| cdc42 |
| ID: | 1501026965 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 191 (172) | ||
| Sequences: | 25639 (15807.4) | ||
| Seq/Len: | 149.064 | ||
| Nf(neff/√len): | 1205.3 |
Jackhmmer Results: (2016_04)
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: 149.064).
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 |
| 11_D | 92_N | 3.264 | 1.00 |
| 22_S | 162_Q | 2.859 | 1.00 |
| 113_V | 168_V | 2.774 | 1.00 |
| 19_L | 81_C | 2.354 | 1.00 |
| 155_V | 171_E | 2.328 | 1.00 |
| 84_V | 114_G | 2.277 | 1.00 |
| 81_C | 115_T | 2.273 | 1.00 |
| 79_L | 113_V | 2.052 | 1.00 |
| 153_K | 171_E | 2.042 | 1.00 |
| 77_V | 172_A | 2.008 | 1.00 |
| 7_V | 75_T | 1.973 | 1.00 |
| 84_V | 117_I | 1.947 | 1.00 |
| 82_F | 154_Y | 1.944 | 1.00 |
| 98_V | 102_T | 1.923 | 1.00 |
| 171_E | 175_A | 1.883 | 1.00 |
| 117_I | 163_K | 1.860 | 1.00 |
| 171_E | 174_L | 1.857 | 1.00 |
| 8_V | 20_L | 1.796 | 1.00 |
| 87_P | 141_T | 1.794 | 1.00 |
| 113_V | 157_C | 1.771 | 1.00 |
| 139_P | 143_E | 1.734 | 1.00 |
| 80_V | 93_V | 1.712 | 1.00 |
| 145_L | 149_L | 1.691 | 1.00 |
| 86_S | 89_S | 1.661 | 1.00 |
| 45_M | 50_P | 1.661 | 1.00 |
| 142_A | 146_A | 1.657 | 1.00 |
| 19_L | 165_L | 1.592 | 1.00 |
| 82_F | 114_G | 1.528 | 1.00 |
| 114_G | 156_E | 1.518 | 1.00 |
| 4_I | 176_A | 1.507 | 1.00 |
| 157_C | 168_V | 1.490 | 1.00 |
| 143_E | 147_R | 1.470 | 1.00 |
| 77_V | 176_A | 1.420 | 1.00 |
| 53_L | 173_I | 1.415 | 1.00 |
| 83_S | 86_S | 1.401 | 0.99 |
| 115_T | 159_A | 1.395 | 0.99 |
| 111_L | 155_V | 1.391 | 0.99 |
| 138_T | 141_T | 1.373 | 0.99 |
| 144_K | 148_D | 1.350 | 0.99 |
| 100_E | 103_H | 1.328 | 0.99 |
| 21_I | 25_T | 1.315 | 0.99 |
| 102_T | 110_F | 1.308 | 0.99 |
| 164_G | 167_N | 1.299 | 0.99 |
| 92_N | 96_K | 1.294 | 0.99 |
| 175_A | 178_E | 1.287 | 0.99 |
| 139_P | 156_E | 1.270 | 0.99 |
| 79_L | 172_A | 1.257 | 0.99 |
| 153_K | 175_A | 1.254 | 0.99 |
| 142_A | 154_Y | 1.246 | 0.98 |
| 135_K | 138_T | 1.243 | 0.98 |
| 18_C | 159_A | 1.238 | 0.98 |
| 43_T | 50_P | 1.227 | 0.98 |
| 43_T | 52_T | 1.222 | 0.98 |
| 99_P | 103_H | 1.221 | 0.98 |
| 5_K | 54_G | 1.220 | 0.98 |
| 83_S | 116_Q | 1.202 | 0.98 |
| 85_V | 119_L | 1.194 | 0.98 |
| 28_F | 160_L | 1.181 | 0.98 |
| 166_K | 170_D | 1.176 | 0.98 |
| 142_A | 145_L | 1.164 | 0.97 |
| 111_L | 171_E | 1.159 | 0.97 |
| 145_L | 148_D | 1.152 | 0.97 |
| 134_Q | 138_T | 1.142 | 0.97 |
| 149_L | 152_V | 1.138 | 0.97 |
| 111_L | 168_V | 1.124 | 0.97 |
| 144_K | 147_R | 1.123 | 0.97 |
| 90_F | 94_K | 1.120 | 0.96 |
| 136_P | 140_E | 1.119 | 0.96 |
| 143_E | 146_A | 1.114 | 0.96 |
| 6_C | 77_V | 1.114 | 0.96 |
| 118_D | 158_S | 1.106 | 0.96 |
| 75_T | 78_F | 1.095 | 0.96 |
| 65_D | 68_R | 1.084 | 0.96 |
| 78_F | 101_I | 1.070 | 0.95 |
| 46_I | 49_E | 1.069 | 0.95 |
| 146_A | 149_L | 1.066 | 0.95 |
| 17_T | 57_D | 1.065 | 0.95 |
| 99_P | 102_T | 1.062 | 0.95 |
| 64_Y | 68_R | 1.050 | 0.94 |
| 8_V | 79_L | 1.049 | 0.94 |
| 109_P | 175_A | 1.048 | 0.94 |
| 90_F | 93_V | 1.048 | 0.94 |
| 141_T | 144_K | 1.048 | 0.94 |
| 72_Y | 100_E | 1.045 | 0.94 |
| 22_S | 26_N | 1.042 | 0.94 |
| 98_V | 149_L | 1.024 | 0.93 |
| 117_I | 156_E | 1.020 | 0.93 |
| 94_K | 148_D | 1.017 | 0.93 |
| 32_Y | 35_T | 1.013 | 0.93 |
| 138_T | 142_A | 1.012 | 0.93 |
| 87_P | 91_E | 1.009 | 0.93 |
| 80_V | 98_V | 1.008 | 0.93 |
| 45_M | 48_G | 1.004 | 0.93 |
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 | |
| 1m7bA | 1 | 0.9319 | 100 | 0.239 | Contact Map |
| 2j0vA | 4 | 0.9267 | 100 | 0.239 | Contact Map |
| 2q3hA | 1 | 0.8953 | 100 | 0.24 | Contact Map |
| 1mh1A | 1 | 0.9476 | 100 | 0.244 | Contact Map |
| 2atxA | 2 | 0.9372 | 100 | 0.253 | Contact Map |
| 3regA | 2 | 0.8953 | 100 | 0.256 | Contact Map |
| 4mitA | 4 | 0.9372 | 100 | 0.257 | Contact Map |
| 2iwrA | 1 | 0.8691 | 100 | 0.261 | Contact Map |
| 3bwdD | 1 | 0.8168 | 100 | 0.262 | Contact Map |
| 3q3jB | 1 | 0.9058 | 100 | 0.267 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)