| mim |
| ID: | 1403703481 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (131) | ||
| Sequences: | 185 (141.7) | ||
| Seq/Len: | 1.412 | ||
| Nf(neff/√len): | 12.4 |
Jackhmmer Results: (2014_04_16)
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: 1.412).
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 |
| 98_S | 102_K | 3.015 | 1.00 |
| 129_E | 132_P | 2.331 | 0.99 |
| 65_E | 86_N | 2.321 | 0.99 |
| 121_K | 125_Y | 1.746 | 0.94 |
| 38_Y | 68_A | 1.734 | 0.94 |
| 83_I | 89_K | 1.630 | 0.91 |
| 129_E | 133_G | 1.610 | 0.90 |
| 65_E | 83_I | 1.553 | 0.88 |
| 119_P | 127_D | 1.451 | 0.82 |
| 37_F | 63_D | 1.451 | 0.82 |
| 79_S | 91_Q | 1.441 | 0.82 |
| 93_Q | 96_Q | 1.410 | 0.80 |
| 56_S | 59_Q | 1.402 | 0.79 |
| 38_Y | 104_A | 1.376 | 0.77 |
| 16_K | 22_F | 1.347 | 0.75 |
| 41_S | 45_Q | 1.335 | 0.74 |
| 100_T | 103_R | 1.311 | 0.72 |
| 65_E | 80_D | 1.287 | 0.70 |
| 40_I | 68_A | 1.285 | 0.70 |
| 100_T | 108_Q | 1.278 | 0.70 |
| 102_K | 106_Q | 1.271 | 0.69 |
| 37_F | 81_R | 1.254 | 0.67 |
| 100_T | 104_A | 1.237 | 0.66 |
| 38_Y | 101_E | 1.234 | 0.66 |
| 92_A | 99_N | 1.229 | 0.65 |
| 126_K | 129_E | 1.227 | 0.65 |
| 67_Q | 71_R | 1.226 | 0.65 |
| 37_F | 84_A | 1.222 | 0.65 |
| 52_D | 72_G | 1.216 | 0.64 |
| 16_K | 107_V | 1.209 | 0.63 |
| 7_W | 10_V | 1.206 | 0.63 |
| 5_G | 11_A | 1.196 | 0.62 |
| 79_S | 85_I | 1.191 | 0.62 |
| 64_L | 68_A | 1.189 | 0.61 |
| 94_L | 101_E | 1.187 | 0.61 |
| 84_A | 88_M | 1.186 | 0.61 |
| 86_N | 89_K | 1.176 | 0.60 |
| 32_G | 65_E | 1.171 | 0.60 |
| 101_E | 104_A | 1.170 | 0.60 |
| 32_G | 86_N | 1.168 | 0.59 |
| 21_D | 65_E | 1.148 | 0.57 |
| 52_D | 75_R | 1.141 | 0.57 |
| 7_W | 91_Q | 1.128 | 0.55 |
| 64_L | 100_T | 1.126 | 0.55 |
| 39_E | 97_D | 1.114 | 0.54 |
| 57_G | 62_P | 1.111 | 0.54 |
| 113_G | 117_H | 1.104 | 0.53 |
| 65_E | 89_K | 1.096 | 0.52 |
| 28_V | 127_D | 1.091 | 0.52 |
| 77_P | 84_A | 1.079 | 0.50 |
| 17_Y | 72_G | 1.073 | 0.50 |
| 32_G | 36_R | 1.069 | 0.49 |
| 121_K | 124_K | 1.049 | 0.47 |
| 64_L | 93_Q | 1.039 | 0.46 |
| 122_F | 129_E | 1.038 | 0.46 |
| 26_N | 67_Q | 1.037 | 0.46 |
| 23_S | 96_Q | 1.024 | 0.45 |
| 21_D | 86_N | 1.023 | 0.45 |
| 48_S | 89_K | 1.023 | 0.45 |
| 32_G | 46_N | 1.022 | 0.45 |
| 130_V | 134_Y | 1.010 | 0.43 |
| 21_D | 32_G | 1.009 | 0.43 |
| 108_Q | 111_G | 1.003 | 0.43 |
| 97_D | 101_E | 1.003 | 0.43 |
| 69_W | 74_R | 1.003 | 0.43 |
| 125_Y | 133_G | 1.000 | 0.42 |
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 | |
| 1ceeB | 1 | 0.4275 | 18.8 | 0.934 | Contact Map |
| 1ej5A | 1 | 0.6377 | 15 | 0.937 | Contact Map |
| 2lnhA | 1 | 0.4493 | 12.4 | 0.939 | Contact Map |
| 2khfA | 1 | 0.1812 | 11.2 | 0.94 | Contact Map |
| 2lzpA | 1 | 0.0942 | 10.5 | 0.941 | Contact Map |
| 4bg7A | 2 | 0.5362 | 7.4 | 0.944 | Contact Map |
| 2bzeA | 1 | 0.6667 | 6.2 | 0.946 | Contact Map |
| 3da7A | 4 | 0.2754 | 5.9 | 0.947 | Contact Map |
| 3u1uA | 2 | 0.6377 | 5.5 | 0.948 | Contact Map |
| 1z87A | 1 | 0.5145 | 4.7 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)