |
| 49_L | 116_L | 1.144 | 0.88 |
| 182_R | 188_L | 1.144 | 0.88 |
| 88_I | 93_L | 1.136 | 0.88 |
| 45_R | 202_E | 1.135 | 0.87 |
| 12_C | 15_N | 1.128 | 0.87 |
| 180_M | 192_E | 1.127 | 0.87 |
| 82_D | 147_V | 1.124 | 0.87 |
| 93_L | 97_H | 1.122 | 0.87 |
| 79_K | 82_D | 1.116 | 0.86 |
| 193_L | 201_M | 1.115 | 0.86 |
| 58_K | 62_T | 1.112 | 0.86 |
| 182_R | 186_Y | 1.094 | 0.85 |
| 158_L | 172_L | 1.092 | 0.85 |
| 137_V | 187_H | 1.091 | 0.85 |
| 86_I | 120_F | 1.089 | 0.84 |
| 11_D | 14_E | 1.088 | 0.84 |
| 9_L | 14_E | 1.087 | 0.84 |
| 204_E | 207_R | 1.083 | 0.84 |
| 157_K | 161_C | 1.080 | 0.84 |
| 115_N | 205_N | 1.078 | 0.84 |
| 66_I | 93_L | 1.077 | 0.83 |
| 51_E | 55_T | 1.077 | 0.83 |
| 181_Q | 185_K | 1.071 | 0.83 |
| 60_T | 101_L | 1.068 | 0.83 |
| 20_G | 25_E | 1.055 | 0.82 |
| 66_I | 90_I | 1.051 | 0.81 |
| 45_R | 87_F | 1.050 | 0.81 |
| 52_I | 120_F | 1.049 | 0.81 |
| 120_F | 186_Y | 1.049 | 0.81 |
| 97_H | 131_G | 1.048 | 0.81 |
| 172_L | 179_P | 1.045 | 0.81 |
| 17_E | 27_L | 1.038 | 0.80 |
| 90_I | 93_L | 1.034 | 0.80 |
| 146_R | 149_A | 1.027 | 0.79 |
| 174_D | 177_M | 1.022 | 0.79 |
| 55_T | 58_K | 1.018 | 0.78 |
| 180_M | 184_L | 1.013 | 0.78 |
| 77_F | 82_D | 1.005 | 0.77 |
| 153_D | 156_M | 1.003 | 0.77 |
| 22_E | 25_E | 1.003 | 0.77 |
| 56_E | 182_R | 1.001 | 0.77 |
| 107_A | 205_N | 1.000 | 0.77 |
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 | |
| 2vrwB | 1 | 0.8143 | 100 | 0.197 | Contact Map |
| 3jzyA | 1 | 0 | 100 | 0.206 | Contact Map |
| 3ky9A | 2 | 0.9381 | 100 | 0.208 | Contact Map |
| 3mpxA | 1 | 0.7667 | 100 | 0.223 | Contact Map |
| 2z0qA | 1 | 0.7667 | 100 | 0.224 | Contact Map |
| 2dfkA | 2 | 0.8524 | 100 | 0.229 | Contact Map |
| 3p6aA | 2 | 0.8143 | 100 | 0.229 | Contact Map |
| 3odwA | 2 | 0.8143 | 100 | 0.23 | Contact Map |
| 3t06A | 2 | 0.8905 | 100 | 0.231 | Contact Map |
| 4d0nB | 1 | 0.9286 | 100 | 0.231 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)