| d2bivc2 |
| ID: | 1448555711 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (90) | ||
| Sequences: | 581 (361.6) | ||
| Seq/Len: | 6.456 | ||
| Nf(neff/√len): | 38.1 |
HHblits Results: (2015_06)
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: 6.456).
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 |
| 25_K | 41_T | 2.515 | 1.00 |
| 28_A | 40_A | 2.286 | 1.00 |
| 3_A | 7_L | 2.141 | 1.00 |
| 78_C | 85_L | 1.818 | 1.00 |
| 69_S | 72_I | 1.792 | 1.00 |
| 3_A | 8_F | 1.756 | 1.00 |
| 57_W | 61_F | 1.545 | 0.99 |
| 64_W | 73_F | 1.467 | 0.99 |
| 76_G | 79_R | 1.432 | 0.99 |
| 41_T | 55_D | 1.359 | 0.98 |
| 29_I | 84_V | 1.349 | 0.98 |
| 40_A | 52_I | 1.337 | 0.98 |
| 4_S | 8_F | 1.335 | 0.98 |
| 53_T | 62_D | 1.328 | 0.98 |
| 20_F | 26_L | 1.326 | 0.98 |
| 25_K | 29_I | 1.324 | 0.98 |
| 31_K | 63_Y | 1.320 | 0.98 |
| 25_K | 55_D | 1.305 | 0.97 |
| 48_D | 66_K | 1.297 | 0.97 |
| 77_W | 83_D | 1.283 | 0.97 |
| 71_D | 83_D | 1.260 | 0.97 |
| 2_M | 11_E | 1.245 | 0.96 |
| 20_F | 42_I | 1.232 | 0.96 |
| 56_G | 71_D | 1.212 | 0.95 |
| 24_M | 45_V | 1.206 | 0.95 |
| 47_G | 56_G | 1.192 | 0.95 |
| 49_E | 66_K | 1.182 | 0.95 |
| 20_F | 72_I | 1.160 | 0.94 |
| 69_S | 74_P | 1.158 | 0.94 |
| 30_D | 54_F | 1.149 | 0.93 |
| 5_A | 10_K | 1.145 | 0.93 |
| 20_F | 25_K | 1.137 | 0.93 |
| 5_A | 22_V | 1.112 | 0.92 |
| 54_F | 61_F | 1.111 | 0.92 |
| 38_C | 76_G | 1.107 | 0.92 |
| 54_F | 57_W | 1.094 | 0.91 |
| 29_I | 37_I | 1.091 | 0.91 |
| 50_V | 56_G | 1.082 | 0.90 |
| 36_L | 61_F | 1.081 | 0.90 |
| 56_G | 62_D | 1.076 | 0.90 |
| 42_I | 59_G | 1.066 | 0.89 |
| 38_C | 54_F | 1.064 | 0.89 |
| 51_H | 64_W | 1.053 | 0.89 |
| 51_H | 65_C | 1.045 | 0.88 |
| 49_E | 63_Y | 1.043 | 0.88 |
| 30_D | 55_D | 1.036 | 0.88 |
| 23_G | 89_G | 1.031 | 0.87 |
| 37_I | 78_C | 1.024 | 0.87 |
| 74_P | 77_W | 1.019 | 0.86 |
| 59_G | 75_A | 1.018 | 0.86 |
| 7_L | 10_K | 1.017 | 0.86 |
| 19_N | 39_P | 1.015 | 0.86 |
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 | |
| 1oz2A | 1 | 1 | 100 | 0.024 | Contact Map |
| 4c5iA | 2 | 0.956 | 100 | 0.025 | Contact Map |
| 3f70A | 2 | 0.967 | 100 | 0.027 | Contact Map |
| 4c5eA | 4 | 0.967 | 100 | 0.035 | Contact Map |
| 3ut1A | 1 | 1 | 100 | 0.037 | Contact Map |
| 2bivA | 3 | 1 | 100 | 0.039 | Contact Map |
| 2r58A | 1 | 1 | 100 | 0.053 | Contact Map |
| 1wjqA | 1 | 0.9341 | 100 | 0.119 | Contact Map |
| 1wjrA | 1 | 0.9121 | 99.9 | 0.182 | Contact Map |
| 2eqmA | 1 | 0.9341 | 99.8 | 0.388 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)