| v2 |
| ID: | 1513311451 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (100) | ||
| Sequences: | 253 (98.4) | ||
| Seq/Len: | 2.530 | ||
| Nf(neff/√len): | 9.8 |
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: 2.530).
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 |
| 48_I | 51_S | 2.299 | 1.00 |
| 29_S | 48_I | 1.961 | 0.99 |
| 101_A | 107_Q | 1.866 | 0.99 |
| 41_L | 64_F | 1.831 | 0.99 |
| 32_Y | 38_G | 1.677 | 0.97 |
| 62_R | 97_M | 1.674 | 0.97 |
| 99_K | 105_E | 1.522 | 0.95 |
| 44_D | 91_R | 1.519 | 0.95 |
| 33_S | 39_Y | 1.505 | 0.94 |
| 62_R | 65_N | 1.491 | 0.94 |
| 80_I | 85_C | 1.431 | 0.92 |
| 35_D | 39_Y | 1.402 | 0.91 |
| 89_C | 92_H | 1.396 | 0.91 |
| 86_C | 89_C | 1.396 | 0.91 |
| 27_L | 37_L | 1.388 | 0.90 |
| 22_V | 26_Q | 1.384 | 0.90 |
| 22_V | 59_C | 1.376 | 0.90 |
| 76_L | 86_C | 1.371 | 0.90 |
| 88_H | 91_R | 1.340 | 0.88 |
| 28_L | 31_D | 1.329 | 0.88 |
| 27_L | 30_Q | 1.315 | 0.87 |
| 68_V | 106_A | 1.280 | 0.85 |
| 99_K | 111_D | 1.261 | 0.84 |
| 109_I | 114_K | 1.249 | 0.83 |
| 98_D | 105_E | 1.224 | 0.81 |
| 21_S | 25_L | 1.208 | 0.80 |
| 44_D | 88_H | 1.207 | 0.80 |
| 47_C | 51_S | 1.199 | 0.79 |
| 51_S | 59_C | 1.187 | 0.78 |
| 42_I | 98_D | 1.180 | 0.78 |
| 29_S | 42_I | 1.152 | 0.75 |
| 78_Q | 90_P | 1.148 | 0.75 |
| 27_L | 113_Q | 1.129 | 0.73 |
| 62_R | 109_I | 1.110 | 0.71 |
| 66_A | 109_I | 1.106 | 0.71 |
| 36_T | 44_D | 1.097 | 0.70 |
| 66_A | 95_T | 1.094 | 0.70 |
| 96_G | 103_E | 1.094 | 0.70 |
| 47_C | 109_I | 1.087 | 0.69 |
| 65_N | 70_S | 1.085 | 0.69 |
| 35_D | 71_T | 1.081 | 0.68 |
| 31_D | 35_D | 1.059 | 0.66 |
| 23_K | 112_V | 1.057 | 0.66 |
| 96_G | 105_E | 1.057 | 0.66 |
| 52_R | 68_V | 1.042 | 0.64 |
| 63_H | 69_E | 1.041 | 0.64 |
| 86_C | 92_H | 1.039 | 0.64 |
| 74_S | 108_N | 1.037 | 0.64 |
| 94_T | 103_E | 1.036 | 0.63 |
| 60_R | 67_R | 1.024 | 0.62 |
| 56_E | 83_P | 1.018 | 0.61 |
| 68_V | 94_T | 1.016 | 0.61 |
| 53_N | 59_C | 1.016 | 0.61 |
| 101_A | 104_Q | 1.014 | 0.61 |
| 65_N | 68_V | 1.009 | 0.60 |
| 31_D | 71_T | 1.008 | 0.60 |
| 84_C | 89_C | 1.008 | 0.60 |
| 100_Q | 103_E | 1.006 | 0.60 |
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 | |
| 4w8yA | 2 | 0.5537 | 5.4 | 0.966 | Contact Map |
| 3x1lA | 1 | 0 | 5 | 0.966 | Contact Map |
| 4mbeH | 4 | 0.1074 | 4.7 | 0.967 | Contact Map |
| 3dc7A | 3 | 0.4959 | 3.9 | 0.968 | Contact Map |
| 1x6eA | 1 | 0.4298 | 3.8 | 0.968 | Contact Map |
| 3pdeA | 4 | 0.4545 | 3.8 | 0.968 | Contact Map |
| 3qkyA | 1 | 0.8595 | 3.6 | 0.969 | Contact Map |
| 4p0gA | 1 | 0.5124 | 3.2 | 0.969 | Contact Map |
| 3nsjA | 1 | 0.8843 | 3 | 0.97 | Contact Map |
| 1zlpA | 2 | 0.5207 | 2.7 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)