| DIM1-2-3 -force run |
| ID: | 1471284650 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 67 (32.5) | ||
| Seq/Len: | 0.957 | ||
| Nf(neff/√len): | 3.9 |
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: 0.957).
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 |
| 30_L | 37_L | 1.997 | 0.95 |
| 20_R | 32_E | 1.633 | 0.83 |
| 13_L | 34_Q | 1.602 | 0.82 |
| 5_I | 50_T | 1.501 | 0.76 |
| 52_T | 55_Y | 1.499 | 0.75 |
| 49_M | 61_T | 1.482 | 0.74 |
| 9_L | 47_E | 1.405 | 0.69 |
| 21_L | 32_E | 1.379 | 0.66 |
| 48_M | 66_V | 1.367 | 0.65 |
| 28_L | 41_L | 1.349 | 0.64 |
| 7_T | 49_M | 1.278 | 0.58 |
| 10_R | 14_K | 1.277 | 0.58 |
| 60_Y | 65_E | 1.275 | 0.58 |
| 49_M | 55_Y | 1.259 | 0.56 |
| 53_E | 62_L | 1.236 | 0.54 |
| 57_Q | 62_L | 1.236 | 0.54 |
| 4_D | 24_A | 1.219 | 0.52 |
| 6_I | 12_R | 1.181 | 0.49 |
| 17_E | 67_E | 1.170 | 0.48 |
| 36_E | 42_D | 1.164 | 0.47 |
| 37_L | 54_S | 1.163 | 0.47 |
| 5_I | 32_E | 1.154 | 0.46 |
| 26_Y | 64_R | 1.142 | 0.45 |
| 12_R | 21_L | 1.136 | 0.45 |
| 66_V | 69_K | 1.133 | 0.45 |
| 25_Q | 47_E | 1.122 | 0.44 |
| 31_V | 45_R | 1.121 | 0.43 |
| 28_L | 38_Q | 1.118 | 0.43 |
| 38_Q | 65_E | 1.107 | 0.42 |
| 53_E | 57_Q | 1.100 | 0.42 |
| 28_L | 68_L | 1.096 | 0.41 |
| 56_E | 61_T | 1.096 | 0.41 |
| 31_V | 55_Y | 1.093 | 0.41 |
| 19_E | 32_E | 1.091 | 0.41 |
| 41_L | 68_L | 1.030 | 0.36 |
| 6_I | 11_C | 1.015 | 0.34 |
| 43_K | 48_M | 1.008 | 0.34 |
| 4_D | 12_R | 1.006 | 0.34 |
| 9_L | 25_Q | 1.001 | 0.33 |
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 | |
| 3ghgA | 4 | 0.9143 | 45.5 | 0.849 | Contact Map |
| 2dfsA | 2 | 1 | 25.7 | 0.868 | Contact Map |
| 2bnxA | 2 | 0.3571 | 23.5 | 0.87 | Contact Map |
| 1deqA | 4 | 0.9857 | 21 | 0.873 | Contact Map |
| 2qagB | 1 | 0 | 19.3 | 0.875 | Contact Map |
| 4rh7A | 1 | 0.9429 | 14.1 | 0.883 | Contact Map |
| 1i84S | 2 | 0 | 13.3 | 0.884 | Contact Map |
| 3u59A | 4 | 1 | 11.7 | 0.887 | Contact Map |
| 4psmA | 4 | 0.8571 | 10.2 | 0.89 | Contact Map |
| 3u1cA | 2 | 1 | 9.5 | 0.891 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)