| 4nn2 |
| ID: | 1500381588 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (123) | ||
| Sequences: | 1759 (1103.1) | ||
| Seq/Len: | 14.301 | ||
| Nf(neff/√len): | 99.5 |
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: 14.301).
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 |
| 94_Y | 117_L | 2.916 | 1.00 |
| 71_M | 84_G | 2.751 | 1.00 |
| 68_G | 82_T | 2.709 | 1.00 |
| 71_M | 93_T | 2.587 | 1.00 |
| 5_C | 8_C | 2.572 | 1.00 |
| 32_H | 35_C | 2.491 | 1.00 |
| 119_C | 122_H | 2.481 | 1.00 |
| 7_F | 31_A | 2.059 | 1.00 |
| 95_H | 98_C | 2.008 | 1.00 |
| 90_C | 95_H | 1.977 | 1.00 |
| 33_Y | 44_Q | 1.963 | 1.00 |
| 90_C | 98_C | 1.933 | 1.00 |
| 41_G | 68_G | 1.907 | 1.00 |
| 73_C | 76_C | 1.805 | 1.00 |
| 84_G | 93_T | 1.751 | 1.00 |
| 75_L | 104_A | 1.751 | 1.00 |
| 67_R | 84_G | 1.626 | 1.00 |
| 19_G | 22_H | 1.533 | 1.00 |
| 39_S | 68_G | 1.509 | 1.00 |
| 85_C | 90_C | 1.464 | 1.00 |
| 92_K | 121_N | 1.426 | 1.00 |
| 64_E | 69_K | 1.424 | 1.00 |
| 76_C | 80_G | 1.407 | 0.99 |
| 64_E | 67_R | 1.401 | 0.99 |
| 76_C | 95_H | 1.377 | 0.99 |
| 84_G | 91_V | 1.351 | 0.99 |
| 25_N | 28_K | 1.343 | 0.99 |
| 85_C | 95_H | 1.331 | 0.99 |
| 64_E | 68_G | 1.298 | 0.99 |
| 39_S | 82_T | 1.252 | 0.99 |
| 65_I | 68_G | 1.245 | 0.98 |
| 110_M | 116_K | 1.225 | 0.98 |
| 30_A | 33_Y | 1.202 | 0.98 |
| 40_S | 84_G | 1.196 | 0.98 |
| 17_A | 20_K | 1.188 | 0.98 |
| 68_G | 71_M | 1.185 | 0.98 |
| 5_C | 35_C | 1.180 | 0.98 |
| 34_K | 97_H | 1.176 | 0.98 |
| 6_G | 29_A | 1.165 | 0.97 |
| 85_C | 98_C | 1.154 | 0.97 |
| 76_C | 85_C | 1.150 | 0.97 |
| 5_C | 32_H | 1.146 | 0.97 |
| 39_S | 96_Y | 1.123 | 0.97 |
| 76_C | 90_C | 1.110 | 0.96 |
| 96_Y | 99_G | 1.104 | 0.96 |
| 31_A | 58_I | 1.094 | 0.96 |
| 18_R | 21_L | 1.087 | 0.96 |
| 34_K | 96_Y | 1.081 | 0.95 |
| 111_S | 114_I | 1.058 | 0.95 |
| 3_P | 21_L | 1.056 | 0.95 |
| 46_T | 49_S | 1.025 | 0.93 |
| 12_E | 94_Y | 1.014 | 0.93 |
| 32_H | 36_M | 1.002 | 0.92 |
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 | |
| 4nn2A | 2 | 1 | 100 | 0.041 | Contact Map |
| 2lq6A | 1 | 0.5081 | 99.2 | 0.53 | Contact Map |
| 4gneA | 1 | 0.7177 | 94.8 | 0.788 | Contact Map |
| 4lk9A | 1 | 0.8226 | 93.6 | 0.799 | Contact Map |
| 3v43A | 1 | 0.8226 | 89.2 | 0.821 | Contact Map |
| 2kwjA | 1 | 0.8145 | 88.4 | 0.824 | Contact Map |
| 2ysmA | 1 | 0.7661 | 85.9 | 0.83 | Contact Map |
| 2g6qA | 1 | 0.3952 | 83.5 | 0.836 | Contact Map |
| 1wewA | 1 | 0.5484 | 82.6 | 0.837 | Contact Map |
| 4cosA | 1 | 0.4032 | 82.5 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)