| his_tail |
| ID: | 1487188409 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (136) | ||
| Sequences: | 622 (439.9) | ||
| Seq/Len: | 4.574 | ||
| Nf(neff/√len): | 37.7 |
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: 4.574).
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 |
| 108_T | 120_I | 3.926 | 1.00 |
| 47_V | 50_R | 3.354 | 1.00 |
| 109_N | 120_I | 2.651 | 1.00 |
| 69_Q | 85_F | 2.173 | 1.00 |
| 1_M | 4_T | 1.976 | 1.00 |
| 1_M | 5_K | 1.797 | 1.00 |
| 76_A | 85_F | 1.766 | 1.00 |
| 88_S | 91_M | 1.722 | 0.99 |
| 124_D | 127_L | 1.715 | 0.99 |
| 7_T | 10_K | 1.700 | 0.99 |
| 112_A | 120_I | 1.613 | 0.99 |
| 104_L | 107_D | 1.564 | 0.99 |
| 109_N | 112_A | 1.547 | 0.99 |
| 97_C | 101_L | 1.469 | 0.98 |
| 7_T | 12_T | 1.453 | 0.98 |
| 103_G | 107_D | 1.428 | 0.97 |
| 130_R | 133_G | 1.423 | 0.97 |
| 77_Q | 82_D | 1.358 | 0.96 |
| 64_R | 69_Q | 1.353 | 0.96 |
| 65_K | 69_Q | 1.322 | 0.95 |
| 52_I | 56_Q | 1.322 | 0.95 |
| 103_G | 134_E | 1.317 | 0.95 |
| 82_D | 85_F | 1.308 | 0.95 |
| 15_K | 18_R | 1.307 | 0.95 |
| 90_V | 99_A | 1.307 | 0.95 |
| 45_G | 48_A | 1.267 | 0.94 |
| 53_R | 70_R | 1.255 | 0.93 |
| 90_V | 108_T | 1.226 | 0.92 |
| 122_P | 134_E | 1.226 | 0.92 |
| 15_K | 19_K | 1.221 | 0.92 |
| 64_R | 67_P | 1.219 | 0.92 |
| 121_M | 131_I | 1.218 | 0.92 |
| 26_A | 30_A | 1.202 | 0.91 |
| 40_H | 47_V | 1.193 | 0.91 |
| 92_A | 95_E | 1.181 | 0.90 |
| 2_A | 5_K | 1.181 | 0.90 |
| 129_R | 133_G | 1.159 | 0.89 |
| 128_A | 132_R | 1.159 | 0.89 |
| 76_A | 83_L | 1.153 | 0.89 |
| 111_C | 126_Q | 1.145 | 0.88 |
| 123_K | 127_L | 1.143 | 0.88 |
| 13_G | 16_A | 1.136 | 0.88 |
| 76_A | 82_D | 1.131 | 0.87 |
| 113_I | 116_K | 1.125 | 0.87 |
| 26_A | 31_P | 1.117 | 0.86 |
| 111_C | 131_I | 1.116 | 0.86 |
| 53_R | 56_Q | 1.109 | 0.86 |
| 71_L | 74_E | 1.087 | 0.84 |
| 31_P | 34_G | 1.086 | 0.84 |
| 86_Q | 89_A | 1.082 | 0.84 |
| 72_V | 118_V | 1.082 | 0.84 |
| 100_Y | 103_G | 1.063 | 0.82 |
| 114_H | 117_R | 1.061 | 0.82 |
| 111_C | 121_M | 1.052 | 0.82 |
| 16_A | 19_K | 1.047 | 0.81 |
| 129_R | 132_R | 1.046 | 0.81 |
| 62_L | 70_R | 1.040 | 0.81 |
| 37_K | 40_H | 1.035 | 0.80 |
| 107_D | 128_A | 1.033 | 0.80 |
| 88_S | 97_C | 1.029 | 0.80 |
| 51_E | 56_Q | 1.023 | 0.79 |
| 56_Q | 62_L | 1.022 | 0.79 |
| 128_A | 133_G | 1.020 | 0.79 |
| 5_K | 71_L | 1.018 | 0.79 |
| 80_K | 85_F | 1.016 | 0.78 |
| 19_K | 22_A | 1.013 | 0.78 |
| 69_Q | 103_G | 1.012 | 0.78 |
| 78_D | 83_L | 1.008 | 0.78 |
| 5_K | 8_A | 1.006 | 0.77 |
| 72_V | 76_A | 1.004 | 0.77 |
| 28_K | 31_P | 1.004 | 0.77 |
| 66_L | 69_Q | 1.004 | 0.77 |
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 | |
| 1tzyC | 2 | 0.7206 | 100 | 0.081 | Contact Map |
| 3r45A | 1 | 0.5662 | 100 | 0.166 | Contact Map |
| 3nquA | 1 | 0.5441 | 100 | 0.174 | Contact Map |
| 2yfvA | 1 | 0.5 | 100 | 0.19 | Contact Map |
| 2l5aA | 1 | 0.5515 | 100 | 0.362 | Contact Map |
| 2hueB | 1 | 0.5515 | 100 | 0.413 | Contact Map |
| 3nqjA | 1 | 0.5441 | 100 | 0.421 | Contact Map |
| 2ly8A | 1 | 0.4926 | 99.9 | 0.533 | Contact Map |
| 4jjnB | 2 | 0.6324 | 99.9 | 0.553 | Contact Map |
| 1tafB | 1 | 0.5147 | 99.7 | 0.631 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)