| 1nmr |
| ID: | 1381525157 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (78) | ||
| Sequences: | 261 (156.3) | ||
| Seq/Len: | 3.346 | ||
| Nf(neff/√len): | 17.7 |
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: 3.346).
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 |
| 32_Y | 36_V | 2.576 | 1.00 |
| 24_K | 55_N | 2.245 | 1.00 |
| 74_E | 78_V | 2.081 | 1.00 |
| 27_L | 72_V | 1.968 | 1.00 |
| 71_K | 78_V | 1.923 | 1.00 |
| 52_E | 72_V | 1.793 | 0.99 |
| 71_K | 74_E | 1.712 | 0.99 |
| 18_L | 26_V | 1.629 | 0.98 |
| 39_N | 61_L | 1.609 | 0.98 |
| 30_R | 82_H | 1.590 | 0.98 |
| 50_L | 68_L | 1.459 | 0.96 |
| 50_L | 67_L | 1.453 | 0.96 |
| 34_H | 65_P | 1.434 | 0.95 |
| 30_R | 62_L | 1.412 | 0.95 |
| 31_L | 62_L | 1.384 | 0.94 |
| 26_V | 54_D | 1.339 | 0.92 |
| 12_S | 59_L | 1.329 | 0.92 |
| 25_N | 58_I | 1.301 | 0.91 |
| 53_M | 61_L | 1.284 | 0.90 |
| 57_E | 78_V | 1.280 | 0.90 |
| 33_N | 68_L | 1.277 | 0.90 |
| 24_K | 58_I | 1.272 | 0.90 |
| 17_N | 70_A | 1.270 | 0.89 |
| 36_V | 40_P | 1.266 | 0.89 |
| 19_T | 22_Q | 1.212 | 0.86 |
| 77_E | 81_R | 1.162 | 0.83 |
| 24_K | 35_I | 1.096 | 0.78 |
| 35_I | 44_A | 1.090 | 0.77 |
| 52_E | 58_I | 1.057 | 0.74 |
| 79_L | 82_H | 1.056 | 0.74 |
| 12_S | 26_V | 1.053 | 0.74 |
| 42_A | 58_I | 1.051 | 0.73 |
| 33_N | 63_D | 1.044 | 0.73 |
| 15_L | 18_L | 1.034 | 0.72 |
| 11_L | 16_A | 1.033 | 0.71 |
| 14_V | 32_Y | 1.030 | 0.71 |
| 34_H | 79_L | 1.028 | 0.71 |
| 39_N | 58_I | 1.016 | 0.70 |
| 36_V | 69_D | 1.011 | 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 | |
| 1nmrA | 1 | 1 | 100 | 0.102 | Contact Map |
| 1g9lA | 1 | 1 | 100 | 0.149 | Contact Map |
| 4iveA | 4 | 0.9176 | 100 | 0.161 | Contact Map |
| 3kujA | 1 | 0.9059 | 100 | 0.176 | Contact Map |
| 2dydA | 1 | 0.9882 | 100 | 0.196 | Contact Map |
| 1ifwA | 1 | 0.9647 | 100 | 0.217 | Contact Map |
| 1i2tA | 1 | 0.7176 | 99.9 | 0.299 | Contact Map |
| 3i16A | 4 | 0.4235 | 8.2 | 0.928 | Contact Map |
| 1yrxA | 3 | 0.8941 | 5.8 | 0.933 | Contact Map |
| 4fgvA | 1 | 0.3294 | 5.5 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)