| z15 |
| ID: | 1487708718 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (119) | ||
| Sequences: | 335 (230.9) | ||
| Seq/Len: | 2.815 | ||
| Nf(neff/√len): | 21.2 |
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: 2.815).
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 |
| 5_M | 8_E | 2.099 | 1.00 |
| 12_A | 98_I | 2.095 | 1.00 |
| 48_W | 60_R | 1.811 | 0.99 |
| 97_W | 106_Q | 1.531 | 0.96 |
| 16_I | 68_V | 1.501 | 0.95 |
| 32_F | 69_D | 1.498 | 0.95 |
| 16_I | 35_E | 1.492 | 0.95 |
| 26_R | 29_V | 1.475 | 0.95 |
| 56_G | 60_R | 1.468 | 0.94 |
| 9_I | 13_L | 1.463 | 0.94 |
| 47_H | 59_F | 1.414 | 0.93 |
| 47_H | 50_P | 1.401 | 0.92 |
| 48_W | 56_G | 1.400 | 0.92 |
| 99_D | 104_S | 1.333 | 0.90 |
| 48_W | 100_P | 1.332 | 0.90 |
| 10_Q | 14_N | 1.326 | 0.89 |
| 99_D | 106_Q | 1.301 | 0.88 |
| 61_C | 93_D | 1.282 | 0.87 |
| 85_D | 98_I | 1.277 | 0.87 |
| 63_H | 93_D | 1.267 | 0.86 |
| 53_P | 60_R | 1.266 | 0.86 |
| 58_G | 97_W | 1.253 | 0.85 |
| 111_G | 116_L | 1.252 | 0.85 |
| 114_K | 117_Y | 1.241 | 0.85 |
| 56_G | 97_W | 1.238 | 0.84 |
| 48_W | 99_D | 1.237 | 0.84 |
| 63_H | 102_E | 1.236 | 0.84 |
| 16_I | 71_V | 1.228 | 0.84 |
| 65_G | 93_D | 1.222 | 0.83 |
| 47_H | 56_G | 1.222 | 0.83 |
| 17_I | 33_G | 1.217 | 0.83 |
| 9_I | 85_D | 1.208 | 0.82 |
| 8_E | 69_D | 1.196 | 0.81 |
| 57_S | 105_Y | 1.196 | 0.81 |
| 20_L | 89_N | 1.191 | 0.81 |
| 22_N | 78_E | 1.180 | 0.80 |
| 14_N | 79_S | 1.160 | 0.79 |
| 88_G | 123_G | 1.155 | 0.78 |
| 42_K | 98_I | 1.154 | 0.78 |
| 63_H | 95_S | 1.149 | 0.78 |
| 10_Q | 38_R | 1.138 | 0.77 |
| 32_F | 36_L | 1.130 | 0.76 |
| 59_F | 97_W | 1.127 | 0.76 |
| 44_Y | 80_G | 1.112 | 0.74 |
| 48_W | 53_P | 1.110 | 0.74 |
| 100_P | 106_Q | 1.109 | 0.74 |
| 6_Q | 119_D | 1.086 | 0.72 |
| 73_E | 76_S | 1.085 | 0.72 |
| 91_P | 105_Y | 1.085 | 0.72 |
| 8_E | 91_P | 1.067 | 0.70 |
| 106_Q | 109_E | 1.066 | 0.70 |
| 28_R | 51_E | 1.065 | 0.70 |
| 69_D | 86_V | 1.060 | 0.69 |
| 79_S | 83_I | 1.048 | 0.68 |
| 52_K | 55_K | 1.042 | 0.67 |
| 13_L | 17_I | 1.037 | 0.67 |
| 64_I | 86_V | 1.036 | 0.67 |
| 49_Y | 55_K | 1.034 | 0.66 |
| 55_K | 58_G | 1.014 | 0.64 |
| 12_A | 55_K | 1.011 | 0.64 |
| 60_R | 99_D | 1.008 | 0.64 |
| 53_P | 56_G | 1.007 | 0.63 |
| 57_S | 99_D | 1.005 | 0.63 |
| 81_L | 86_V | 1.001 | 0.63 |
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 | |
| 2z15A | 4 | 0.9528 | 100 | 0.036 | Contact Map |
| 3e9vA | 1 | 0.9291 | 100 | 0.075 | Contact Map |
| 1ghhA | 1 | 0.6142 | 14.1 | 0.935 | Contact Map |
| 2p41A | 1 | 0.1102 | 12.7 | 0.936 | Contact Map |
| 3shrA | 2 | 0.5354 | 12.1 | 0.937 | Contact Map |
| 1e5eA | 2 | 0.3543 | 11.3 | 0.938 | Contact Map |
| 3iaiA | 4 | 0.4961 | 9.4 | 0.94 | Contact Map |
| 4k36A | 2 | 0.2756 | 9.3 | 0.94 | Contact Map |
| 2kmfA | 1 | 0.3701 | 9 | 0.94 | Contact Map |
| 1wyrA | 1 | 0.874 | 7.2 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)