| ac2 |
| ID: | 1517552860 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 134 (134) | ||
| Sequences: | 470 (186.8) | ||
| Seq/Len: | 3.507 | ||
| Nf(neff/√len): | 16.1 |
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: 3.507).
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 |
| 122_D | 129_S | 2.577 | 1.00 |
| 122_D | 125_P | 2.234 | 1.00 |
| 125_P | 129_S | 2.209 | 1.00 |
| 48_N | 60_S | 2.188 | 1.00 |
| 107_S | 111_A | 2.090 | 1.00 |
| 122_D | 128_W | 1.892 | 1.00 |
| 118_P | 121_D | 1.797 | 0.99 |
| 27_N | 44_I | 1.728 | 0.99 |
| 57_H | 61_S | 1.653 | 0.99 |
| 6_H | 10_P | 1.603 | 0.98 |
| 1_M | 4_S | 1.572 | 0.98 |
| 26_R | 43_S | 1.550 | 0.98 |
| 17_K | 20_H | 1.550 | 0.98 |
| 125_P | 128_W | 1.549 | 0.98 |
| 16_I | 20_H | 1.537 | 0.97 |
| 32_V | 49_H | 1.523 | 0.97 |
| 73_K | 78_Q | 1.501 | 0.97 |
| 3_S | 12_T | 1.416 | 0.95 |
| 12_T | 18_V | 1.399 | 0.95 |
| 2_R | 22_E | 1.375 | 0.94 |
| 1_M | 5_S | 1.360 | 0.94 |
| 102_L | 111_A | 1.315 | 0.92 |
| 124_T | 130_F | 1.308 | 0.92 |
| 12_T | 104_H | 1.288 | 0.91 |
| 113_V | 119_N | 1.283 | 0.91 |
| 19_Q | 22_E | 1.268 | 0.90 |
| 3_S | 19_Q | 1.229 | 0.88 |
| 14_V | 18_V | 1.228 | 0.88 |
| 111_A | 125_P | 1.224 | 0.88 |
| 89_D | 97_Q | 1.213 | 0.87 |
| 67_I | 107_S | 1.199 | 0.86 |
| 21_R | 111_A | 1.185 | 0.86 |
| 21_R | 26_R | 1.183 | 0.85 |
| 107_S | 110_T | 1.174 | 0.85 |
| 22_E | 25_R | 1.172 | 0.85 |
| 124_T | 127_D | 1.172 | 0.85 |
| 15_P | 18_V | 1.168 | 0.84 |
| 55_G | 58_H | 1.152 | 0.83 |
| 17_K | 23_A | 1.149 | 0.83 |
| 99_P | 102_L | 1.144 | 0.83 |
| 32_V | 40_Y | 1.132 | 0.82 |
| 3_S | 8_I | 1.131 | 0.82 |
| 7_L | 10_P | 1.130 | 0.82 |
| 30_R | 70_G | 1.127 | 0.81 |
| 56_T | 65_W | 1.122 | 0.81 |
| 81_Q | 86_S | 1.109 | 0.80 |
| 66_R | 69_L | 1.097 | 0.79 |
| 52_T | 68_Y | 1.091 | 0.78 |
| 113_V | 124_T | 1.076 | 0.77 |
| 127_D | 130_F | 1.069 | 0.76 |
| 47_H | 116_N | 1.067 | 0.76 |
| 61_S | 65_W | 1.063 | 0.76 |
| 59_C | 68_Y | 1.055 | 0.75 |
| 74_S | 78_Q | 1.054 | 0.75 |
| 108_S | 111_A | 1.053 | 0.75 |
| 2_R | 19_Q | 1.050 | 0.75 |
| 41_Y | 73_K | 1.050 | 0.75 |
| 41_Y | 45_N | 1.036 | 0.73 |
| 43_S | 70_G | 1.035 | 0.73 |
| 129_S | 132_K | 1.034 | 0.73 |
| 30_R | 63_R | 1.031 | 0.73 |
| 30_R | 115_S | 1.031 | 0.73 |
| 41_Y | 44_I | 1.029 | 0.72 |
| 110_T | 117_L | 1.027 | 0.72 |
| 17_K | 21_R | 1.024 | 0.72 |
| 70_G | 122_D | 1.022 | 0.72 |
| 104_H | 126_S | 1.017 | 0.71 |
| 21_R | 24_K | 1.011 | 0.71 |
| 3_S | 10_P | 1.003 | 0.70 |
| 76_L | 96_D | 1.003 | 0.70 |
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 | |
| 4uz8A | 2 | 0.3657 | 10.4 | 0.961 | Contact Map |
| 3tirA | 1 | 0.4179 | 7.4 | 0.964 | Contact Map |
| 3uitA | 4 | 0.5896 | 6.5 | 0.964 | Contact Map |
| 3gv2A | 6 | 0.4104 | 6 | 0.965 | Contact Map |
| 2d8sA | 1 | 0.5672 | 5.9 | 0.965 | Contact Map |
| 3fhkA | 4 | 0.3358 | 4.9 | 0.966 | Contact Map |
| 1w9nA | 1 | 0.1642 | 4.5 | 0.967 | Contact Map |
| 4u0cA | 1 | 0.403 | 4.4 | 0.967 | Contact Map |
| 1d1dA | 1 | 0.3433 | 3.9 | 0.968 | Contact Map |
| 1rsoB | 2 | 0.2463 | 3.8 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)