| shortest |
| ID: | 1488503689 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (105) | ||
| Sequences: | 2212 (186.1) | ||
| Seq/Len: | 21.067 | ||
| Nf(neff/√len): | 18.2 |
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: 21.067).
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 |
| 75_G | 79_V | 2.078 | 1.00 |
| 99_Q | 102_E | 2.002 | 1.00 |
| 87_C | 91_R | 1.877 | 1.00 |
| 102_E | 105_L | 1.874 | 1.00 |
| 55_Q | 59_N | 1.869 | 1.00 |
| 11_R | 15_L | 1.774 | 1.00 |
| 74_E | 79_V | 1.736 | 1.00 |
| 58_K | 62_V | 1.622 | 1.00 |
| 13_L | 22_R | 1.549 | 1.00 |
| 33_E | 36_G | 1.511 | 1.00 |
| 88_R | 91_R | 1.503 | 1.00 |
| 80_I | 83_V | 1.456 | 1.00 |
| 38_R | 47_W | 1.383 | 0.99 |
| 92_H | 103_R | 1.380 | 0.99 |
| 48_N | 51_Q | 1.378 | 0.99 |
| 63_S | 67_A | 1.373 | 0.99 |
| 91_R | 96_R | 1.342 | 0.99 |
| 3_L | 11_R | 1.341 | 0.99 |
| 99_Q | 105_L | 1.313 | 0.99 |
| 86_A | 89_A | 1.301 | 0.99 |
| 8_D | 14_C | 1.284 | 0.99 |
| 72_V | 75_G | 1.282 | 0.99 |
| 94_P | 98_R | 1.277 | 0.99 |
| 2_S | 6_I | 1.275 | 0.99 |
| 67_A | 71_A | 1.258 | 0.99 |
| 96_R | 99_Q | 1.243 | 0.98 |
| 1_G | 9_D | 1.234 | 0.98 |
| 94_P | 99_Q | 1.216 | 0.98 |
| 96_R | 102_E | 1.207 | 0.98 |
| 98_R | 102_E | 1.202 | 0.98 |
| 32_V | 35_L | 1.196 | 0.98 |
| 30_R | 35_L | 1.187 | 0.98 |
| 20_R | 23_D | 1.181 | 0.98 |
| 95_R | 99_Q | 1.152 | 0.97 |
| 51_Q | 75_G | 1.150 | 0.97 |
| 49_L | 64_L | 1.144 | 0.97 |
| 32_V | 36_G | 1.143 | 0.97 |
| 101_L | 104_I | 1.136 | 0.97 |
| 61_A | 64_L | 1.134 | 0.97 |
| 75_G | 83_V | 1.125 | 0.97 |
| 100_G | 105_L | 1.124 | 0.97 |
| 84_Q | 88_R | 1.106 | 0.96 |
| 65_L | 68_T | 1.090 | 0.96 |
| 44_K | 48_N | 1.086 | 0.96 |
| 53_W | 56_E | 1.082 | 0.96 |
| 25_L | 46_W | 1.074 | 0.95 |
| 16_F | 20_R | 1.073 | 0.95 |
| 57_L | 61_A | 1.069 | 0.95 |
| 47_W | 59_N | 1.061 | 0.95 |
| 98_R | 105_L | 1.056 | 0.95 |
| 74_E | 78_R | 1.051 | 0.94 |
| 38_R | 55_Q | 1.050 | 0.94 |
| 43_L | 50_L | 1.046 | 0.94 |
| 19_H | 23_D | 1.039 | 0.94 |
| 43_L | 54_S | 1.031 | 0.94 |
| 90_I | 94_P | 1.026 | 0.94 |
| 52_Y | 56_E | 1.016 | 0.93 |
| 30_R | 33_E | 1.016 | 0.93 |
| 28_V | 87_C | 1.015 | 0.93 |
| 29_T | 33_E | 1.010 | 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 | |
| 2lpdA | 1 | 0.3048 | 3.1 | 0.942 | Contact Map |
| 2qfaC | 1 | 0.4286 | 2.2 | 0.946 | Contact Map |
| 2a01A | 3 | 0.7143 | 1.7 | 0.95 | Contact Map |
| 4rnwA | 2 | 0.5714 | 1.2 | 0.954 | Contact Map |
| 1oz9A | 1 | 0.3048 | 1.1 | 0.954 | Contact Map |
| 4hneA | 2 | 0.5238 | 1 | 0.957 | Contact Map |
| 1oefA | 1 | 0.2286 | 0.9 | 0.957 | Contact Map |
| 4nkgB | 2 | 0.2381 | 0.9 | 0.957 | Contact Map |
| 3libA | 10 | 0.4571 | 0.9 | 0.958 | Contact Map |
| 2x7lM | 6 | 0.0762 | 0.8 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)