| cdc48_1 |
| ID: | 1487742654 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (186) | ||
| Sequences: | 980 (613.8) | ||
| Seq/Len: | 5.269 | ||
| Nf(neff/√len): | 45.0 |
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: 5.269).
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 |
| 29_I | 74_I | 4.139 | 1.00 |
| 41_L | 61_V | 2.958 | 1.00 |
| 158_V | 164_G | 2.825 | 1.00 |
| 136_V | 166_V | 2.715 | 1.00 |
| 48_L | 93_H | 2.636 | 1.00 |
| 4_T | 7_L | 2.424 | 1.00 |
| 32_S | 69_D | 2.281 | 1.00 |
| 56_D | 137_R | 2.217 | 1.00 |
| 101_A | 164_G | 2.184 | 1.00 |
| 29_I | 47_V | 2.169 | 1.00 |
| 18_V | 160_P | 2.063 | 1.00 |
| 81_N | 140_D | 1.946 | 1.00 |
| 53_K | 140_D | 1.926 | 1.00 |
| 49_V | 59_L | 1.764 | 1.00 |
| 36_M | 61_V | 1.667 | 0.99 |
| 16_L | 160_P | 1.661 | 0.99 |
| 51_G | 81_N | 1.628 | 0.99 |
| 79_R | 86_H | 1.601 | 0.99 |
| 21_A | 30_A | 1.586 | 0.99 |
| 84_V | 88_D | 1.583 | 0.99 |
| 57_T | 140_D | 1.583 | 0.99 |
| 35_T | 38_A | 1.565 | 0.99 |
| 49_V | 90_I | 1.544 | 0.99 |
| 36_M | 133_Y | 1.536 | 0.99 |
| 50_R | 93_H | 1.493 | 0.99 |
| 29_I | 59_L | 1.439 | 0.98 |
| 109_I | 112_T | 1.426 | 0.98 |
| 99_K | 138_Q | 1.418 | 0.98 |
| 156_V | 173_H | 1.405 | 0.98 |
| 25_D | 62_L | 1.395 | 0.98 |
| 25_D | 28_I | 1.394 | 0.98 |
| 29_I | 72_A | 1.393 | 0.98 |
| 103_R | 173_H | 1.378 | 0.97 |
| 58_V | 135_P | 1.375 | 0.97 |
| 26_N | 63_A | 1.325 | 0.96 |
| 104_I | 136_V | 1.312 | 0.96 |
| 80_H | 141_L | 1.293 | 0.96 |
| 49_V | 82_L | 1.279 | 0.95 |
| 102_K | 159_D | 1.268 | 0.95 |
| 106_V | 122_D | 1.251 | 0.95 |
| 72_A | 94_P | 1.248 | 0.95 |
| 41_L | 92_I | 1.216 | 0.93 |
| 57_T | 82_L | 1.183 | 0.92 |
| 58_V | 137_R | 1.175 | 0.92 |
| 59_L | 78_V | 1.171 | 0.92 |
| 122_D | 125_L | 1.170 | 0.92 |
| 24_D | 147_G | 1.163 | 0.91 |
| 106_V | 142_F | 1.160 | 0.91 |
| 25_D | 63_A | 1.153 | 0.91 |
| 76_R | 139_G | 1.138 | 0.90 |
| 32_S | 49_V | 1.138 | 0.90 |
| 151_V | 154_K | 1.133 | 0.90 |
| 29_I | 49_V | 1.124 | 0.89 |
| 53_K | 81_N | 1.124 | 0.89 |
| 166_V | 170_T | 1.115 | 0.89 |
| 5_A | 8_K | 1.090 | 0.87 |
| 81_N | 135_P | 1.080 | 0.87 |
| 108_P | 153_F | 1.077 | 0.86 |
| 14_N | 18_V | 1.074 | 0.86 |
| 67_L | 158_V | 1.071 | 0.86 |
| 36_M | 41_L | 1.069 | 0.86 |
| 58_V | 163_Y | 1.067 | 0.86 |
| 9_K | 12_K | 1.067 | 0.86 |
| 66_D | 129_F | 1.060 | 0.85 |
| 27_S | 75_N | 1.054 | 0.85 |
| 76_R | 79_R | 1.051 | 0.85 |
| 159_D | 166_V | 1.049 | 0.84 |
| 44_G | 88_D | 1.047 | 0.84 |
| 74_I | 78_V | 1.045 | 0.84 |
| 42_F | 46_T | 1.043 | 0.84 |
| 144_V | 153_F | 1.041 | 0.84 |
| 50_R | 91_T | 1.040 | 0.84 |
| 31_L | 92_I | 1.037 | 0.84 |
| 25_D | 129_F | 1.036 | 0.83 |
| 52_K | 81_N | 1.035 | 0.83 |
| 74_I | 86_H | 1.034 | 0.83 |
| 67_L | 128_Y | 1.029 | 0.83 |
| 185_E | 188_L | 1.025 | 0.83 |
| 81_N | 153_F | 1.022 | 0.82 |
| 61_V | 155_V | 1.019 | 0.82 |
| 121_F | 125_L | 1.019 | 0.82 |
| 79_R | 88_D | 1.016 | 0.82 |
| 33_N | 84_V | 1.015 | 0.82 |
| 6_I | 9_K | 1.015 | 0.82 |
| 76_R | 85_K | 1.012 | 0.81 |
| 121_F | 124_F | 1.010 | 0.81 |
| 57_T | 61_V | 1.000 | 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 | |
| 1cz4A | 1 | 0.9211 | 100 | 0.086 | Contact Map |
| 3tiwA | 2 | 0.8526 | 100 | 0.127 | Contact Map |
| 3cf2A | 4 | 0.9474 | 100 | 0.253 | Contact Map |
| 4ko8A | 2 | 0.9842 | 100 | 0.254 | Contact Map |
| 3j94A | 6 | 0.0158 | 99.4 | 0.623 | Contact Map |
| 2m3xA | 6 | 0.4526 | 99.1 | 0.676 | Contact Map |
| 2jv2A | 1 | 0.4 | 98.9 | 0.691 | Contact Map |
| 1zc1A | 1 | 0.9421 | 98.4 | 0.745 | Contact Map |
| 2yujA | 1 | 0.9053 | 98.3 | 0.751 | Contact Map |
| 1wlfA | 1 | 0.8316 | 98.1 | 0.764 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)