| T0814 300-424 |
| ID: | 1404854217 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 125 (119) | ||
| Sequences: | 233 (214) | ||
| Seq/Len: | 1.958 | ||
| Nf(neff/√len): | 19.6 |
Jackhmmer Results: (2014_04_16)
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: 1.958).
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 |
| 49_N | 56_E | 6.348 | 1.00 |
| 103_R | 110_D | 3.537 | 1.00 |
| 97_S | 115_V | 2.635 | 1.00 |
| 46_M | 57_K | 2.554 | 1.00 |
| 99_Y | 112_L | 2.240 | 1.00 |
| 28_S | 45_K | 2.171 | 0.99 |
| 30_Y | 44_S | 1.927 | 0.98 |
| 104_P | 107_A | 1.770 | 0.97 |
| 41_D | 44_S | 1.635 | 0.95 |
| 36_F | 44_S | 1.624 | 0.94 |
| 35_L | 44_S | 1.610 | 0.94 |
| 30_Y | 45_K | 1.510 | 0.91 |
| 19_L | 85_I | 1.476 | 0.90 |
| 63_Q | 110_D | 1.409 | 0.87 |
| 61_L | 66_Y | 1.408 | 0.87 |
| 31_L | 59_V | 1.385 | 0.86 |
| 16_H | 66_Y | 1.344 | 0.83 |
| 17_F | 61_L | 1.317 | 0.81 |
| 67_N | 85_I | 1.317 | 0.81 |
| 14_I | 58_A | 1.309 | 0.81 |
| 44_S | 59_V | 1.284 | 0.79 |
| 65_S | 85_I | 1.249 | 0.76 |
| 52_T | 56_E | 1.242 | 0.76 |
| 10_A | 35_L | 1.240 | 0.76 |
| 93_Q | 120_N | 1.233 | 0.75 |
| 108_R | 112_L | 1.223 | 0.74 |
| 29_V | 85_I | 1.201 | 0.72 |
| 32_N | 71_L | 1.197 | 0.72 |
| 97_S | 109_Y | 1.172 | 0.70 |
| 39_V | 88_N | 1.170 | 0.69 |
| 23_P | 50_F | 1.165 | 0.69 |
| 104_P | 111_R | 1.145 | 0.67 |
| 86_E | 108_R | 1.135 | 0.66 |
| 19_L | 92_T | 1.132 | 0.66 |
| 65_S | 99_Y | 1.130 | 0.66 |
| 36_F | 86_E | 1.115 | 0.64 |
| 106_G | 109_Y | 1.115 | 0.64 |
| 98_I | 113_I | 1.113 | 0.64 |
| 83_G | 88_N | 1.110 | 0.64 |
| 87_G | 94_N | 1.102 | 0.63 |
| 66_Y | 106_G | 1.094 | 0.62 |
| 13_Y | 116_T | 1.071 | 0.59 |
| 5_D | 118_V | 1.070 | 0.59 |
| 35_L | 65_S | 1.043 | 0.56 |
| 67_N | 104_P | 1.026 | 0.55 |
| 15_V | 50_F | 1.019 | 0.54 |
| 23_P | 31_L | 1.008 | 0.53 |
| 21_C | 24_L | 1.008 | 0.53 |
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 | |
| 2qlvB | 2 | 0.688 | 96.2 | 0.865 | Contact Map |
| 4aeeA | 2 | 0.912 | 94.9 | 0.878 | Contact Map |
| 4aefA | 2 | 0.92 | 94.8 | 0.879 | Contact Map |
| 4pyhA | 1 | 0.92 | 94.2 | 0.882 | Contact Map |
| 2lu3A | 1 | 0.776 | 94.1 | 0.883 | Contact Map |
| 4cfeB | 2 | 0.768 | 93.9 | 0.883 | Contact Map |
| 1z0nA | 3 | 0.696 | 93.6 | 0.885 | Contact Map |
| 1gcyA | 1 | 0.016 | 92.9 | 0.888 | Contact Map |
| 1ac0A | 1 | 0.808 | 92.6 | 0.889 | Contact Map |
| 1vemA | 1 | 0.8 | 92.4 | 0.89 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)