| spot_449_607 |
| ID: | 1422378262 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (158) | ||
| Sequences: | 1757 (1219.5) | ||
| Seq/Len: | 11.120 | ||
| Nf(neff/√len): | 97.0 |
HHblits Results: (2013_03)
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: 11.120).
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_V | 22_I | 4.462 | 1.00 |
| 35_V | 77_A | 3.819 | 1.00 |
| 42_L | 79_I | 2.905 | 1.00 |
| 15_S | 18_A | 2.789 | 1.00 |
| 69_L | 78_E | 2.747 | 1.00 |
| 139_S | 145_V | 2.624 | 1.00 |
| 71_T | 74_D | 2.569 | 1.00 |
| 135_I | 154_I | 2.188 | 1.00 |
| 30_K | 33_D | 2.016 | 1.00 |
| 126_C | 151_C | 1.938 | 1.00 |
| 147_H | 151_C | 1.903 | 1.00 |
| 125_C | 151_C | 1.891 | 1.00 |
| 7_A | 26_L | 1.823 | 1.00 |
| 61_Q | 65_D | 1.822 | 1.00 |
| 133_P | 149_E | 1.819 | 1.00 |
| 25_L | 29_L | 1.742 | 1.00 |
| 126_C | 147_H | 1.735 | 1.00 |
| 125_C | 147_H | 1.684 | 1.00 |
| 70_A | 74_D | 1.604 | 1.00 |
| 38_G | 80_G | 1.591 | 1.00 |
| 31_R | 74_D | 1.554 | 1.00 |
| 121_T | 142_K | 1.530 | 1.00 |
| 35_V | 73_D | 1.475 | 1.00 |
| 64_L | 72_L | 1.463 | 1.00 |
| 31_R | 35_V | 1.445 | 1.00 |
| 69_L | 75_L | 1.424 | 1.00 |
| 86_S | 90_A | 1.408 | 1.00 |
| 78_E | 84_A | 1.392 | 0.99 |
| 66_R | 92_N | 1.381 | 0.99 |
| 139_S | 153_N | 1.364 | 0.99 |
| 80_G | 130_P | 1.362 | 0.99 |
| 114_G | 130_P | 1.343 | 0.99 |
| 115_A | 118_V | 1.294 | 0.99 |
| 62_R | 65_D | 1.279 | 0.99 |
| 17_K | 21_K | 1.264 | 0.99 |
| 13_V | 18_A | 1.262 | 0.99 |
| 128_P | 151_C | 1.253 | 0.99 |
| 24_Q | 28_N | 1.249 | 0.99 |
| 12_F | 17_K | 1.244 | 0.98 |
| 55_I | 112_I | 1.209 | 0.98 |
| 6_N | 26_L | 1.209 | 0.98 |
| 123_A | 145_V | 1.200 | 0.98 |
| 97_D | 106_S | 1.190 | 0.98 |
| 124_K | 127_R | 1.183 | 0.98 |
| 42_L | 76_L | 1.165 | 0.97 |
| 125_C | 128_P | 1.146 | 0.97 |
| 16_S | 20_A | 1.130 | 0.97 |
| 39_R | 76_L | 1.129 | 0.97 |
| 153_N | 156_G | 1.101 | 0.96 |
| 7_A | 30_K | 1.088 | 0.96 |
| 110_L | 134_I | 1.078 | 0.95 |
| 21_K | 137_H | 1.070 | 0.95 |
| 20_A | 24_Q | 1.061 | 0.95 |
| 72_L | 76_L | 1.058 | 0.95 |
| 67_M | 84_A | 1.043 | 0.94 |
| 34_S | 83_N | 1.034 | 0.94 |
| 21_K | 24_Q | 1.026 | 0.94 |
| 15_S | 88_V | 1.023 | 0.93 |
| 136_A | 144_L | 1.017 | 0.93 |
| 74_D | 77_A | 1.016 | 0.93 |
| 77_A | 80_G | 1.008 | 0.93 |
| 44_H | 47_G | 1.002 | 0.92 |
| 43_N | 66_R | 1.001 | 0.92 |
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 | |
| 1nubA | 2 | 0.6604 | 40 | 0.923 | Contact Map |
| 2kz2A | 1 | 0.5346 | 25.6 | 0.931 | Contact Map |
| 1vx5T | 1 | 0.6101 | 18.5 | 0.935 | Contact Map |
| 3iz6S | 1 | 0.6038 | 18.5 | 0.935 | Contact Map |
| 4i2yA | 2 | 0.5157 | 13.1 | 0.939 | Contact Map |
| 2mysC | 1 | 0.522 | 11.2 | 0.941 | Contact Map |
| 3u0kA | 1 | 0.4591 | 10.8 | 0.942 | Contact Map |
| 2jnfA | 1 | 0.5472 | 10.8 | 0.942 | Contact Map |
| 3j38T | 1 | 0.673 | 10.7 | 0.942 | Contact Map |
| 2k85A | 1 | 0.2013 | 10.6 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)