| ccdc84 |
| ID: | 1476355182 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (86) | ||
| Sequences: | 107 (68.1) | ||
| Seq/Len: | 1.244 | ||
| Nf(neff/√len): | 7.3 |
Jackhmmer Results: (2016_04)
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: 1.244).
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 |
| 69_R | 86_E | 1.974 | 0.97 |
| 5_H | 8_A | 1.948 | 0.96 |
| 35_E | 41_L | 1.931 | 0.96 |
| 6_S | 75_R | 1.792 | 0.94 |
| 69_R | 79_S | 1.685 | 0.91 |
| 84_K | 87_A | 1.668 | 0.90 |
| 17_E | 42_K | 1.575 | 0.86 |
| 52_N | 72_N | 1.498 | 0.82 |
| 40_K | 44_L | 1.451 | 0.79 |
| 7_G | 48_R | 1.441 | 0.79 |
| 30_E | 34_K | 1.390 | 0.75 |
| 80_R | 86_E | 1.370 | 0.73 |
| 64_L | 76_R | 1.312 | 0.69 |
| 17_E | 66_S | 1.292 | 0.67 |
| 58_R | 73_N | 1.274 | 0.65 |
| 3_N | 8_A | 1.269 | 0.65 |
| 5_H | 43_K | 1.263 | 0.64 |
| 49_V | 76_R | 1.238 | 0.62 |
| 2_G | 58_R | 1.232 | 0.62 |
| 4_I | 72_N | 1.228 | 0.61 |
| 51_A | 76_R | 1.210 | 0.60 |
| 66_S | 72_N | 1.181 | 0.57 |
| 66_S | 77_W | 1.160 | 0.55 |
| 72_N | 81_H | 1.159 | 0.55 |
| 69_R | 80_R | 1.148 | 0.54 |
| 53_F | 66_S | 1.141 | 0.53 |
| 13_M | 21_G | 1.129 | 0.52 |
| 18_Y | 42_K | 1.122 | 0.51 |
| 75_R | 82_Q | 1.114 | 0.50 |
| 45_P | 82_Q | 1.114 | 0.50 |
| 41_L | 62_G | 1.112 | 0.50 |
| 29_Y | 33_L | 1.108 | 0.50 |
| 52_N | 57_S | 1.105 | 0.49 |
| 27_P | 30_E | 1.104 | 0.49 |
| 49_V | 64_L | 1.104 | 0.49 |
| 27_P | 32_F | 1.101 | 0.49 |
| 53_F | 77_W | 1.101 | 0.49 |
| 44_L | 70_V | 1.093 | 0.48 |
| 51_A | 64_L | 1.088 | 0.48 |
| 76_R | 83_F | 1.079 | 0.47 |
| 8_A | 79_S | 1.074 | 0.46 |
| 51_A | 54_D | 1.074 | 0.46 |
| 48_R | 51_A | 1.056 | 0.45 |
| 7_G | 50_G | 1.055 | 0.44 |
| 19_I | 37_E | 1.034 | 0.42 |
| 60_S | 66_S | 1.025 | 0.42 |
| 28_S | 35_E | 1.019 | 0.41 |
| 3_N | 6_S | 1.017 | 0.41 |
| 44_L | 49_V | 1.014 | 0.40 |
| 44_L | 75_R | 1.009 | 0.40 |
| 6_S | 73_N | 1.001 | 0.39 |
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 | |
| 4blpA | 6 | 0.1136 | 11.4 | 0.935 | Contact Map |
| 3m3wA | 2 | 0.2045 | 9.2 | 0.937 | Contact Map |
| 2xfrA | 1 | 0.6932 | 7.8 | 0.939 | Contact Map |
| 1x6mA | 4 | 0.5227 | 7.1 | 0.94 | Contact Map |
| 1wdpA | 1 | 0.6932 | 7 | 0.94 | Contact Map |
| 1p90A | 1 | 0.1932 | 3.6 | 0.948 | Contact Map |
| 1fa2A | 1 | 0.6932 | 3.5 | 0.949 | Contact Map |
| 2bjrA | 2 | 0.6477 | 2.6 | 0.952 | Contact Map |
| 1ka8A | 6 | 0.7273 | 2.5 | 0.952 | Contact Map |
| 3l3bA | 2 | 0.3977 | 2.3 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)