| fliaPentaGremlin |
| ID: | 1430148698 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 78 (78) | ||
| Sequences: | 3189 (2693) | ||
| Seq/Len: | 40.885 | ||
| Nf(neff/√len): | 304.9 |
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: 40.885).
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 |
| 48_A | 66_K | 2.290 | 1.00 |
| 51_D | 71_K | 2.140 | 1.00 |
| 14_T | 32_K | 2.085 | 1.00 |
| 3_L | 23_L | 2.082 | 1.00 |
| 54_N | 74_G | 2.076 | 1.00 |
| 53_N | 71_K | 2.062 | 1.00 |
| 49_G | 69_G | 2.045 | 1.00 |
| 9_S | 27_D | 1.920 | 1.00 |
| 18_F | 38_W | 1.788 | 1.00 |
| 10_G | 30_A | 1.769 | 1.00 |
| 5_E | 25_K | 1.749 | 1.00 |
| 67_F | 72_L | 1.695 | 1.00 |
| 15_G | 35_G | 1.688 | 1.00 |
| 43_S | 61_T | 1.651 | 1.00 |
| 44_E | 64_S | 1.613 | 1.00 |
| 42_L | 62_L | 1.608 | 1.00 |
| 8_L | 28_C | 1.582 | 1.00 |
| 7_D | 27_D | 1.548 | 1.00 |
| 62_L | 67_F | 1.532 | 1.00 |
| 4_E | 22_N | 1.518 | 1.00 |
| 40_A | 60_A | 1.481 | 1.00 |
| 48_A | 68_V | 1.440 | 1.00 |
| 50_G | 70_T | 1.417 | 1.00 |
| 19_E | 37_I | 1.409 | 1.00 |
| 12_D | 32_K | 1.399 | 0.99 |
| 47_F | 67_F | 1.395 | 0.99 |
| 43_S | 63_T | 1.351 | 0.99 |
| 19_E | 39_Q | 1.348 | 0.99 |
| 17_R | 37_I | 1.308 | 0.99 |
| 34_E | 51_D | 1.267 | 0.99 |
| 57_W | 62_L | 1.256 | 0.99 |
| 28_C | 31_A | 1.251 | 0.99 |
| 28_C | 47_F | 1.183 | 0.98 |
| 72_L | 77_F | 1.153 | 0.97 |
| 52_F | 55_S | 1.120 | 0.96 |
| 6_A | 26_A | 1.102 | 0.96 |
| 57_W | 77_F | 1.085 | 0.96 |
| 58_R | 76_D | 1.081 | 0.95 |
| 53_N | 73_T | 1.065 | 0.95 |
| 16_W | 36_S | 1.061 | 0.95 |
| 61_T | 65_A | 1.031 | 0.94 |
| 25_K | 44_E | 1.025 | 0.93 |
| 38_W | 57_W | 1.025 | 0.93 |
| 33_L | 38_W | 1.021 | 0.93 |
| 46_A | 66_K | 1.012 | 0.93 |
| 47_F | 52_F | 1.009 | 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 | |
| 3n90A | 1 | 1 | 99.4 | 0.148 | Contact Map |
| 3nb2A | 4 | 1 | 99.4 | 0.156 | Contact Map |
| 2o6wA | 1 | 1 | 99.4 | 0.181 | Contact Map |
| 3du1X | 1 | 1 | 99.4 | 0.182 | Contact Map |
| 2f3lA | 1 | 1 | 99.3 | 0.193 | Contact Map |
| 2bm5A | 2 | 1 | 99.3 | 0.205 | Contact Map |
| 2j8kA | 1 | 1 | 99.3 | 0.208 | Contact Map |
| 4jraC | 2 | 0.9872 | 99.3 | 0.22 | Contact Map |
| 2xtyA | 2 | 1 | 99.3 | 0.222 | Contact Map |
| 3pssA | 2 | 1 | 99.3 | 0.222 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)