| 4nn2 |
| ID: | 1501760704 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 124 (120) | ||
| Sequences: | 716 (689.3) | ||
| Seq/Len: | 5.967 | ||
| Nf(neff/√len): | 62.9 |
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: 5.967).
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 |
| 71_M | 93_T | 3.098 | 1.00 |
| 71_M | 84_G | 2.645 | 1.00 |
| 32_H | 35_C | 2.564 | 1.00 |
| 95_H | 98_C | 2.460 | 1.00 |
| 119_C | 122_H | 2.402 | 1.00 |
| 68_G | 82_T | 2.262 | 1.00 |
| 19_G | 22_H | 2.230 | 1.00 |
| 84_G | 93_T | 2.145 | 1.00 |
| 73_C | 76_C | 2.101 | 1.00 |
| 73_C | 95_H | 1.846 | 1.00 |
| 33_Y | 44_Q | 1.815 | 1.00 |
| 7_F | 31_A | 1.713 | 1.00 |
| 90_C | 98_C | 1.702 | 1.00 |
| 94_Y | 117_L | 1.649 | 1.00 |
| 85_C | 98_C | 1.575 | 0.99 |
| 76_C | 95_H | 1.573 | 0.99 |
| 73_C | 98_C | 1.565 | 0.99 |
| 85_C | 95_H | 1.558 | 0.99 |
| 25_N | 28_K | 1.532 | 0.99 |
| 75_L | 104_A | 1.529 | 0.99 |
| 96_Y | 99_G | 1.509 | 0.99 |
| 76_C | 85_C | 1.498 | 0.99 |
| 34_K | 96_Y | 1.446 | 0.99 |
| 39_S | 81_A | 1.428 | 0.98 |
| 73_C | 85_C | 1.423 | 0.98 |
| 90_C | 95_H | 1.414 | 0.98 |
| 5_C | 35_C | 1.395 | 0.98 |
| 85_C | 90_C | 1.355 | 0.98 |
| 84_G | 91_V | 1.323 | 0.97 |
| 30_A | 33_Y | 1.321 | 0.97 |
| 41_G | 68_G | 1.310 | 0.97 |
| 65_I | 68_G | 1.293 | 0.97 |
| 5_C | 32_H | 1.292 | 0.97 |
| 76_C | 98_C | 1.286 | 0.97 |
| 73_C | 80_G | 1.226 | 0.95 |
| 64_E | 69_K | 1.183 | 0.94 |
| 39_S | 96_Y | 1.174 | 0.93 |
| 94_Y | 102_D | 1.165 | 0.93 |
| 3_P | 12_E | 1.142 | 0.92 |
| 4_K | 9_H | 1.116 | 0.91 |
| 80_G | 95_H | 1.110 | 0.91 |
| 39_S | 82_T | 1.105 | 0.90 |
| 82_T | 96_Y | 1.101 | 0.90 |
| 38_F | 83_I | 1.097 | 0.90 |
| 65_I | 69_K | 1.059 | 0.88 |
| 67_R | 84_G | 1.032 | 0.86 |
| 39_S | 68_G | 1.007 | 0.84 |
| 73_C | 90_C | 1.000 | 0.83 |
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 | 0.05 | Contact Map |
| 2lq6A | 1 | 0.5081 | 99.1 | 0.546 | Contact Map |
| 4lk9A | 1 | 0.8226 | 94.8 | 0.785 | Contact Map |
| 4gneA | 1 | 0.7177 | 93.8 | 0.794 | Contact Map |
| 3v43A | 1 | 0.8226 | 92 | 0.807 | Contact Map |
| 2kwjA | 1 | 0.8145 | 90.2 | 0.815 | Contact Map |
| 2ysmA | 1 | 0.7661 | 84.8 | 0.831 | Contact Map |
| 2g6qA | 1 | 0.3952 | 82.4 | 0.835 | Contact Map |
| 1wewA | 1 | 0.5484 | 82 | 0.836 | Contact Map |
| 4cosA | 1 | 0.379 | 80.7 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)