| test |
| ID: | 1431377950 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (76) | ||
| Sequences: | 2137 (1494.9) | ||
| Seq/Len: | 28.118 | ||
| Nf(neff/√len): | 171.5 |
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: 28.118).
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 |
| 27_K | 52_D | 4.137 | 1.00 |
| 21_D | 29_K | 2.547 | 1.00 |
| 24_E | 28_A | 2.047 | 1.00 |
| 21_D | 25_N | 2.025 | 1.00 |
| 55_T | 58_D | 2.022 | 1.00 |
| 54_R | 58_D | 1.997 | 1.00 |
| 54_R | 59_Y | 1.759 | 1.00 |
| 62_Q | 65_S | 1.709 | 1.00 |
| 36_I | 41_Q | 1.696 | 1.00 |
| 51_E | 54_R | 1.595 | 1.00 |
| 31_Q | 38_P | 1.567 | 1.00 |
| 37_P | 41_Q | 1.555 | 1.00 |
| 44_I | 70_V | 1.555 | 1.00 |
| 3_I | 17_V | 1.527 | 1.00 |
| 29_K | 32_D | 1.515 | 1.00 |
| 25_N | 28_A | 1.496 | 1.00 |
| 1_M | 16_E | 1.481 | 1.00 |
| 21_D | 26_V | 1.462 | 1.00 |
| 30_I | 43_L | 1.460 | 1.00 |
| 18_E | 21_D | 1.433 | 1.00 |
| 24_E | 52_D | 1.396 | 0.99 |
| 4_F | 14_T | 1.396 | 0.99 |
| 22_T | 25_N | 1.318 | 0.99 |
| 44_I | 49_Q | 1.265 | 0.99 |
| 44_I | 68_H | 1.238 | 0.98 |
| 29_K | 33_K | 1.211 | 0.98 |
| 17_V | 21_D | 1.201 | 0.98 |
| 2_Q | 14_T | 1.163 | 0.97 |
| 23_I | 56_L | 1.163 | 0.97 |
| 45_F | 48_K | 1.155 | 0.97 |
| 61_I | 67_L | 1.145 | 0.97 |
| 4_F | 66_T | 1.098 | 0.96 |
| 73_L | 76_G | 1.062 | 0.95 |
| 6_K | 47_G | 1.061 | 0.95 |
| 45_F | 65_S | 1.054 | 0.95 |
| 3_I | 26_V | 1.042 | 0.94 |
| 2_Q | 16_E | 1.026 | 0.94 |
| 15_L | 26_V | 1.018 | 0.93 |
| 19_P | 57_S | 1.006 | 0.93 |
| 2_Q | 63_K | 1.005 | 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 | |
| 3a9jA | 1 | 1 | 99.8 | -0.078 | Contact Map |
| 3ai5A | 1 | 0.9342 | 99.7 | -0.032 | Contact Map |
| 3b1lX | 1 | 1 | 99.7 | 0.003 | Contact Map |
| 3j80f | 1 | 0 | 99.6 | 0.014 | Contact Map |
| 4k95A | 12 | 0.9605 | 99.6 | 0.015 | Contact Map |
| 4adx5 | 1 | 0 | 99.6 | 0.023 | Contact Map |
| 3q3fA | 1 | 1 | 99.6 | 0.034 | Contact Map |
| 4hcnB | 1 | 1 | 99.6 | 0.041 | Contact Map |
| 4npnA | 1 | 0.9211 | 99.6 | 0.043 | Contact Map |
| 3l0wB | 1 | 0.9868 | 99.6 | 0.043 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)