| contact map |
| ID: | 1504442236 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (139) | ||
| Sequences: | 3824 (2165.2) | ||
| Seq/Len: | 27.511 | ||
| Nf(neff/√len): | 183.6 |
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: 27.511).
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_V | 137_K | 4.084 | 1.00 |
| 86_N | 89_D | 2.595 | 1.00 |
| 123_A | 132_A | 2.589 | 1.00 |
| 19_R | 85_D | 2.584 | 1.00 |
| 26_G | 82_D | 2.463 | 1.00 |
| 35_A | 124_S | 2.444 | 1.00 |
| 107_S | 110_E | 2.322 | 1.00 |
| 43_D | 120_K | 2.104 | 1.00 |
| 39_T | 120_K | 2.101 | 1.00 |
| 11_T | 14_V | 2.026 | 1.00 |
| 21_S | 135_W | 2.004 | 1.00 |
| 43_D | 117_P | 2.002 | 1.00 |
| 12_A | 16_K | 2.000 | 1.00 |
| 22_W | 78_Q | 1.965 | 1.00 |
| 40_L | 113_K | 1.941 | 1.00 |
| 28_D | 31_G | 1.825 | 1.00 |
| 127_F | 132_A | 1.798 | 1.00 |
| 30_K | 71_I | 1.793 | 1.00 |
| 115_N | 139_V | 1.777 | 1.00 |
| 80_F | 142_V | 1.760 | 1.00 |
| 133_N | 137_K | 1.742 | 1.00 |
| 13_D | 16_K | 1.718 | 1.00 |
| 132_A | 136_A | 1.696 | 1.00 |
| 14_V | 133_N | 1.662 | 1.00 |
| 21_S | 131_Y | 1.650 | 1.00 |
| 98_A | 146_L | 1.629 | 1.00 |
| 33_G | 74_M | 1.617 | 1.00 |
| 18_L | 138_L | 1.613 | 1.00 |
| 128_G | 131_Y | 1.612 | 1.00 |
| 115_N | 140_A | 1.598 | 1.00 |
| 15_K | 85_D | 1.594 | 1.00 |
| 17_D | 134_A | 1.593 | 1.00 |
| 37_M | 69_H | 1.556 | 1.00 |
| 39_T | 124_S | 1.533 | 1.00 |
| 16_K | 20_D | 1.528 | 1.00 |
| 35_A | 38_T | 1.526 | 1.00 |
| 39_T | 117_P | 1.507 | 1.00 |
| 17_D | 131_Y | 1.477 | 1.00 |
| 35_A | 39_T | 1.450 | 1.00 |
| 13_D | 130_K | 1.367 | 0.99 |
| 119_K | 136_A | 1.359 | 0.99 |
| 24_V | 126_N | 1.336 | 0.99 |
| 39_T | 43_D | 1.286 | 0.99 |
| 11_T | 137_K | 1.275 | 0.99 |
| 76_A | 79_N | 1.272 | 0.99 |
| 78_Q | 82_D | 1.240 | 0.98 |
| 136_A | 140_A | 1.216 | 0.98 |
| 41_F | 51_F | 1.211 | 0.98 |
| 36_L | 118_I | 1.207 | 0.98 |
| 51_F | 101_H | 1.183 | 0.98 |
| 22_W | 25_I | 1.179 | 0.98 |
| 119_K | 132_A | 1.179 | 0.98 |
| 69_H | 73_L | 1.165 | 0.97 |
| 123_A | 129_D | 1.164 | 0.97 |
| 139_V | 143_Q | 1.163 | 0.97 |
| 44_N | 117_P | 1.162 | 0.97 |
| 44_N | 47_T | 1.160 | 0.97 |
| 43_D | 116_G | 1.147 | 0.97 |
| 71_I | 75_Y | 1.109 | 0.96 |
| 116_G | 120_K | 1.096 | 0.96 |
| 41_F | 45_Q | 1.095 | 0.96 |
| 100_N | 103_T | 1.080 | 0.95 |
| 34_V | 70_S | 1.078 | 0.95 |
| 40_L | 47_T | 1.061 | 0.95 |
| 127_F | 131_Y | 1.053 | 0.95 |
| 40_L | 117_P | 1.040 | 0.94 |
| 15_K | 19_R | 1.028 | 0.94 |
| 100_N | 104_R | 1.013 | 0.93 |
| 140_A | 144_A | 1.004 | 0.93 |
| 83_Q | 86_N | 1.002 | 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 | |
| 3g46A | 2 | 1 | 99.9 | 0.124 | Contact Map |
| 4hrrB | 4 | 1 | 99.9 | 0.136 | Contact Map |
| 4hrrA | 4 | 0.9863 | 99.9 | 0.153 | Contact Map |
| 2wtgA | 1 | 0.9452 | 99.9 | 0.156 | Contact Map |
| 3pt8A | 1 | 0.9521 | 99.9 | 0.161 | Contact Map |
| 1hlbA | 1 | 0.9863 | 99.9 | 0.161 | Contact Map |
| 2dc3A | 2 | 1 | 99.9 | 0.166 | Contact Map |
| 1mbaA | 1 | 0.9452 | 99.9 | 0.166 | Contact Map |
| 3pt8B | 1 | 0.9589 | 99.9 | 0.168 | Contact Map |
| 1hlmA | 1 | 0.9932 | 99.9 | 0.174 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)