| dysf_c2b |
| ID: | 1475705893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 134 (120) | ||
| Sequences: | 14903 (8785.6) | ||
| Seq/Len: | 124.192 | ||
| Nf(neff/√len): | 802.0 |
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: 124.192).
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 |
| 39_R | 50_E | 3.495 | 1.00 |
| 67_P | 88_R | 2.875 | 1.00 |
| 14_E | 47_L | 2.506 | 1.00 |
| 87_F | 107_L | 2.433 | 1.00 |
| 73_V | 83_L | 2.420 | 1.00 |
| 15_G | 48_F | 2.385 | 1.00 |
| 12_V | 38_T | 2.339 | 1.00 |
| 76_R | 82_A | 2.312 | 1.00 |
| 36_K | 52_L | 2.284 | 1.00 |
| 15_G | 18_L | 2.205 | 1.00 |
| 9_R | 53_F | 2.194 | 1.00 |
| 69_F | 86_E | 2.124 | 1.00 |
| 14_E | 124_K | 2.103 | 1.00 |
| 11_Q | 51_T | 2.093 | 1.00 |
| 69_F | 88_R | 1.781 | 1.00 |
| 12_V | 27_V | 1.759 | 1.00 |
| 25_P | 74_D | 1.736 | 1.00 |
| 40_I | 75_S | 1.725 | 1.00 |
| 27_V | 70_I | 1.663 | 1.00 |
| 106_W | 124_K | 1.651 | 1.00 |
| 9_R | 51_T | 1.647 | 1.00 |
| 71_T | 86_E | 1.634 | 1.00 |
| 11_Q | 49_N | 1.620 | 1.00 |
| 83_L | 86_E | 1.618 | 1.00 |
| 29_V | 52_L | 1.596 | 1.00 |
| 71_T | 83_L | 1.595 | 1.00 |
| 16_R | 122_Y | 1.594 | 1.00 |
| 30_T | 71_T | 1.567 | 1.00 |
| 28_K | 71_T | 1.511 | 1.00 |
| 26_V | 81_D | 1.487 | 1.00 |
| 75_S | 81_D | 1.457 | 1.00 |
| 15_G | 46_P | 1.447 | 1.00 |
| 27_V | 72_V | 1.436 | 1.00 |
| 106_W | 122_Y | 1.422 | 1.00 |
| 30_T | 69_F | 1.375 | 0.99 |
| 67_P | 90_D | 1.350 | 0.99 |
| 27_V | 48_F | 1.339 | 0.99 |
| 14_E | 106_W | 1.331 | 0.99 |
| 27_V | 38_T | 1.316 | 0.99 |
| 36_K | 54_F | 1.313 | 0.99 |
| 104_R | 124_K | 1.298 | 0.99 |
| 13_I | 126_S | 1.295 | 0.99 |
| 29_V | 70_I | 1.287 | 0.99 |
| 16_R | 106_W | 1.254 | 0.99 |
| 7_Q | 53_F | 1.242 | 0.98 |
| 20_G | 44_N | 1.234 | 0.98 |
| 30_T | 35_T | 1.224 | 0.98 |
| 13_I | 49_N | 1.215 | 0.98 |
| 108_L | 122_Y | 1.210 | 0.98 |
| 43_G | 46_P | 1.187 | 0.98 |
| 24_K | 40_I | 1.186 | 0.98 |
| 73_V | 81_D | 1.178 | 0.98 |
| 7_Q | 55_N | 1.178 | 0.98 |
| 12_V | 29_V | 1.171 | 0.98 |
| 18_L | 72_V | 1.167 | 0.97 |
| 107_L | 125_T | 1.156 | 0.97 |
| 32_A | 66_E | 1.147 | 0.97 |
| 23_I | 84_L | 1.142 | 0.97 |
| 26_V | 73_V | 1.139 | 0.97 |
| 21_V | 84_L | 1.118 | 0.96 |
| 20_G | 23_I | 1.073 | 0.95 |
| 41_H | 48_F | 1.065 | 0.95 |
| 90_D | 93_T | 1.054 | 0.95 |
| 20_G | 43_G | 1.035 | 0.94 |
| 10_V | 29_V | 1.032 | 0.94 |
| 72_V | 109_L | 1.023 | 0.93 |
| 22_N | 44_N | 1.010 | 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 | |
| 3l9bA | 1 | 0.9179 | 99.4 | 0.127 | Contact Map |
| 3m7fB | 1 | 0.8657 | 99.3 | 0.19 | Contact Map |
| 1wfjA | 1 | 0.9179 | 99.3 | 0.191 | Contact Map |
| 1djxA | 2 | 0.8955 | 99.3 | 0.198 | Contact Map |
| 2nq3A | 1 | 0.9403 | 99.3 | 0.2 | Contact Map |
| 3b7yA | 2 | 0.9328 | 99.3 | 0.205 | Contact Map |
| 2dmhA | 1 | 0.9701 | 99.3 | 0.205 | Contact Map |
| 3bxjA | 2 | 0.2537 | 99.3 | 0.207 | Contact Map |
| 4v29A | 2 | 0.9179 | 99.2 | 0.211 | Contact Map |
| 2fk9A | 1 | 0.8657 | 99.2 | 0.212 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)