| 1A6M |
| ID: | 1411070488 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (147) | ||
| Sequences: | 1955 (1107.1) | ||
| Seq/Len: | 13.299 | ||
| Nf(neff/√len): | 91.3 |
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: 13.299).
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 |
| 6_E | 133_K | 3.909 | 1.00 |
| 18_E | 77_K | 2.671 | 1.00 |
| 123_F | 128_Q | 2.565 | 1.00 |
| 75_I | 138_F | 2.445 | 1.00 |
| 32_L | 106_F | 2.302 | 1.00 |
| 100_P | 103_Y | 2.261 | 1.00 |
| 3_S | 6_E | 2.242 | 1.00 |
| 116_H | 128_Q | 2.131 | 1.00 |
| 90_A | 145_K | 2.081 | 1.00 |
| 3_S | 133_K | 2.053 | 1.00 |
| 11_L | 80_G | 2.036 | 1.00 |
| 14_W | 73_G | 1.944 | 1.00 |
| 108_S | 135_L | 1.921 | 1.00 |
| 124_G | 127_A | 1.868 | 1.00 |
| 9_L | 130_A | 1.844 | 1.00 |
| 8_Q | 12_H | 1.821 | 1.00 |
| 87_K | 145_K | 1.777 | 1.00 |
| 92_S | 96_K | 1.776 | 1.00 |
| 13_V | 131_M | 1.768 | 1.00 |
| 20_D | 23_G | 1.756 | 1.00 |
| 31_R | 113_H | 1.730 | 1.00 |
| 10_V | 134_A | 1.670 | 1.00 |
| 9_L | 127_A | 1.625 | 1.00 |
| 27_D | 117_S | 1.579 | 1.00 |
| 4_E | 8_Q | 1.568 | 1.00 |
| 13_V | 127_A | 1.552 | 1.00 |
| 64_H | 68_V | 1.532 | 1.00 |
| 7_W | 80_G | 1.518 | 1.00 |
| 9_L | 13_V | 1.503 | 1.00 |
| 22_A | 66_V | 1.489 | 1.00 |
| 35_S | 110_A | 1.483 | 1.00 |
| 112_I | 132_N | 1.472 | 1.00 |
| 29_L | 64_H | 1.461 | 1.00 |
| 16_K | 122_D | 1.453 | 1.00 |
| 4_E | 7_W | 1.439 | 1.00 |
| 25_G | 69_L | 1.431 | 1.00 |
| 129_G | 133_K | 1.416 | 1.00 |
| 14_W | 76_L | 1.400 | 0.99 |
| 108_S | 136_E | 1.399 | 0.99 |
| 127_A | 130_A | 1.328 | 0.99 |
| 90_A | 142_I | 1.326 | 0.99 |
| 27_D | 30_I | 1.268 | 0.99 |
| 140_K | 144_A | 1.262 | 0.99 |
| 36_H | 110_A | 1.245 | 0.98 |
| 114_V | 118_R | 1.243 | 0.98 |
| 27_D | 31_R | 1.239 | 0.98 |
| 31_R | 117_S | 1.236 | 0.98 |
| 28_I | 111_I | 1.225 | 0.98 |
| 26_Q | 30_I | 1.207 | 0.98 |
| 71_A | 74_A | 1.197 | 0.98 |
| 36_H | 39_T | 1.183 | 0.98 |
| 32_L | 131_M | 1.166 | 0.97 |
| 6_E | 129_G | 1.162 | 0.97 |
| 105_E | 143_A | 1.158 | 0.97 |
| 139_R | 143_A | 1.142 | 0.97 |
| 111_I | 135_L | 1.135 | 0.97 |
| 24_H | 114_V | 1.132 | 0.97 |
| 73_G | 77_K | 1.131 | 0.97 |
| 132_N | 136_E | 1.109 | 0.96 |
| 24_H | 27_D | 1.102 | 0.96 |
| 111_I | 115_L | 1.095 | 0.96 |
| 29_L | 68_V | 1.093 | 0.96 |
| 14_W | 25_G | 1.084 | 0.96 |
| 35_S | 109_E | 1.079 | 0.95 |
| 116_H | 125_A | 1.059 | 0.95 |
| 92_S | 97_H | 1.050 | 0.94 |
| 35_S | 113_H | 1.039 | 0.94 |
| 109_E | 113_H | 1.038 | 0.94 |
| 68_V | 107_I | 1.033 | 0.94 |
| 5_G | 126_D | 1.031 | 0.94 |
| 32_L | 107_I | 1.028 | 0.94 |
| 134_A | 138_F | 1.025 | 0.93 |
| 2_L | 137_L | 1.019 | 0.93 |
| 31_R | 114_V | 1.011 | 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 | |
| 1lhsA | 1 | 1 | 100 | 0.102 | Contact Map |
| 1a6mA | 1 | 1 | 100 | 0.114 | Contact Map |
| 2r80B | 2 | 0.9603 | 100 | 0.131 | Contact Map |
| 1v4xB | 2 | 0.9603 | 100 | 0.134 | Contact Map |
| 1outB | 1 | 0.9603 | 100 | 0.137 | Contact Map |
| 3bomB | 2 | 0.9603 | 100 | 0.139 | Contact Map |
| 2w72B | 2 | 0.9603 | 100 | 0.14 | Contact Map |
| 3d1kB | 1 | 0.9603 | 100 | 0.143 | Contact Map |
| 2aa1B | 2 | 0.9603 | 100 | 0.143 | Contact Map |
| 2dc3A | 2 | 1 | 100 | 0.148 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)