| j27 |
| ID: | 1487704482 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (85) | ||
| Sequences: | 653 (478.9) | ||
| Seq/Len: | 7.682 | ||
| Nf(neff/√len): | 51.9 |
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: 7.682).
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 |
| 44_L | 56_G | 2.696 | 1.00 |
| 47_L | 62_N | 2.402 | 1.00 |
| 16_A | 21_E | 2.340 | 1.00 |
| 6_G | 71_M | 2.259 | 1.00 |
| 11_R | 52_Y | 2.113 | 1.00 |
| 33_L | 41_A | 2.112 | 1.00 |
| 6_G | 67_V | 2.088 | 1.00 |
| 45_Y | 54_V | 2.024 | 1.00 |
| 33_L | 57_F | 1.895 | 1.00 |
| 40_S | 59_L | 1.803 | 1.00 |
| 29_A | 84_F | 1.765 | 1.00 |
| 61_G | 67_V | 1.693 | 1.00 |
| 16_A | 25_L | 1.585 | 1.00 |
| 10_A | 78_L | 1.553 | 1.00 |
| 30_L | 41_A | 1.508 | 0.99 |
| 22_K | 43_R | 1.501 | 0.99 |
| 46_G | 54_V | 1.469 | 0.99 |
| 27_K | 31_E | 1.468 | 0.99 |
| 14_T | 25_L | 1.444 | 0.99 |
| 27_K | 30_L | 1.433 | 0.99 |
| 44_L | 60_L | 1.420 | 0.99 |
| 24_A | 28_P | 1.419 | 0.99 |
| 44_L | 54_V | 1.374 | 0.99 |
| 73_A | 76_R | 1.350 | 0.99 |
| 46_G | 52_Y | 1.328 | 0.98 |
| 8_Y | 71_M | 1.289 | 0.98 |
| 12_L | 78_L | 1.286 | 0.98 |
| 12_L | 53_E | 1.278 | 0.98 |
| 42_A | 62_N | 1.227 | 0.97 |
| 22_K | 48_D | 1.222 | 0.97 |
| 17_R | 51_G | 1.195 | 0.96 |
| 29_A | 78_L | 1.194 | 0.96 |
| 65_A | 69_E | 1.185 | 0.96 |
| 4_Y | 64_P | 1.152 | 0.95 |
| 46_G | 49_A | 1.145 | 0.95 |
| 33_L | 39_V | 1.140 | 0.95 |
| 59_L | 67_V | 1.130 | 0.95 |
| 64_P | 68_E | 1.129 | 0.95 |
| 16_A | 50_W | 1.118 | 0.94 |
| 13_E | 52_Y | 1.100 | 0.93 |
| 71_M | 74_A | 1.097 | 0.93 |
| 8_Y | 57_F | 1.089 | 0.93 |
| 4_Y | 7_L | 1.077 | 0.93 |
| 33_L | 74_A | 1.058 | 0.92 |
| 68_E | 72_R | 1.057 | 0.92 |
| 14_T | 53_E | 1.053 | 0.91 |
| 31_E | 35_A | 1.051 | 0.91 |
| 37_F | 77_F | 1.033 | 0.90 |
| 34_K | 38_P | 1.009 | 0.89 |
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 | |
| 1j27A | 1 | 0.9796 | 100 | 0.078 | Contact Map |
| 3mf7A | 1 | 0.5612 | 17 | 0.913 | Contact Map |
| 2qkdA | 1 | 0.8469 | 6.6 | 0.928 | Contact Map |
| 2ch1A | 4 | 0.8265 | 6.2 | 0.929 | Contact Map |
| 1otgA | 3 | 0.6122 | 6 | 0.929 | Contact Map |
| 2aalA | 6 | 0.6633 | 5.9 | 0.93 | Contact Map |
| 4u5rA | 3 | 0.898 | 5.8 | 0.93 | Contact Map |
| 2abkA | 1 | 0.7653 | 5.5 | 0.93 | Contact Map |
| 3hvwA | 1 | 0.9286 | 4.8 | 0.932 | Contact Map |
| 1ve4A | 1 | 0.398 | 4.8 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)