| d4kodk1 |
| ID: | 1449333707 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (79) | ||
| Sequences: | 683 (425.3) | ||
| Seq/Len: | 8.646 | ||
| Nf(neff/√len): | 47.8 |
HHblits Results: (2015_06)
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: 8.646).
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 |
| 17_V | 62_M | 4.239 | 1.00 |
| 29_L | 49_V | 2.760 | 1.00 |
| 17_V | 35_V | 2.393 | 1.00 |
| 47_C | 66_V | 1.855 | 1.00 |
| 20_S | 57_D | 1.851 | 1.00 |
| 37_L | 78_I | 1.630 | 1.00 |
| 24_M | 49_V | 1.627 | 1.00 |
| 72_V | 76_D | 1.601 | 1.00 |
| 36_L | 44_E | 1.587 | 1.00 |
| 37_L | 47_C | 1.581 | 1.00 |
| 40_K | 69_N | 1.555 | 1.00 |
| 17_V | 47_C | 1.534 | 1.00 |
| 23_K | 26_E | 1.511 | 1.00 |
| 56_S | 81_Q | 1.422 | 0.99 |
| 67_R | 74_L | 1.419 | 0.99 |
| 15_S | 52_D | 1.404 | 0.99 |
| 45_A | 70_L | 1.389 | 0.99 |
| 58_E | 81_Q | 1.350 | 0.99 |
| 34_T | 69_N | 1.297 | 0.99 |
| 45_A | 75_G | 1.281 | 0.98 |
| 54_T | 57_D | 1.259 | 0.98 |
| 38_K | 79_S | 1.217 | 0.98 |
| 54_T | 80_I | 1.194 | 0.97 |
| 27_L | 39_G | 1.187 | 0.97 |
| 2_N | 25_D | 1.176 | 0.97 |
| 65_V | 75_G | 1.175 | 0.97 |
| 24_M | 33_D | 1.150 | 0.96 |
| 17_V | 60_I | 1.148 | 0.96 |
| 21_Q | 25_D | 1.139 | 0.96 |
| 35_V | 62_M | 1.097 | 0.95 |
| 23_K | 27_L | 1.053 | 0.93 |
| 31_R | 51_S | 1.050 | 0.93 |
| 54_T | 58_E | 1.032 | 0.92 |
| 15_S | 19_L | 1.028 | 0.92 |
| 60_I | 82_P | 1.026 | 0.92 |
| 16_V | 75_G | 1.022 | 0.91 |
| 54_T | 81_Q | 1.020 | 0.91 |
| 17_V | 37_L | 1.019 | 0.91 |
| 24_M | 29_L | 1.003 | 0.90 |
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 | |
| 1cz4A | 1 | 0.9762 | 99.8 | 0.088 | Contact Map |
| 3tiwA | 2 | 1 | 99.8 | 0.128 | Contact Map |
| 4ko8A | 2 | 1 | 99.7 | 0.169 | Contact Map |
| 3cf2A | 4 | 1 | 99.7 | 0.193 | Contact Map |
| 3j94A | 6 | 0 | 98.5 | 0.532 | Contact Map |
| 1qcsA | 1 | 0.9405 | 95.4 | 0.712 | Contact Map |
| 1cr5A | 3 | 0.8929 | 94.3 | 0.728 | Contact Map |
| 2ivfA | 1 | 0.9286 | 92.2 | 0.748 | Contact Map |
| 4aayA | 4 | 0.9405 | 91.8 | 0.751 | Contact Map |
| 2napA | 1 | 0.9286 | 91.8 | 0.751 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)