| beps_core_with 4 iterations |
| ID: | 1507630006 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (123) | ||
| Sequences: | 168 (115) | ||
| Seq/Len: | 1.366 | ||
| Nf(neff/√len): | 10.4 |
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: 1.366).
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 |
| 84_H | 92_R | 1.978 | 0.97 |
| 81_N | 91_G | 1.939 | 0.97 |
| 70_N | 117_E | 1.931 | 0.97 |
| 58_K | 72_E | 1.874 | 0.96 |
| 84_H | 87_R | 1.834 | 0.95 |
| 65_T | 77_F | 1.781 | 0.94 |
| 81_N | 94_Q | 1.769 | 0.94 |
| 81_N | 92_R | 1.731 | 0.93 |
| 88_E | 92_R | 1.724 | 0.93 |
| 8_A | 12_R | 1.626 | 0.90 |
| 87_R | 92_R | 1.620 | 0.90 |
| 64_L | 105_A | 1.543 | 0.86 |
| 28_E | 31_R | 1.530 | 0.86 |
| 73_A | 107_H | 1.527 | 0.86 |
| 6_E | 107_H | 1.520 | 0.85 |
| 91_G | 95_R | 1.504 | 0.84 |
| 81_N | 119_M | 1.463 | 0.82 |
| 100_N | 103_K | 1.444 | 0.81 |
| 51_L | 76_L | 1.402 | 0.78 |
| 20_D | 44_I | 1.383 | 0.77 |
| 44_I | 49_Q | 1.357 | 0.75 |
| 29_M | 123_S | 1.329 | 0.73 |
| 84_H | 88_E | 1.328 | 0.73 |
| 38_F | 84_H | 1.316 | 0.72 |
| 70_N | 110_N | 1.309 | 0.71 |
| 2_K | 62_Q | 1.299 | 0.70 |
| 115_T | 118_R | 1.279 | 0.69 |
| 50_R | 53_Q | 1.271 | 0.68 |
| 63_G | 106_G | 1.271 | 0.68 |
| 38_F | 91_G | 1.239 | 0.65 |
| 5_F | 115_T | 1.236 | 0.65 |
| 8_A | 89_G | 1.226 | 0.64 |
| 61_L | 105_A | 1.216 | 0.63 |
| 97_F | 105_A | 1.200 | 0.61 |
| 28_E | 103_K | 1.182 | 0.60 |
| 3_N | 60_N | 1.172 | 0.59 |
| 31_R | 123_S | 1.158 | 0.57 |
| 5_F | 18_F | 1.145 | 0.56 |
| 7_W | 12_R | 1.131 | 0.55 |
| 12_R | 89_G | 1.127 | 0.54 |
| 66_R | 107_H | 1.113 | 0.53 |
| 19_A | 33_G | 1.112 | 0.53 |
| 117_E | 123_S | 1.093 | 0.51 |
| 38_F | 85_P | 1.083 | 0.50 |
| 31_R | 34_W | 1.077 | 0.49 |
| 91_G | 119_M | 1.064 | 0.48 |
| 81_N | 123_S | 1.056 | 0.47 |
| 74_I | 117_E | 1.054 | 0.47 |
| 1_F | 69_F | 1.052 | 0.47 |
| 93_T | 97_F | 1.051 | 0.47 |
| 51_L | 83_L | 1.050 | 0.47 |
| 14_I | 79_S | 1.046 | 0.46 |
| 94_Q | 118_R | 1.043 | 0.46 |
| 46_E | 93_T | 1.035 | 0.45 |
| 41_G | 122_A | 1.035 | 0.45 |
| 100_N | 110_N | 1.035 | 0.45 |
| 50_R | 80_L | 1.021 | 0.44 |
| 9_G | 86_F | 1.020 | 0.44 |
| 54_T | 57_E | 1.017 | 0.43 |
| 15_P | 23_T | 1.014 | 0.43 |
| 92_R | 95_R | 1.012 | 0.43 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4n67A | 1 | 1 | 99.9 | 0.506 | Contact Map |
| 4npsA | 1 | 0.9187 | 99.9 | 0.507 | Contact Map |
| 2jk8A | 2 | 1 | 99.9 | 0.509 | Contact Map |
| 4py3A | 10 | 0 | 99.9 | 0.511 | Contact Map |
| 4m16A | 1 | 1 | 99.9 | 0.516 | Contact Map |
| 3zc7A | 1 | 0.878 | 99.9 | 0.559 | Contact Map |
| 3shgA | 1 | 0.878 | 99.9 | 0.58 | Contact Map |
| 3se5A | 4 | 0.7886 | 99.6 | 0.669 | Contact Map |
| 2f6sA | 2 | 0.7886 | 99.6 | 0.675 | Contact Map |
| 3zlmA | 1 | 0.7886 | 99.6 | 0.685 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)