| 2mmz |
| ID: | 1397938799 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (105) | ||
| Sequences: | 1783 (1138.3) | ||
| Seq/Len: | 16.981 | ||
| Nf(neff/√len): | 111.1 |
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: 16.981).
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 |
| 19_L | 28_F | 3.051 | 1.00 |
| 24_K | 86_N | 3.051 | 1.00 |
| 27_V | 83_V | 2.920 | 1.00 |
| 33_P | 58_A | 2.719 | 1.00 |
| 17_D | 21_K | 2.578 | 1.00 |
| 18_A | 22_K | 2.557 | 1.00 |
| 49_R | 56_Y | 2.350 | 1.00 |
| 71_I | 80_I | 2.291 | 1.00 |
| 17_D | 74_Y | 2.267 | 1.00 |
| 44_V | 93_C | 2.108 | 1.00 |
| 60_N | 63_D | 2.095 | 1.00 |
| 44_V | 96_L | 2.094 | 1.00 |
| 43_A | 97_L | 2.083 | 1.00 |
| 82_Q | 89_F | 1.985 | 1.00 |
| 77_W | 82_Q | 1.973 | 1.00 |
| 75_S | 84_Y | 1.871 | 1.00 |
| 93_C | 97_L | 1.867 | 1.00 |
| 51_H | 100_H | 1.709 | 1.00 |
| 43_A | 93_C | 1.647 | 1.00 |
| 15_Q | 19_L | 1.576 | 1.00 |
| 32_T | 60_N | 1.539 | 1.00 |
| 50_L | 100_H | 1.515 | 1.00 |
| 83_V | 96_L | 1.428 | 1.00 |
| 61_V | 80_I | 1.417 | 1.00 |
| 45_V | 60_N | 1.370 | 0.99 |
| 85_L | 108_E | 1.365 | 0.99 |
| 106_V | 110_K | 1.350 | 0.99 |
| 90_V | 99_M | 1.349 | 0.99 |
| 27_V | 48_L | 1.336 | 0.99 |
| 69_Q | 73_D | 1.325 | 0.99 |
| 46_Q | 50_L | 1.307 | 0.99 |
| 80_I | 89_F | 1.295 | 0.99 |
| 47_I | 93_C | 1.254 | 0.99 |
| 77_W | 89_F | 1.240 | 0.98 |
| 99_M | 104_D | 1.194 | 0.98 |
| 47_I | 97_L | 1.188 | 0.98 |
| 15_Q | 64_D | 1.177 | 0.98 |
| 21_K | 87_G | 1.156 | 0.97 |
| 100_H | 105_L | 1.152 | 0.97 |
| 75_S | 82_Q | 1.152 | 0.97 |
| 19_L | 26_V | 1.138 | 0.97 |
| 65_P | 69_Q | 1.135 | 0.97 |
| 30_K | 38_C | 1.134 | 0.97 |
| 19_L | 59_Y | 1.097 | 0.96 |
| 72_K | 78_P | 1.080 | 0.95 |
| 90_V | 108_E | 1.075 | 0.95 |
| 30_K | 41_S | 1.065 | 0.95 |
| 44_V | 83_V | 1.059 | 0.95 |
| 99_M | 105_L | 1.056 | 0.95 |
| 100_H | 106_V | 1.049 | 0.94 |
| 26_V | 57_A | 1.018 | 0.93 |
| 13_A | 17_D | 1.013 | 0.93 |
| 47_I | 96_L | 1.007 | 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 | |
| 2jadA | 1 | 0.8678 | 99.9 | 0.392 | Contact Map |
| 2wemA | 4 | 0.9091 | 99.8 | 0.43 | Contact Map |
| 2wciA | 2 | 0.9256 | 99.8 | 0.457 | Contact Map |
| 3zywA | 2 | 0.9174 | 99.8 | 0.461 | Contact Map |
| 3ipzA | 1 | 0.9008 | 99.8 | 0.467 | Contact Map |
| 3gx8A | 1 | 0.8926 | 99.8 | 0.469 | Contact Map |
| 2ltkA | 1 | 0.9091 | 99.8 | 0.471 | Contact Map |
| 2yanA | 2 | 0.8678 | 99.8 | 0.475 | Contact Map |
| 1wikA | 1 | 0.9008 | 99.8 | 0.479 | Contact Map |
| 1u6tA | 1 | 0.7603 | 99.8 | 0.489 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)