| 1f21 |
| ID: | 1408343321 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 152 (142) | ||
| Sequences: | 2845 (1873.8) | ||
| Seq/Len: | 20.035 | ||
| Nf(neff/√len): | 157.2 |
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: 20.035).
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 |
| 70_Q | 74_Q | 3.453 | 1.00 |
| 52_V | 55_E | 3.440 | 1.00 |
| 84_K | 106_D | 3.391 | 1.00 |
| 55_E | 104_R | 3.388 | 1.00 |
| 64_I | 117_E | 3.239 | 1.00 |
| 99_V | 103_Q | 3.140 | 1.00 |
| 74_Q | 78_Q | 3.114 | 1.00 |
| 5_I | 53_A | 3.031 | 1.00 |
| 124_G | 129_E | 3.028 | 1.00 |
| 50_A | 72_V | 2.875 | 1.00 |
| 12_L | 136_R | 2.627 | 1.00 |
| 32_T | 130_R | 2.511 | 1.00 |
| 12_L | 140_M | 2.183 | 1.00 |
| 50_A | 65_L | 2.160 | 1.00 |
| 62_E | 113_Q | 2.072 | 1.00 |
| 19_G | 139_A | 2.012 | 1.00 |
| 44_R | 100_D | 1.991 | 1.00 |
| 12_L | 139_A | 1.989 | 1.00 |
| 82_N | 86_R | 1.836 | 1.00 |
| 55_E | 108_A | 1.801 | 1.00 |
| 7_T | 67_T | 1.757 | 1.00 |
| 67_T | 73_R | 1.745 | 1.00 |
| 10_S | 139_A | 1.706 | 1.00 |
| 66_S | 117_E | 1.683 | 1.00 |
| 20_Y | 52_V | 1.626 | 1.00 |
| 130_R | 133_E | 1.605 | 1.00 |
| 21_G | 138_A | 1.581 | 1.00 |
| 120_K | 123_A | 1.569 | 1.00 |
| 64_I | 115_K | 1.562 | 1.00 |
| 48_M | 52_V | 1.516 | 1.00 |
| 4_E | 25_R | 1.470 | 1.00 |
| 18_G | 45_M | 1.464 | 1.00 |
| 22_A | 33_F | 1.434 | 1.00 |
| 75_G | 102_W | 1.388 | 0.99 |
| 136_R | 140_M | 1.375 | 0.99 |
| 10_S | 135_A | 1.351 | 0.99 |
| 23_I | 131_A | 1.301 | 0.99 |
| 4_E | 66_S | 1.299 | 0.99 |
| 20_Y | 35_A | 1.279 | 0.99 |
| 136_R | 139_A | 1.276 | 0.99 |
| 125_H | 129_E | 1.237 | 0.98 |
| 6_F | 66_S | 1.228 | 0.98 |
| 6_F | 127_E | 1.190 | 0.98 |
| 7_T | 49_A | 1.183 | 0.98 |
| 10_S | 136_R | 1.179 | 0.98 |
| 25_R | 30_E | 1.174 | 0.98 |
| 108_A | 111_Q | 1.171 | 0.98 |
| 2_Q | 64_I | 1.167 | 0.97 |
| 133_E | 137_A | 1.162 | 0.97 |
| 4_E | 64_I | 1.160 | 0.97 |
| 34_S | 137_A | 1.156 | 0.97 |
| 51_I | 105_L | 1.149 | 0.97 |
| 21_G | 134_L | 1.148 | 0.97 |
| 18_G | 40_T | 1.143 | 0.97 |
| 131_A | 138_A | 1.125 | 0.97 |
| 6_F | 125_H | 1.118 | 0.96 |
| 80_I | 106_D | 1.090 | 0.96 |
| 25_R | 127_E | 1.084 | 0.96 |
| 36_G | 138_A | 1.075 | 0.95 |
| 123_A | 129_E | 1.068 | 0.95 |
| 19_G | 135_A | 1.050 | 0.94 |
| 2_Q | 62_E | 1.044 | 0.94 |
| 104_R | 108_A | 1.040 | 0.94 |
| 34_S | 138_A | 1.039 | 0.94 |
| 109_L | 116_W | 1.034 | 0.94 |
| 23_I | 127_E | 1.026 | 0.94 |
| 70_Q | 118_W | 1.023 | 0.93 |
| 20_Y | 49_A | 1.019 | 0.93 |
| 134_L | 138_A | 1.016 | 0.93 |
| 86_R | 93_K | 1.013 | 0.93 |
| 40_T | 44_R | 1.009 | 0.93 |
| 51_I | 104_R | 1.005 | 0.93 |
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 | |
| 1jl1A | 1 | 1 | 100 | 0.166 | Contact Map |
| 2e4lA | 1 | 1 | 100 | 0.171 | Contact Map |
| 4ibnA | 1 | 0.9934 | 100 | 0.195 | Contact Map |
| 1rilA | 1 | 0.9539 | 100 | 0.209 | Contact Map |
| 3h08A | 2 | 0.9211 | 100 | 0.216 | Contact Map |
| 4mh8A | 1 | 0 | 100 | 0.25 | Contact Map |
| 2lsnA | 1 | 0.9408 | 100 | 0.27 | Contact Map |
| 3qioA | 1 | 0.8224 | 100 | 0.278 | Contact Map |
| 2qkbA | 2 | 0.9276 | 100 | 0.283 | Contact Map |
| 1mu2A | 1 | 0.7961 | 99.9 | 0.393 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)