| CHEY_3q9s |
| ID: | 1444979830 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (118) | ||
| Sequences: | 105392 (77996.4) | ||
| Seq/Len: | 893.153 | ||
| Nf(neff/√len): | 7180.2 |
HHblits Results: (2015_06)
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: 893.153).
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 |
| 14_A | 30_H | 3.027 | 1.00 |
| 18_R | 30_H | 2.764 | 1.00 |
| 14_A | 32_D | 2.736 | 1.00 |
| 7_I | 37_G | 2.313 | 1.00 |
| 54_G | 81_R | 2.111 | 1.00 |
| 38_L | 66_R | 2.051 | 1.00 |
| 29_D | 46_P | 1.951 | 1.00 |
| 3_R | 29_D | 1.935 | 1.00 |
| 24_A | 109_L | 1.900 | 1.00 |
| 35_M | 57_D | 1.887 | 1.00 |
| 31_A | 40_K | 1.847 | 1.00 |
| 97_D | 111_R | 1.843 | 1.00 |
| 51_L | 63_V | 1.829 | 1.00 |
| 58_F | 66_R | 1.817 | 1.00 |
| 77_V | 95_A | 1.747 | 1.00 |
| 20_D | 105_P | 1.697 | 1.00 |
| 64_V | 75_I | 1.696 | 1.00 |
| 34_A | 58_F | 1.664 | 1.00 |
| 3_R | 27_V | 1.620 | 1.00 |
| 29_D | 40_K | 1.584 | 1.00 |
| 32_D | 36_N | 1.582 | 1.00 |
| 42_R | 70_N | 1.570 | 1.00 |
| 65_Q | 93_L | 1.541 | 1.00 |
| 33_S | 57_D | 1.536 | 1.00 |
| 29_D | 44_D | 1.504 | 1.00 |
| 53_L | 61_G | 1.433 | 1.00 |
| 68_R | 96_D | 1.432 | 1.00 |
| 5_L | 31_A | 1.398 | 0.99 |
| 18_R | 22_T | 1.391 | 0.99 |
| 3_R | 47_D | 1.389 | 0.99 |
| 66_R | 70_N | 1.382 | 0.99 |
| 49_I | 73_L | 1.377 | 0.99 |
| 33_S | 36_N | 1.340 | 0.99 |
| 81_R | 86_E | 1.305 | 0.99 |
| 34_A | 63_V | 1.303 | 0.99 |
| 2_Q | 116_L | 1.288 | 0.99 |
| 40_K | 46_P | 1.255 | 0.99 |
| 88_V | 92_G | 1.224 | 0.98 |
| 59_D | 62_D | 1.196 | 0.98 |
| 35_M | 58_F | 1.196 | 0.98 |
| 89_R | 93_L | 1.195 | 0.98 |
| 58_F | 62_D | 1.193 | 0.98 |
| 41_A | 67_L | 1.190 | 0.98 |
| 3_R | 44_D | 1.181 | 0.98 |
| 111_R | 114_V | 1.160 | 0.97 |
| 61_G | 90_L | 1.141 | 0.97 |
| 97_D | 114_V | 1.138 | 0.97 |
| 78_L | 103_F | 1.136 | 0.97 |
| 2_Q | 26_Y | 1.133 | 0.97 |
| 66_R | 69_K | 1.125 | 0.97 |
| 38_L | 63_V | 1.122 | 0.97 |
| 107_E | 111_R | 1.111 | 0.96 |
| 64_V | 77_V | 1.104 | 0.96 |
| 5_L | 46_P | 1.104 | 0.96 |
| 84_V | 88_V | 1.090 | 0.96 |
| 40_K | 44_D | 1.090 | 0.96 |
| 6_V | 17_L | 1.090 | 0.96 |
| 96_D | 115_Q | 1.060 | 0.95 |
| 61_G | 89_R | 1.042 | 0.94 |
| 83_T | 86_E | 1.042 | 0.94 |
| 77_V | 90_L | 1.036 | 0.94 |
| 11_H | 32_D | 1.027 | 0.94 |
| 15_N | 18_R | 1.019 | 0.93 |
| 109_L | 113_K | 1.006 | 0.93 |
| 37_G | 63_V | 1.003 | 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
- 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 | |
| 4g97A | 1 | 0.9835 | 99.5 | -0.188 | Contact Map |
| 3n0rA | 1 | 0.9835 | 99.5 | -0.183 | Contact Map |
| 2gwrA | 1 | 1 | 99.5 | -0.178 | Contact Map |
| 4kfcA | 2 | 1 | 99.5 | -0.178 | Contact Map |
| 2oqrA | 1 | 1 | 99.5 | -0.177 | Contact Map |
| 4b09A | 12 | 0.9504 | 99.5 | -0.17 | Contact Map |
| 2a9oA | 1 | 0.9669 | 99.5 | -0.167 | Contact Map |
| 1w25A | 2 | 1 | 99.4 | -0.165 | Contact Map |
| 3q9sA | 1 | 1 | 99.4 | -0.165 | Contact Map |
| 3dzdA | 2 | 0.9917 | 99.4 | -0.164 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)