| FYVE |
| ID: | 1511976286 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (91) | ||
| Sequences: | 411 (270.2) | ||
| Seq/Len: | 4.516 | ||
| Nf(neff/√len): | 28.3 |
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: 4.516).
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 |
| 55_F | 60_S | 2.253 | 1.00 |
| 51_C | 56_C | 2.044 | 1.00 |
| 45_R | 54_L | 1.768 | 1.00 |
| 23_W | 44_R | 1.711 | 0.99 |
| 29_G | 54_L | 1.709 | 0.99 |
| 32_C | 39_F | 1.658 | 0.99 |
| 62_F | 79_Q | 1.641 | 0.99 |
| 78_C | 81_C | 1.628 | 0.99 |
| 32_C | 35_C | 1.623 | 0.99 |
| 44_R | 49_R | 1.605 | 0.99 |
| 23_W | 49_R | 1.555 | 0.99 |
| 49_R | 52_G | 1.516 | 0.98 |
| 1_D | 5_R | 1.481 | 0.98 |
| 44_R | 47_H | 1.473 | 0.98 |
| 5_R | 10_S | 1.463 | 0.98 |
| 23_W | 47_H | 1.423 | 0.97 |
| 52_G | 56_C | 1.398 | 0.97 |
| 7_F | 10_S | 1.349 | 0.96 |
| 66_I | 77_V | 1.325 | 0.95 |
| 23_W | 32_C | 1.293 | 0.94 |
| 52_G | 59_C | 1.269 | 0.94 |
| 48_C | 56_C | 1.262 | 0.93 |
| 35_C | 39_F | 1.262 | 0.93 |
| 84_N | 88_E | 1.257 | 0.93 |
| 60_S | 76_R | 1.255 | 0.93 |
| 47_H | 52_G | 1.250 | 0.93 |
| 77_V | 82_Y | 1.243 | 0.93 |
| 67_K | 70_K | 1.209 | 0.91 |
| 23_W | 46_H | 1.208 | 0.91 |
| 46_H | 49_R | 1.194 | 0.91 |
| 44_R | 48_C | 1.182 | 0.90 |
| 23_W | 26_D | 1.179 | 0.90 |
| 3_R | 8_S | 1.176 | 0.90 |
| 23_W | 39_F | 1.142 | 0.88 |
| 23_W | 35_C | 1.133 | 0.87 |
| 34_G | 55_F | 1.121 | 0.86 |
| 39_F | 49_R | 1.117 | 0.86 |
| 62_F | 82_Y | 1.110 | 0.86 |
| 48_C | 51_C | 1.100 | 0.85 |
| 37_V | 43_E | 1.097 | 0.85 |
| 2_S | 6_V | 1.092 | 0.84 |
| 34_G | 53_Q | 1.089 | 0.84 |
| 16_G | 20_A | 1.081 | 0.84 |
| 26_D | 47_H | 1.071 | 0.83 |
| 56_C | 59_C | 1.049 | 0.81 |
| 58_K | 79_Q | 1.048 | 0.81 |
| 32_C | 48_C | 1.039 | 0.80 |
| 48_C | 59_C | 1.037 | 0.80 |
| 4_G | 8_S | 1.032 | 0.80 |
| 5_R | 12_S | 1.029 | 0.79 |
| 50_N | 85_L | 1.021 | 0.78 |
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 | |
| 1x4uA | 1 | 0.7959 | 99.8 | 0.349 | Contact Map |
| 1z2qA | 1 | 0.8571 | 99.8 | 0.36 | Contact Map |
| 2yw8A | 1 | 0.6224 | 99.8 | 0.362 | Contact Map |
| 3zyqA | 1 | 0.8571 | 99.7 | 0.366 | Contact Map |
| 1dvpA | 1 | 0.8469 | 99.7 | 0.373 | Contact Map |
| 1jocA | 2 | 0.8469 | 99.7 | 0.373 | Contact Map |
| 3mpxA | 1 | 0 | 99.7 | 0.375 | Contact Map |
| 3t7lA | 1 | 0.7551 | 99.7 | 0.376 | Contact Map |
| 1vfyA | 1 | 0.6837 | 99.7 | 0.382 | Contact Map |
| 1y02A | 1 | 0.5816 | 99.6 | 0.422 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)