| mad3II |
| ID: | 1434121668 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (66) | ||
| Sequences: | 142 (114.5) | ||
| Seq/Len: | 2.152 | ||
| Nf(neff/√len): | 14.1 |
Jackhmmer Results: (2015_01_07)
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: 2.152).
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_D | 36_L | 2.155 | 1.00 |
| 36_L | 46_L | 1.965 | 0.99 |
| 31_C | 49_I | 1.816 | 0.98 |
| 23_G | 35_L | 1.579 | 0.94 |
| 42_E | 49_I | 1.509 | 0.92 |
| 25_K | 34_D | 1.460 | 0.91 |
| 24_K | 56_V | 1.424 | 0.89 |
| 41_E | 44_Y | 1.420 | 0.89 |
| 38_P | 48_E | 1.381 | 0.87 |
| 36_L | 53_S | 1.376 | 0.87 |
| 55_N | 61_K | 1.374 | 0.87 |
| 20_E | 50_L | 1.356 | 0.86 |
| 32_N | 54_R | 1.324 | 0.84 |
| 4_I | 15_V | 1.297 | 0.82 |
| 42_E | 45_S | 1.259 | 0.80 |
| 57_Y | 62_Q | 1.245 | 0.79 |
| 20_E | 24_K | 1.226 | 0.77 |
| 21_N | 61_K | 1.215 | 0.76 |
| 63_K | 66_K | 1.137 | 0.69 |
| 3_P | 36_L | 1.126 | 0.68 |
| 3_P | 29_I | 1.123 | 0.68 |
| 12_S | 58_Y | 1.099 | 0.65 |
| 10_G | 29_I | 1.075 | 0.63 |
| 6_K | 41_E | 1.070 | 0.62 |
| 12_S | 52_I | 1.070 | 0.62 |
| 19_I | 54_R | 1.066 | 0.62 |
| 25_K | 49_I | 1.060 | 0.61 |
| 30_D | 33_F | 1.059 | 0.61 |
| 4_I | 51_A | 1.056 | 0.61 |
| 38_P | 56_V | 1.034 | 0.58 |
| 31_C | 53_S | 1.030 | 0.58 |
| 18_L | 25_K | 1.010 | 0.56 |
| 27_E | 30_D | 1.005 | 0.55 |
| 33_F | 55_N | 1.003 | 0.55 |
| 17_K | 45_S | 1.000 | 0.54 |
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 | |
| 4bl0B | 2 | 0.6765 | 99.9 | 0.145 | Contact Map |
| 2i3sB | 3 | 0.5294 | 99.4 | 0.42 | Contact Map |
| 2i3tB | 4 | 0.5441 | 99.1 | 0.506 | Contact Map |
| 3exmA | 1 | 1 | 9.6 | 0.899 | Contact Map |
| 1lm5A | 2 | 0.8529 | 6.7 | 0.905 | Contact Map |
| 4mzyA | 1 | 0.9412 | 4.2 | 0.914 | Contact Map |
| 2r51A | 1 | 0.9412 | 4.2 | 0.914 | Contact Map |
| 3iceA | 6 | 0.4853 | 3.8 | 0.915 | Contact Map |
| 2hp0A | 1 | 0.9412 | 3.2 | 0.919 | Contact Map |
| 4f0lA | 2 | 0.8824 | 3 | 0.92 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)