| 4n8nA |
| ID: | 1491921394 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (92) | ||
| Sequences: | 2830 (2168.7) | ||
| Seq/Len: | 30.761 | ||
| Nf(neff/√len): | 226.1 |
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: 30.761).
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 |
| 30_R | 34_E | 3.726 | 1.00 |
| 30_R | 74_F | 2.924 | 1.00 |
| 24_T | 27_K | 2.082 | 1.00 |
| 45_L | 50_A | 2.072 | 1.00 |
| 15_S | 25_A | 2.035 | 1.00 |
| 54_A | 70_F | 2.012 | 1.00 |
| 5_E | 77_K | 2.000 | 1.00 |
| 46_N | 49_Q | 1.861 | 1.00 |
| 78_L | 87_F | 1.788 | 1.00 |
| 49_Q | 52_D | 1.762 | 1.00 |
| 47_R | 72_A | 1.759 | 1.00 |
| 11_T | 98_L | 1.658 | 1.00 |
| 45_L | 75_I | 1.641 | 1.00 |
| 36_R | 90_A | 1.636 | 1.00 |
| 42_V | 74_F | 1.598 | 1.00 |
| 31_E | 34_E | 1.585 | 1.00 |
| 45_L | 53_D | 1.569 | 1.00 |
| 32_K | 94_Q | 1.552 | 1.00 |
| 8_V | 76_V | 1.548 | 1.00 |
| 48_Q | 52_D | 1.527 | 1.00 |
| 43_R | 49_Q | 1.477 | 1.00 |
| 29_L | 94_Q | 1.461 | 1.00 |
| 27_K | 30_R | 1.457 | 1.00 |
| 89_T | 92_K | 1.442 | 1.00 |
| 10_L | 29_L | 1.412 | 1.00 |
| 25_A | 28_A | 1.409 | 1.00 |
| 52_D | 55_I | 1.397 | 0.99 |
| 8_V | 91_M | 1.379 | 0.99 |
| 41_A | 77_K | 1.319 | 0.99 |
| 26_C | 30_R | 1.318 | 0.99 |
| 26_C | 72_A | 1.277 | 0.99 |
| 50_A | 73_S | 1.276 | 0.99 |
| 88_D | 92_K | 1.273 | 0.99 |
| 28_A | 32_K | 1.271 | 0.99 |
| 40_K | 79_E | 1.215 | 0.98 |
| 38_D | 87_F | 1.200 | 0.98 |
| 5_E | 75_I | 1.193 | 0.98 |
| 33_I | 74_F | 1.170 | 0.97 |
| 85_K | 89_T | 1.165 | 0.97 |
| 49_Q | 53_D | 1.141 | 0.97 |
| 55_I | 63_D | 1.136 | 0.97 |
| 33_I | 91_M | 1.135 | 0.97 |
| 7_Q | 73_S | 1.132 | 0.97 |
| 83_Q | 86_D | 1.127 | 0.97 |
| 44_F | 72_A | 1.102 | 0.96 |
| 10_L | 74_F | 1.099 | 0.96 |
| 6_S | 88_D | 1.084 | 0.96 |
| 39_V | 76_V | 1.066 | 0.95 |
| 53_D | 56_R | 1.038 | 0.94 |
| 46_N | 72_A | 1.030 | 0.94 |
| 43_R | 75_I | 1.014 | 0.93 |
| 8_V | 97_V | 1.013 | 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 | |
| 4n8nA | 4 | 1 | 99.9 | 0.107 | Contact Map |
| 4dx5A | 3 | 0.9706 | 50 | 0.849 | Contact Map |
| 4k0jA | 6 | 0.9706 | 47.2 | 0.851 | Contact Map |
| 3ne5A | 1 | 0.9804 | 42.2 | 0.855 | Contact Map |
| 4mt1A | 1 | 0.9608 | 41.2 | 0.856 | Contact Map |
| 2djwA | 10 | 0.6863 | 39.3 | 0.858 | Contact Map |
| 2cviA | 2 | 0.6863 | 34.8 | 0.862 | Contact Map |
| 4pcqA | 4 | 0 | 34.6 | 0.862 | Contact Map |
| 4un1A | 2 | 0.6961 | 32.6 | 0.864 | Contact Map |
| 3w9iA | 6 | 0.9706 | 31.4 | 0.865 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)