| sdfsd |
| ID: | 1481798929 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 125 (124) | ||
| Sequences: | 839 (681.7) | ||
| Seq/Len: | 6.766 | ||
| Nf(neff/√len): | 61.2 |
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: 6.766).
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 |
| 5_K | 16_E | 3.472 | 1.00 |
| 16_E | 121_K | 2.311 | 1.00 |
| 18_S | 28_E | 2.299 | 1.00 |
| 30_R | 62_T | 2.230 | 1.00 |
| 7_I | 14_A | 2.158 | 1.00 |
| 64_N | 104_L | 2.046 | 1.00 |
| 91_R | 94_R | 1.971 | 1.00 |
| 60_F | 109_L | 1.905 | 1.00 |
| 16_E | 119_K | 1.854 | 1.00 |
| 65_D | 69_E | 1.835 | 1.00 |
| 91_R | 95_K | 1.833 | 1.00 |
| 30_R | 66_W | 1.779 | 1.00 |
| 14_A | 123_V | 1.772 | 1.00 |
| 33_L | 101_I | 1.754 | 1.00 |
| 77_W | 81_R | 1.726 | 1.00 |
| 84_N | 88_V | 1.699 | 1.00 |
| 114_D | 117_V | 1.665 | 1.00 |
| 25_L | 120_T | 1.662 | 1.00 |
| 19_G | 28_E | 1.603 | 1.00 |
| 38_G | 42_D | 1.520 | 0.99 |
| 71_S | 100_E | 1.519 | 0.99 |
| 37_E | 40_V | 1.518 | 0.99 |
| 48_K | 54_E | 1.503 | 0.99 |
| 63_V | 104_L | 1.465 | 0.99 |
| 29_A | 59_F | 1.455 | 0.99 |
| 20_N | 24_E | 1.453 | 0.99 |
| 26_L | 62_T | 1.430 | 0.99 |
| 52_L | 61_D | 1.428 | 0.99 |
| 49_M | 87_K | 1.417 | 0.99 |
| 37_E | 42_D | 1.405 | 0.99 |
| 48_K | 52_L | 1.346 | 0.98 |
| 85_E | 88_V | 1.342 | 0.98 |
| 90_F | 97_E | 1.342 | 0.98 |
| 114_D | 119_K | 1.327 | 0.98 |
| 39_I | 42_D | 1.323 | 0.98 |
| 101_I | 124_F | 1.317 | 0.98 |
| 82_E | 85_E | 1.307 | 0.98 |
| 46_K | 72_K | 1.278 | 0.97 |
| 110_K | 121_K | 1.270 | 0.97 |
| 34_L | 66_W | 1.267 | 0.97 |
| 17_I | 25_L | 1.262 | 0.97 |
| 83_G | 86_L | 1.254 | 0.97 |
| 56_E | 109_L | 1.223 | 0.96 |
| 106_Y | 109_L | 1.223 | 0.96 |
| 47_E | 54_E | 1.220 | 0.96 |
| 37_E | 41_L | 1.135 | 0.93 |
| 64_N | 109_L | 1.100 | 0.92 |
| 6_P | 35_E | 1.095 | 0.92 |
| 51_P | 85_E | 1.085 | 0.91 |
| 3_M | 28_E | 1.075 | 0.91 |
| 14_A | 121_K | 1.072 | 0.91 |
| 15_Y | 32_I | 1.065 | 0.90 |
| 37_E | 43_T | 1.057 | 0.90 |
| 17_I | 101_I | 1.044 | 0.89 |
| 26_L | 59_F | 1.044 | 0.89 |
| 15_Y | 124_F | 1.034 | 0.88 |
| 103_A | 107_H | 1.030 | 0.88 |
| 110_K | 119_K | 1.017 | 0.87 |
| 67_I | 70_I | 1.008 | 0.87 |
| 4_R | 28_E | 1.005 | 0.86 |
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 | |
| 1jw3A | 1 | 0.992 | 100 | 0.111 | Contact Map |
| 4n2pA | 4 | 1 | 100 | 0.147 | Contact Map |
| 1j5uA | 1 | 0.968 | 100 | 0.171 | Contact Map |
| 3gkuA | 3 | 0.888 | 47.7 | 0.905 | Contact Map |
| 1wv8A | 1 | 0.456 | 24.4 | 0.919 | Contact Map |
| 1r7lA | 2 | 0.312 | 19.2 | 0.923 | Contact Map |
| 2yztA | 1 | 0.44 | 12.5 | 0.929 | Contact Map |
| 4dv8A | 1 | 0.52 | 10.4 | 0.931 | Contact Map |
| 2pt7G | 2 | 0.552 | 8.7 | 0.934 | Contact Map |
| 4e5xG | 2 | 0.392 | 8.6 | 0.934 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)