| 6_1_333 166-260 -force run |
| ID: | 1432245204 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (94) | ||
| Sequences: | 63 (52.7) | ||
| Seq/Len: | 0.670 | ||
| Nf(neff/√len): | 5.4 |
Jackhmmer Results: (2015_01_07)
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: 0.670).
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 |
| 17_L | 71_F | 1.823 | 0.85 |
| 48_S | 87_L | 1.821 | 0.85 |
| 2_L | 35_Y | 1.611 | 0.73 |
| 29_R | 48_S | 1.594 | 0.72 |
| 29_R | 87_L | 1.559 | 0.70 |
| 13_I | 17_L | 1.526 | 0.67 |
| 8_V | 27_I | 1.485 | 0.64 |
| 51_H | 87_L | 1.394 | 0.57 |
| 53_G | 61_M | 1.355 | 0.54 |
| 49_M | 59_Y | 1.341 | 0.52 |
| 25_K | 30_N | 1.327 | 0.51 |
| 35_Y | 49_M | 1.288 | 0.48 |
| 14_Y | 52_A | 1.280 | 0.47 |
| 40_E | 59_Y | 1.279 | 0.47 |
| 19_P | 49_M | 1.269 | 0.46 |
| 55_T | 59_Y | 1.264 | 0.46 |
| 18_T | 79_S | 1.252 | 0.45 |
| 13_I | 56_S | 1.227 | 0.43 |
| 27_I | 87_L | 1.208 | 0.41 |
| 43_N | 65_I | 1.206 | 0.41 |
| 22_I | 32_V | 1.191 | 0.40 |
| 25_K | 78_I | 1.185 | 0.40 |
| 49_M | 54_S | 1.183 | 0.39 |
| 4_Q | 43_N | 1.178 | 0.39 |
| 33_K | 60_Y | 1.169 | 0.38 |
| 12_I | 22_I | 1.157 | 0.37 |
| 10_T | 77_E | 1.143 | 0.36 |
| 13_I | 39_A | 1.143 | 0.36 |
| 35_Y | 47_K | 1.141 | 0.36 |
| 26_N | 61_M | 1.132 | 0.35 |
| 12_I | 80_V | 1.123 | 0.35 |
| 58_I | 78_I | 1.119 | 0.34 |
| 59_Y | 89_A | 1.118 | 0.34 |
| 38_G | 71_F | 1.116 | 0.34 |
| 4_Q | 9_R | 1.101 | 0.33 |
| 24_D | 64_T | 1.097 | 0.33 |
| 45_T | 92_I | 1.089 | 0.32 |
| 47_K | 82_A | 1.082 | 0.32 |
| 2_L | 47_K | 1.076 | 0.31 |
| 67_G | 76_G | 1.060 | 0.30 |
| 19_P | 78_I | 1.059 | 0.30 |
| 44_W | 64_T | 1.058 | 0.30 |
| 56_S | 76_G | 1.053 | 0.30 |
| 12_I | 59_Y | 1.052 | 0.30 |
| 33_K | 56_S | 1.052 | 0.30 |
| 18_T | 31_Q | 1.051 | 0.30 |
| 31_Q | 59_Y | 1.042 | 0.29 |
| 10_T | 52_A | 1.036 | 0.29 |
| 40_E | 58_I | 1.034 | 0.28 |
| 71_F | 80_V | 1.015 | 0.27 |
| 48_S | 92_I | 1.012 | 0.27 |
| 25_K | 81_N | 1.011 | 0.27 |
| 15_D | 50_V | 1.005 | 0.26 |
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 | |
| 4wrtC | 1 | 0 | 7 | 0.936 | Contact Map |
| 3e8tA | 1 | 0.9579 | 5.3 | 0.94 | Contact Map |
| 4wsbC | 1 | 0.1789 | 3.5 | 0.945 | Contact Map |
| 2vvfA | 6 | 0.8421 | 3.2 | 0.946 | Contact Map |
| 4dgwC | 1 | 0.6316 | 3.1 | 0.947 | Contact Map |
| 2wjsA | 1 | 0.8211 | 3.1 | 0.947 | Contact Map |
| 1k0eA | 2 | 0.7053 | 2.9 | 0.947 | Contact Map |
| 2vl7A | 1 | 0.3789 | 2.9 | 0.948 | Contact Map |
| 3ky7A | 1 | 0.3053 | 2.8 | 0.948 | Contact Map |
| 1oy5A | 3 | 0.4211 | 2.7 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)