| 2M3K |
| ID: | 1515674516 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (100) | ||
| Sequences: | 190 (166.2) | ||
| Seq/Len: | 1.900 | ||
| Nf(neff/√len): | 16.6 |
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: 1.900).
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 |
| 77_D | 80_P | 3.534 | 1.00 |
| 86_N | 90_V | 2.212 | 1.00 |
| 69_L | 85_M | 2.198 | 1.00 |
| 18_E | 22_F | 1.907 | 0.98 |
| 9_I | 80_P | 1.833 | 0.98 |
| 20_A | 67_F | 1.779 | 0.97 |
| 25_K | 83_I | 1.774 | 0.97 |
| 16_L | 71_A | 1.649 | 0.95 |
| 9_I | 77_D | 1.598 | 0.94 |
| 10_N | 62_A | 1.594 | 0.93 |
| 9_I | 51_F | 1.593 | 0.93 |
| 54_R | 72_V | 1.446 | 0.88 |
| 9_I | 23_M | 1.431 | 0.87 |
| 16_L | 100_S | 1.367 | 0.84 |
| 11_A | 48_A | 1.300 | 0.79 |
| 33_F | 91_T | 1.270 | 0.77 |
| 52_C | 74_I | 1.259 | 0.76 |
| 23_M | 33_F | 1.258 | 0.76 |
| 5_E | 79_N | 1.256 | 0.76 |
| 12_V | 81_F | 1.208 | 0.72 |
| 51_F | 73_A | 1.186 | 0.70 |
| 69_L | 88_N | 1.180 | 0.70 |
| 3_E | 30_N | 1.171 | 0.69 |
| 7_A | 29_Q | 1.158 | 0.67 |
| 10_N | 39_K | 1.158 | 0.67 |
| 58_I | 66_K | 1.141 | 0.66 |
| 36_T | 67_F | 1.138 | 0.65 |
| 7_A | 79_N | 1.137 | 0.65 |
| 41_P | 44_P | 1.128 | 0.64 |
| 26_F | 29_Q | 1.118 | 0.63 |
| 64_D | 69_L | 1.112 | 0.63 |
| 62_A | 69_L | 1.091 | 0.61 |
| 26_F | 30_N | 1.084 | 0.60 |
| 55_L | 87_E | 1.075 | 0.59 |
| 11_A | 53_I | 1.063 | 0.58 |
| 39_K | 61_G | 1.057 | 0.57 |
| 6_K | 83_I | 1.048 | 0.56 |
| 19_N | 90_V | 1.028 | 0.54 |
| 21_H | 45_I | 1.028 | 0.54 |
| 51_F | 75_D | 1.027 | 0.54 |
| 36_T | 74_I | 1.020 | 0.53 |
| 7_A | 31_G | 1.015 | 0.52 |
| 25_K | 29_Q | 1.014 | 0.52 |
| 30_N | 56_N | 1.014 | 0.52 |
| 3_E | 78_K | 1.004 | 0.51 |
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 | |
| 2m3kA | 1 | 0.9916 | 99.9 | 0.281 | Contact Map |
| 4d40A | 2 | 0 | 99.6 | 0.516 | Contact Map |
| 4noaA | 1 | 0.8571 | 99.5 | 0.551 | Contact Map |
| 2opeA | 4 | 0.9328 | 99 | 0.644 | Contact Map |
| 1x6zA | 1 | 0.8739 | 95.8 | 0.814 | Contact Map |
| 3g20A | 2 | 0.8571 | 95.7 | 0.815 | Contact Map |
| 2hi2A | 1 | 0.9748 | 93.9 | 0.832 | Contact Map |
| 3sokA | 2 | 0.916 | 93.7 | 0.833 | Contact Map |
| 3jyzA | 1 | 0.9496 | 89.9 | 0.85 | Contact Map |
| 1oqwA | 2 | 0.8908 | 88.9 | 0.853 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)