| 1n9n |
| ID: | 1452700546 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (106) | ||
| Sequences: | 27014 (21208.2) | ||
| Seq/Len: | 254.849 | ||
| Nf(neff/√len): | 2059.9 |
HHblits Results: (2015_06)
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: 254.849).
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_R | 79_T | 3.111 | 1.00 |
| 4_H | 105_V | 2.586 | 1.00 |
| 72_L | 82_W | 2.219 | 1.00 |
| 24_G | 27_A | 2.198 | 1.00 |
| 72_L | 80_P | 2.171 | 1.00 |
| 21_A | 25_F | 2.015 | 1.00 |
| 68_S | 84_L | 1.992 | 1.00 |
| 26_Y | 33_P | 1.990 | 1.00 |
| 39_H | 43_F | 1.984 | 1.00 |
| 33_P | 37_L | 1.956 | 1.00 |
| 5_T | 28_M | 1.921 | 1.00 |
| 10_D | 15_D | 1.885 | 1.00 |
| 7_V | 102_G | 1.829 | 1.00 |
| 74_Y | 80_P | 1.804 | 1.00 |
| 31_Y | 76_K | 1.792 | 1.00 |
| 84_L | 105_V | 1.773 | 1.00 |
| 21_A | 36_V | 1.730 | 1.00 |
| 17_P | 40_N | 1.716 | 1.00 |
| 75_R | 81_F | 1.715 | 1.00 |
| 91_K | 97_V | 1.714 | 1.00 |
| 10_D | 17_P | 1.705 | 1.00 |
| 20_Y | 33_P | 1.656 | 1.00 |
| 7_V | 18_L | 1.585 | 1.00 |
| 23_E | 27_A | 1.584 | 1.00 |
| 71_L | 85_L | 1.515 | 1.00 |
| 5_T | 104_Q | 1.513 | 1.00 |
| 73_N | 83_N | 1.504 | 1.00 |
| 89_P | 97_V | 1.497 | 1.00 |
| 59_D | 63_K | 1.489 | 1.00 |
| 92_T | 96_R | 1.489 | 1.00 |
| 85_L | 104_Q | 1.481 | 1.00 |
| 68_S | 86_T | 1.469 | 1.00 |
| 32_G | 35_E | 1.406 | 0.99 |
| 26_Y | 32_G | 1.398 | 0.99 |
| 46_G | 49_T | 1.388 | 0.99 |
| 21_A | 26_Y | 1.380 | 0.99 |
| 23_E | 26_Y | 1.371 | 0.99 |
| 19_V | 99_K | 1.351 | 0.99 |
| 8_V | 101_V | 1.340 | 0.99 |
| 35_E | 76_K | 1.268 | 0.99 |
| 11_A | 15_D | 1.268 | 0.99 |
| 10_D | 19_V | 1.215 | 0.98 |
| 83_N | 104_Q | 1.203 | 0.98 |
| 31_Y | 35_E | 1.200 | 0.98 |
| 49_T | 53_E | 1.192 | 0.98 |
| 8_V | 99_K | 1.191 | 0.98 |
| 7_V | 25_F | 1.182 | 0.98 |
| 70_R | 84_L | 1.169 | 0.97 |
| 9_A | 102_G | 1.161 | 0.97 |
| 2_L | 6_F | 1.149 | 0.97 |
| 25_F | 29_T | 1.149 | 0.97 |
| 88_T | 101_V | 1.113 | 0.96 |
| 40_N | 43_F | 1.072 | 0.95 |
| 25_F | 36_V | 1.057 | 0.95 |
| 60_A | 65_E | 1.039 | 0.94 |
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 | |
| 2gj3A | 2 | 0.9725 | 99.1 | -0.293 | Contact Map |
| 3lyxA | 2 | 0.9725 | 99.1 | -0.28 | Contact Map |
| 2wkqA | 1 | 1 | 99.1 | -0.278 | Contact Map |
| 3gdiA | 2 | 0.9725 | 99 | -0.254 | Contact Map |
| 4eetB | 2 | 1 | 99 | -0.252 | Contact Map |
| 3rtyA | 8 | 0.9725 | 99 | -0.248 | Contact Map |
| 3f1pA | 1 | 0.9725 | 99 | -0.244 | Contact Map |
| 3f1pB | 1 | 0.9725 | 98.9 | -0.237 | Contact Map |
| 3ewkA | 1 | 0.9358 | 98.9 | -0.212 | Contact Map |
| 4wujA | 4 | 0.9541 | 98.8 | -0.207 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)