| 1EL4A |
| ID: | 1411763253 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 194 (176) | ||
| Sequences: | 1882 (1307.5) | ||
| Seq/Len: | 10.693 | ||
| Nf(neff/√len): | 98.6 |
HHblits Results: (2013_03)
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: 10.693).
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 |
| 158_D | 169_E | 3.636 | 1.00 |
| 75_G | 86_Q | 3.471 | 1.00 |
| 126_S | 133_E | 3.256 | 1.00 |
| 124_D | 133_E | 3.098 | 1.00 |
| 33_N | 40_E | 3.031 | 1.00 |
| 162_S | 169_E | 2.913 | 1.00 |
| 128_T | 164_D | 2.770 | 1.00 |
| 75_G | 80_K | 2.663 | 1.00 |
| 79_G | 86_Q | 2.653 | 1.00 |
| 77_E | 86_Q | 2.564 | 1.00 |
| 158_D | 162_S | 2.531 | 1.00 |
| 158_D | 163_G | 2.445 | 1.00 |
| 75_G | 79_G | 2.430 | 1.00 |
| 31_N | 40_E | 2.408 | 1.00 |
| 160_D | 169_E | 2.189 | 1.00 |
| 122_D | 127_G | 2.145 | 1.00 |
| 35_K | 81_E | 2.073 | 1.00 |
| 158_D | 161_N | 1.915 | 1.00 |
| 25_F | 87_F | 1.809 | 1.00 |
| 160_D | 166_D | 1.795 | 1.00 |
| 123_K | 133_E | 1.752 | 1.00 |
| 115_D | 167_V | 1.744 | 1.00 |
| 166_D | 169_E | 1.670 | 1.00 |
| 121_F | 129_I | 1.639 | 1.00 |
| 75_G | 78_Y | 1.609 | 1.00 |
| 71_F | 154_F | 1.599 | 1.00 |
| 29_D | 40_E | 1.482 | 1.00 |
| 162_S | 166_D | 1.411 | 1.00 |
| 183_P | 186_D | 1.400 | 0.99 |
| 13_D | 18_I | 1.395 | 0.99 |
| 181_L | 186_D | 1.387 | 0.99 |
| 182_D | 186_D | 1.291 | 0.99 |
| 26_D | 32_G | 1.280 | 0.99 |
| 22_K | 84_F | 1.275 | 0.99 |
| 74_C | 157_C | 1.268 | 0.99 |
| 38_L | 68_E | 1.267 | 0.99 |
| 131_L | 151_E | 1.244 | 0.98 |
| 181_L | 184_E | 1.233 | 0.98 |
| 29_D | 34_G | 1.230 | 0.98 |
| 180_T | 186_D | 1.227 | 0.98 |
| 37_T | 40_E | 1.206 | 0.98 |
| 167_V | 170_M | 1.206 | 0.98 |
| 87_F | 170_M | 1.188 | 0.98 |
| 86_Q | 89_D | 1.183 | 0.98 |
| 33_N | 146_S | 1.172 | 0.98 |
| 181_L | 185_A | 1.168 | 0.97 |
| 133_E | 160_D | 1.166 | 0.97 |
| 25_F | 84_F | 1.145 | 0.97 |
| 122_D | 133_E | 1.129 | 0.97 |
| 179_Y | 183_P | 1.121 | 0.97 |
| 118_F | 122_D | 1.109 | 0.96 |
| 120_I | 137_Y | 1.084 | 0.96 |
| 84_F | 167_V | 1.084 | 0.96 |
| 28_L | 40_E | 1.075 | 0.95 |
| 12_F | 15_P | 1.072 | 0.95 |
| 30_I | 43_S | 1.047 | 0.94 |
| 126_S | 130_T | 1.041 | 0.94 |
| 41_I | 50_C | 1.037 | 0.94 |
| 29_D | 32_G | 1.033 | 0.94 |
| 29_D | 33_N | 1.022 | 0.93 |
| 154_F | 157_C | 1.018 | 0.93 |
| 71_F | 134_W | 1.017 | 0.93 |
| 124_D | 130_T | 1.015 | 0.93 |
| 182_D | 185_A | 1.013 | 0.93 |
| 179_Y | 185_A | 1.011 | 0.93 |
| 32_G | 78_Y | 1.008 | 0.93 |
| 36_I | 137_Y | 1.006 | 0.93 |
| 24_M | 117_V | 1.005 | 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 | |
| 1qv0A | 1 | 0.9536 | 100 | 0.21 | Contact Map |
| 1uhkA | 2 | 0.9845 | 100 | 0.261 | Contact Map |
| 1q80A | 1 | 0.8299 | 99.9 | 0.41 | Contact Map |
| 2hpsA | 1 | 0.8969 | 99.9 | 0.411 | Contact Map |
| 3mwuA | 1 | 0.7577 | 99.9 | 0.417 | Contact Map |
| 4mn0A | 1 | 0.8196 | 99.9 | 0.418 | Contact Map |
| 2ccmA | 2 | 0.9072 | 99.9 | 0.419 | Contact Map |
| 4mvfA | 1 | 0.7938 | 99.9 | 0.423 | Contact Map |
| 2obhA | 2 | 0.7371 | 99.9 | 0.438 | Contact Map |
| 3cs1A | 1 | 0.8557 | 99.9 | 0.438 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)