| dcp2 1-98 |
| ID: | 1502389065 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (97) | ||
| Sequences: | 303 (201.7) | ||
| Seq/Len: | 3.124 | ||
| Nf(neff/√len): | 20.5 |
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: 3.124).
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 |
| 13_D | 71_H | 2.548 | 1.00 |
| 26_E | 54_D | 2.238 | 1.00 |
| 32_E | 89_F | 2.105 | 1.00 |
| 17_A | 40_Q | 1.893 | 0.99 |
| 69_F | 75_L | 1.870 | 0.99 |
| 38_I | 61_L | 1.489 | 0.96 |
| 61_L | 86_F | 1.470 | 0.95 |
| 39_E | 93_K | 1.470 | 0.95 |
| 84_E | 88_D | 1.431 | 0.94 |
| 16_S | 68_L | 1.429 | 0.94 |
| 65_S | 83_E | 1.425 | 0.94 |
| 35_C | 85_A | 1.360 | 0.92 |
| 39_E | 44_F | 1.360 | 0.92 |
| 43_W | 47_D | 1.358 | 0.92 |
| 79_S | 82_H | 1.357 | 0.92 |
| 60_G | 86_F | 1.332 | 0.91 |
| 8_F | 11_V | 1.317 | 0.90 |
| 20_I | 23_L | 1.277 | 0.89 |
| 24_P | 97_P | 1.271 | 0.88 |
| 30_S | 89_F | 1.254 | 0.87 |
| 37_Q | 48_F | 1.246 | 0.87 |
| 27_E | 33_R | 1.239 | 0.87 |
| 81_V | 84_E | 1.235 | 0.86 |
| 50_R | 57_P | 1.208 | 0.85 |
| 16_S | 72_C | 1.200 | 0.84 |
| 2_S | 5_N | 1.189 | 0.83 |
| 27_E | 96_I | 1.174 | 0.82 |
| 29_S | 57_P | 1.156 | 0.81 |
| 3_F | 6_A | 1.143 | 0.80 |
| 23_L | 37_Q | 1.138 | 0.79 |
| 11_V | 42_H | 1.137 | 0.79 |
| 10_Q | 31_V | 1.117 | 0.78 |
| 46_E | 58_S | 1.109 | 0.77 |
| 22_N | 48_F | 1.092 | 0.75 |
| 18_R | 36_F | 1.087 | 0.75 |
| 14_D | 18_R | 1.085 | 0.75 |
| 3_F | 55_Q | 1.082 | 0.74 |
| 13_D | 38_I | 1.073 | 0.74 |
| 32_E | 98_V | 1.068 | 0.73 |
| 83_E | 87_D | 1.060 | 0.72 |
| 37_Q | 94_T | 1.058 | 0.72 |
| 29_S | 63_V | 1.050 | 0.71 |
| 9_S | 77_K | 1.048 | 0.71 |
| 7_T | 98_V | 1.037 | 0.70 |
| 8_F | 57_P | 1.036 | 0.70 |
| 54_D | 81_V | 1.031 | 0.69 |
| 8_F | 14_D | 1.031 | 0.69 |
| 29_S | 66_A | 1.029 | 0.69 |
| 2_S | 6_A | 1.029 | 0.69 |
| 44_F | 49_I | 1.028 | 0.69 |
| 53_N | 76_W | 1.022 | 0.68 |
| 53_N | 59_L | 1.010 | 0.67 |
| 95_R | 98_V | 1.006 | 0.67 |
| 80_K | 84_E | 1.003 | 0.66 |
| 3_F | 38_I | 1.001 | 0.66 |
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 | |
| 2qklB | 1 | 0.9184 | 100 | 0.055 | Contact Map |
| 2a6tA | 2 | 0.9694 | 100 | 0.265 | Contact Map |
| 1h2vC | 1 | 0.7959 | 8.3 | 0.93 | Contact Map |
| 1h7dA | 1 | 0.3776 | 7.9 | 0.931 | Contact Map |
| 2r09A | 2 | 0.8776 | 7.7 | 0.931 | Contact Map |
| 3gcgB | 1 | 0.9592 | 6 | 0.935 | Contact Map |
| 3trkA | 1 | 0.9184 | 5.8 | 0.935 | Contact Map |
| 3o8sA | 1 | 0.051 | 5.8 | 0.935 | Contact Map |
| 2hfiA | 1 | 0.6429 | 5.4 | 0.936 | Contact Map |
| 2hwkA | 1 | 0.9184 | 5.4 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)