| DIM1-2-3 |
| ID: | 1471276132 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (65) | ||
| Sequences: | 1910 (1695.1) | ||
| Seq/Len: | 29.385 | ||
| Nf(neff/√len): | 210.3 |
Jackhmmer Results: (2016_04)
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: 29.385).
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 |
| 15_E | 26_Y | 2.233 | 1.00 |
| 18_E | 29_Q | 2.126 | 1.00 |
| 22_K | 33_S | 1.750 | 1.00 |
| 29_Q | 46_N | 1.705 | 1.00 |
| 26_Y | 43_K | 1.540 | 1.00 |
| 14_K | 25_Q | 1.536 | 1.00 |
| 48_M | 52_T | 1.517 | 1.00 |
| 39_N | 50_T | 1.484 | 1.00 |
| 25_Q | 42_D | 1.450 | 1.00 |
| 55_Y | 59_K | 1.366 | 0.99 |
| 13_L | 24_A | 1.363 | 0.99 |
| 20_R | 31_V | 1.323 | 0.99 |
| 45_R | 63_Q | 1.316 | 0.99 |
| 11_C | 22_K | 1.298 | 0.99 |
| 37_L | 41_L | 1.265 | 0.99 |
| 59_K | 62_L | 1.224 | 0.98 |
| 46_N | 64_R | 1.216 | 0.98 |
| 19_E | 30_L | 1.202 | 0.98 |
| 41_L | 52_T | 1.202 | 0.98 |
| 43_K | 61_T | 1.175 | 0.98 |
| 26_Y | 36_E | 1.174 | 0.98 |
| 18_E | 46_N | 1.174 | 0.98 |
| 14_K | 42_D | 1.157 | 0.97 |
| 16_A | 27_G | 1.147 | 0.97 |
| 9_L | 13_L | 1.145 | 0.97 |
| 36_E | 54_S | 1.127 | 0.97 |
| 22_K | 39_N | 1.115 | 0.96 |
| 39_N | 57_Q | 1.104 | 0.96 |
| 33_S | 50_T | 1.103 | 0.96 |
| 58_E | 63_Q | 1.093 | 0.96 |
| 15_E | 43_K | 1.092 | 0.96 |
| 43_K | 54_S | 1.044 | 0.94 |
| 35_N | 53_E | 1.016 | 0.93 |
| 34_Q | 38_Q | 1.008 | 0.93 |
| 42_D | 60_Y | 1.004 | 0.93 |
| 12_R | 23_A | 1.004 | 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 | |
| 3c9iA | 6 | 0.9571 | 82.7 | 0.628 | Contact Map |
| 3qprA | 7 | 0 | 51.3 | 0.703 | Contact Map |
| 4linA | 12 | 1 | 46.5 | 0.711 | Contact Map |
| 2l7bA | 1 | 1 | 44.5 | 0.715 | Contact Map |
| 3ghgA | 4 | 1 | 43.1 | 0.717 | Contact Map |
| 1deqA | 4 | 1 | 38.1 | 0.726 | Contact Map |
| 2bnxA | 2 | 0.2143 | 33.8 | 0.733 | Contact Map |
| 4q4gX | 1 | 0 | 30.5 | 0.739 | Contact Map |
| 2dfsA | 2 | 0.7714 | 29.9 | 0.74 | Contact Map |
| 4y66B | 3 | 0.9286 | 27.6 | 0.744 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)