| 4qnc |
| ID: | 1416966170 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 93 (84) | ||
| Sequences: | 294 (252.8) | ||
| Seq/Len: | 3.500 | ||
| Nf(neff/√len): | 27.6 |
HHblits Results: (2013_03)
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: 3.500).
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 |
| 29_Q | 32_D | 4.099 | 1.00 |
| 10_A | 63_A | 2.154 | 1.00 |
| 17_F | 41_F | 1.954 | 1.00 |
| 55_R | 60_I | 1.734 | 0.99 |
| 3_N | 57_D | 1.614 | 0.98 |
| 14_T | 67_T | 1.570 | 0.98 |
| 40_M | 79_L | 1.544 | 0.97 |
| 9_A | 48_W | 1.451 | 0.96 |
| 5_I | 40_M | 1.448 | 0.96 |
| 28_K | 81_E | 1.448 | 0.96 |
| 13_T | 44_G | 1.442 | 0.96 |
| 49_F | 61_I | 1.421 | 0.95 |
| 42_F | 71_V | 1.417 | 0.95 |
| 24_V | 30_T | 1.402 | 0.95 |
| 25_V | 77_Y | 1.389 | 0.94 |
| 30_T | 33_I | 1.370 | 0.94 |
| 17_F | 37_M | 1.325 | 0.92 |
| 21_V | 70_F | 1.276 | 0.90 |
| 12_L | 41_F | 1.268 | 0.90 |
| 29_Q | 38_Y | 1.261 | 0.90 |
| 41_F | 67_T | 1.252 | 0.89 |
| 26_M | 50_V | 1.244 | 0.89 |
| 17_F | 67_T | 1.214 | 0.87 |
| 38_Y | 71_V | 1.200 | 0.86 |
| 53_I | 61_I | 1.189 | 0.86 |
| 50_V | 69_F | 1.176 | 0.85 |
| 77_Y | 81_E | 1.166 | 0.84 |
| 14_T | 41_F | 1.158 | 0.84 |
| 52_G | 64_N | 1.156 | 0.84 |
| 39_I | 79_L | 1.151 | 0.83 |
| 49_F | 65_V | 1.149 | 0.83 |
| 33_I | 59_P | 1.149 | 0.83 |
| 45_V | 67_T | 1.148 | 0.83 |
| 35_R | 78_K | 1.114 | 0.80 |
| 28_K | 80_T | 1.108 | 0.80 |
| 48_W | 52_G | 1.078 | 0.77 |
| 23_R | 27_T | 1.069 | 0.76 |
| 6_G | 52_G | 1.062 | 0.76 |
| 3_N | 46_V | 1.023 | 0.72 |
| 4_L | 28_K | 1.003 | 0.70 |
| 5_I | 56_S | 1.002 | 0.69 |
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 | |
| 3l1lA | 1 | 0.9785 | 9.1 | 0.917 | Contact Map |
| 4oo9A | 1 | 0.8925 | 8.9 | 0.917 | Contact Map |
| 4or2A | 2 | 0.9032 | 8.8 | 0.917 | Contact Map |
| 3giaA | 1 | 0.9785 | 7.7 | 0.919 | Contact Map |
| 3tdsE | 5 | 0.9247 | 7 | 0.921 | Contact Map |
| 4tllA | 2 | 0.0108 | 4.7 | 0.927 | Contact Map |
| 3ne5A | 1 | 0.3226 | 4.5 | 0.928 | Contact Map |
| 1afoA | 2 | 0.3011 | 4.3 | 0.928 | Contact Map |
| 4nv5A | 2 | 0.957 | 3.9 | 0.93 | Contact Map |
| 3b9wA | 1 | 0.9462 | 3.9 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)