| ncor 1-96 -force run -force run |
| ID: | 1464871957 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 96 (92) | ||
| Sequences: | 57 (24.9) | ||
| Seq/Len: | 0.620 | ||
| Nf(neff/√len): | 2.6 |
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: 0.620).
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 |
| 65_D | 74_D | 2.330 | 0.96 |
| 39_Q | 42_T | 1.926 | 0.87 |
| 15_K | 18_K | 1.660 | 0.74 |
| 39_Q | 44_I | 1.583 | 0.69 |
| 39_Q | 45_F | 1.583 | 0.69 |
| 40_P | 44_I | 1.583 | 0.69 |
| 40_P | 45_F | 1.583 | 0.69 |
| 42_T | 45_F | 1.583 | 0.69 |
| 57_S | 85_D | 1.495 | 0.62 |
| 3_F | 6_K | 1.487 | 0.62 |
| 30_G | 35_M | 1.480 | 0.61 |
| 13_M | 25_L | 1.476 | 0.61 |
| 5_T | 23_R | 1.405 | 0.55 |
| 5_T | 12_P | 1.396 | 0.55 |
| 43_E | 48_P | 1.335 | 0.50 |
| 84_F | 91_H | 1.313 | 0.48 |
| 39_Q | 43_E | 1.284 | 0.45 |
| 40_P | 43_E | 1.284 | 0.45 |
| 39_Q | 48_P | 1.271 | 0.44 |
| 40_P | 48_P | 1.271 | 0.44 |
| 42_T | 48_P | 1.271 | 0.44 |
| 60_S | 74_D | 1.261 | 0.44 |
| 63_F | 70_L | 1.233 | 0.41 |
| 3_F | 16_S | 1.225 | 0.41 |
| 6_K | 16_S | 1.225 | 0.41 |
| 56_V | 61_H | 1.222 | 0.41 |
| 54_G | 60_S | 1.221 | 0.40 |
| 54_G | 57_S | 1.219 | 0.40 |
| 13_M | 21_I | 1.207 | 0.39 |
| 44_I | 48_P | 1.185 | 0.38 |
| 45_F | 48_P | 1.185 | 0.38 |
| 58_S | 61_H | 1.184 | 0.38 |
| 60_S | 64_A | 1.157 | 0.36 |
| 66_P | 70_L | 1.153 | 0.35 |
| 36_A | 53_S | 1.147 | 0.35 |
| 62_S | 86_D | 1.146 | 0.35 |
| 65_D | 84_F | 1.133 | 0.34 |
| 12_P | 47_L | 1.122 | 0.33 |
| 22_F | 85_D | 1.100 | 0.31 |
| 64_A | 70_L | 1.099 | 0.31 |
| 38_A | 47_L | 1.094 | 0.31 |
| 7_L | 17_K | 1.078 | 0.30 |
| 5_T | 22_F | 1.060 | 0.29 |
| 39_Q | 46_N | 1.052 | 0.28 |
| 40_P | 46_N | 1.052 | 0.28 |
| 42_T | 46_N | 1.052 | 0.28 |
| 51_T | 59_R | 1.042 | 0.27 |
| 87_K | 92_G | 1.041 | 0.27 |
| 8_E | 11_S | 1.037 | 0.27 |
| 43_E | 49_A | 1.031 | 0.27 |
| 33_S | 89_E | 1.017 | 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 | |
| 2ovmB | 1 | 0.1146 | 99.1 | 0.756 | Contact Map |
| 2gpvG | 3 | 0.125 | 98.7 | 0.792 | Contact Map |
| 2wh0Q | 2 | 0.1146 | 7.5 | 0.952 | Contact Map |
| 1a32A | 1 | 0.8125 | 5.1 | 0.956 | Contact Map |
| 1b4uA | 2 | 0.7188 | 4.5 | 0.957 | Contact Map |
| 1hn0A | 1 | 0.2917 | 4.3 | 0.957 | Contact Map |
| 4a5uB | 1 | 0.7188 | 3.5 | 0.959 | Contact Map |
| 3a6pA | 2 | 0.1042 | 3.4 | 0.959 | Contact Map |
| 4m7wA | 3 | 0.8854 | 3.4 | 0.959 | Contact Map |
| 4iylA | 1 | 0.7917 | 3 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)