| bromodomain |
| ID: | 1430261379 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 100 (97) | ||
| Sequences: | 781 (520.5) | ||
| Seq/Len: | 8.052 | ||
| Nf(neff/√len): | 52.8 |
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: 8.052).
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 |
| 34_D | 77_Y | 5.539 | 1.00 |
| 29_T | 36_Y | 3.000 | 1.00 |
| 51_R | 56_E | 2.938 | 1.00 |
| 57_Y | 66_D | 2.619 | 1.00 |
| 39_I | 76_Y | 2.501 | 1.00 |
| 75_R | 89_E | 2.194 | 1.00 |
| 75_R | 92_E | 1.992 | 1.00 |
| 15_Q | 49_E | 1.898 | 1.00 |
| 74_C | 88_A | 1.884 | 1.00 |
| 26_P | 44_D | 1.871 | 1.00 |
| 44_D | 47_T | 1.778 | 1.00 |
| 67_M | 95_F | 1.764 | 1.00 |
| 48_M | 70_I | 1.754 | 1.00 |
| 26_P | 47_T | 1.698 | 1.00 |
| 79_P | 85_Y | 1.612 | 1.00 |
| 51_R | 66_D | 1.569 | 1.00 |
| 14_L | 67_M | 1.562 | 1.00 |
| 48_M | 67_M | 1.510 | 1.00 |
| 10_I | 99_L | 1.421 | 0.99 |
| 45_L | 70_I | 1.402 | 0.99 |
| 15_Q | 24_L | 1.398 | 0.99 |
| 84_F | 88_A | 1.385 | 0.99 |
| 75_R | 88_A | 1.347 | 0.99 |
| 71_F | 91_L | 1.327 | 0.99 |
| 20_A | 24_L | 1.301 | 0.98 |
| 3_D | 7_L | 1.297 | 0.98 |
| 22_P | 87_C | 1.290 | 0.98 |
| 74_C | 85_Y | 1.285 | 0.98 |
| 92_E | 96_V | 1.285 | 0.98 |
| 64_V | 95_F | 1.268 | 0.98 |
| 35_Y | 39_I | 1.259 | 0.98 |
| 21_W | 84_F | 1.238 | 0.97 |
| 68_T | 96_V | 1.207 | 0.97 |
| 17_H | 21_W | 1.170 | 0.96 |
| 81_D | 86_Q | 1.152 | 0.96 |
| 19_M | 90_V | 1.142 | 0.95 |
| 46_S | 70_I | 1.131 | 0.95 |
| 64_V | 99_L | 1.120 | 0.95 |
| 35_Y | 42_P | 1.120 | 0.95 |
| 68_T | 92_E | 1.116 | 0.95 |
| 43_M | 70_I | 1.112 | 0.94 |
| 64_V | 68_T | 1.077 | 0.93 |
| 28_D | 31_D | 1.066 | 0.93 |
| 94_F | 98_K | 1.007 | 0.90 |
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 | |
| 4donA | 1 | 1 | 100 | 0.129 | Contact Map |
| 4uydA | 1 | 1 | 100 | 0.134 | Contact Map |
| 4bhwA | 2 | 1 | 100 | 0.135 | Contact Map |
| 3fkmX | 1 | 0.97 | 100 | 0.135 | Contact Map |
| 4algA | 1 | 1 | 100 | 0.136 | Contact Map |
| 3d7cA | 2 | 1 | 100 | 0.138 | Contact Map |
| 1e6iA | 1 | 1 | 100 | 0.141 | Contact Map |
| 3mb3A | 1 | 1 | 100 | 0.145 | Contact Map |
| 4nudA | 1 | 1 | 100 | 0.145 | Contact Map |
| 3q2eA | 1 | 0.99 | 100 | 0.146 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)