| jul1BP2 |
| ID: | 1478214163 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (122) | ||
| Sequences: | 970 (568.9) | ||
| Seq/Len: | 7.951 | ||
| Nf(neff/√len): | 51.5 |
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: 7.951).
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 |
| 5_F | 102_A | 3.235 | 1.00 |
| 102_A | 106_F | 3.154 | 1.00 |
| 11_C | 77_C | 2.998 | 1.00 |
| 61_C | 91_C | 2.828 | 1.00 |
| 30_G | 49_D | 2.372 | 1.00 |
| 46_Q | 50_N | 2.218 | 1.00 |
| 32_G | 49_D | 2.038 | 1.00 |
| 44_C | 48_H | 2.020 | 1.00 |
| 100_R | 104_I | 1.937 | 1.00 |
| 84_C | 96_C | 1.831 | 1.00 |
| 1_A | 4_Q | 1.789 | 1.00 |
| 28_Y | 33_G | 1.682 | 1.00 |
| 44_C | 105_C | 1.655 | 1.00 |
| 5_F | 106_F | 1.643 | 1.00 |
| 55_A | 94_F | 1.526 | 1.00 |
| 44_C | 49_D | 1.455 | 0.99 |
| 39_D | 42_D | 1.451 | 0.99 |
| 30_G | 44_C | 1.443 | 0.99 |
| 49_D | 52_Y | 1.419 | 0.99 |
| 115_H | 118_L | 1.418 | 0.99 |
| 45_C | 51_C | 1.398 | 0.99 |
| 19_L | 23_N | 1.395 | 0.99 |
| 45_C | 48_H | 1.386 | 0.99 |
| 1_A | 72_N | 1.372 | 0.99 |
| 82_I | 104_I | 1.358 | 0.99 |
| 34_S | 38_V | 1.348 | 0.99 |
| 40_D | 109_V | 1.344 | 0.99 |
| 30_G | 105_C | 1.287 | 0.98 |
| 93_A | 97_N | 1.281 | 0.98 |
| 44_C | 52_Y | 1.281 | 0.98 |
| 82_I | 100_R | 1.276 | 0.98 |
| 119_D | 122_N | 1.267 | 0.98 |
| 48_H | 51_C | 1.230 | 0.97 |
| 3_W | 6_N | 1.218 | 0.97 |
| 27_C | 37_P | 1.197 | 0.97 |
| 53_K | 56_K | 1.184 | 0.96 |
| 97_N | 100_R | 1.176 | 0.96 |
| 29_C | 42_D | 1.161 | 0.96 |
| 97_N | 101_N | 1.157 | 0.96 |
| 29_C | 39_D | 1.133 | 0.95 |
| 91_C | 98_C | 1.123 | 0.95 |
| 48_H | 52_Y | 1.122 | 0.95 |
| 28_Y | 49_D | 1.118 | 0.95 |
| 41_L | 109_V | 1.101 | 0.94 |
| 76_S | 85_S | 1.073 | 0.93 |
| 12_K | 82_I | 1.056 | 0.92 |
| 52_Y | 105_C | 1.055 | 0.92 |
| 48_H | 105_C | 1.054 | 0.92 |
| 55_A | 77_C | 1.039 | 0.91 |
| 1_A | 6_N | 1.036 | 0.91 |
| 5_F | 47_T | 1.033 | 0.91 |
| 70_T | 92_E | 1.031 | 0.91 |
| 98_C | 105_C | 1.028 | 0.91 |
| 74_S | 90_A | 1.024 | 0.90 |
| 71_N | 95_I | 1.024 | 0.90 |
| 117_N | 120_K | 1.019 | 0.90 |
| 4_Q | 72_N | 1.012 | 0.90 |
| 28_Y | 34_S | 1.002 | 0.89 |
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 | |
| 1gp7A | 3 | 0.9919 | 100 | 0.042 | Contact Map |
| 1g4iA | 1 | 0.9919 | 100 | 0.042 | Contact Map |
| 1p7oA | 6 | 0.9919 | 100 | 0.044 | Contact Map |
| 3jqlA | 1 | 0.9512 | 100 | 0.06 | Contact Map |
| 4ntwC | 1 | 0.9431 | 100 | 0.062 | Contact Map |
| 1m8tA | 6 | 0.9512 | 100 | 0.062 | Contact Map |
| 1le6A | 3 | 0.935 | 100 | 0.063 | Contact Map |
| 1bunA | 1 | 0.9512 | 100 | 0.064 | Contact Map |
| 3u8iA | 2 | 0.9268 | 100 | 0.073 | Contact Map |
| 1g0zA | 2 | 0.9431 | 100 | 0.074 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)