| ccdc84 1-320 230-320 |
| ID: | 1457539425 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (88) | ||
| Sequences: | 99 (62.4) | ||
| Seq/Len: | 1.125 | ||
| Nf(neff/√len): | 6.7 |
Jackhmmer Results: (2015_08)
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: 1.125).
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 |
| 8_H | 11_A | 2.379 | 0.99 |
| 39_E | 45_L | 2.152 | 0.98 |
| 73_R | 90_E | 2.010 | 0.97 |
| 9_S | 79_R | 1.784 | 0.92 |
| 84_R | 90_E | 1.632 | 0.87 |
| 6_N | 11_A | 1.631 | 0.87 |
| 56_N | 76_N | 1.562 | 0.83 |
| 44_K | 48_L | 1.525 | 0.81 |
| 41_E | 63_T | 1.406 | 0.73 |
| 21_E | 46_K | 1.392 | 0.72 |
| 9_S | 73_R | 1.371 | 0.71 |
| 57_F | 70_S | 1.356 | 0.69 |
| 55_A | 80_R | 1.349 | 0.69 |
| 73_R | 83_S | 1.332 | 0.67 |
| 20_E | 46_K | 1.303 | 0.65 |
| 9_S | 43_Q | 1.269 | 0.62 |
| 56_N | 61_S | 1.259 | 0.61 |
| 16_M | 20_E | 1.229 | 0.58 |
| 5_G | 62_R | 1.203 | 0.56 |
| 70_S | 76_N | 1.194 | 0.55 |
| 64_S | 70_S | 1.172 | 0.53 |
| 68_L | 80_R | 1.172 | 0.53 |
| 70_S | 81_W | 1.172 | 0.53 |
| 20_E | 50_P | 1.159 | 0.52 |
| 9_S | 21_E | 1.146 | 0.50 |
| 8_H | 47_K | 1.141 | 0.50 |
| 35_E | 42_K | 1.127 | 0.49 |
| 3_G | 43_Q | 1.114 | 0.47 |
| 49_P | 86_Q | 1.109 | 0.47 |
| 29_I | 34_E | 1.109 | 0.47 |
| 52_R | 55_A | 1.101 | 0.46 |
| 17_I | 60_S | 1.095 | 0.45 |
| 23_I | 46_K | 1.076 | 0.44 |
| 10_G | 58_D | 1.071 | 0.43 |
| 57_F | 81_W | 1.068 | 0.43 |
| 76_N | 85_H | 1.063 | 0.42 |
| 6_N | 10_G | 1.062 | 0.42 |
| 28_E | 64_S | 1.062 | 0.42 |
| 12_T | 60_S | 1.052 | 0.41 |
| 10_G | 52_R | 1.051 | 0.41 |
| 57_F | 61_S | 1.034 | 0.40 |
| 53_V | 80_R | 1.028 | 0.39 |
| 44_K | 65_A | 1.026 | 0.39 |
| 65_A | 90_E | 1.021 | 0.39 |
| 9_S | 87_F | 1.016 | 0.38 |
| 5_G | 8_H | 1.010 | 0.38 |
| 58_D | 61_S | 1.005 | 0.37 |
| 80_R | 87_F | 1.000 | 0.37 |
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 | 0.1429 | 6.1 | 0.945 | Contact Map |
| 2bjrA | 2 | 0.8901 | 5.3 | 0.946 | Contact Map |
| 4b4hA | 2 | 0.3407 | 4.5 | 0.948 | Contact Map |
| 3jszA | 1 | 0.4066 | 3.6 | 0.951 | Contact Map |
| 3m3wA | 2 | 0.2308 | 3 | 0.952 | Contact Map |
| 1b35D | 1 | 0.2967 | 2.9 | 0.953 | Contact Map |
| 1x6mA | 4 | 0.5495 | 2.7 | 0.954 | Contact Map |
| 1wdpA | 1 | 0.6923 | 2.6 | 0.954 | Contact Map |
| 2xfrA | 1 | 0.6923 | 2.5 | 0.954 | Contact Map |
| 1fa2A | 1 | 0.6813 | 2.1 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)