| prot |
| ID: | 1387274880 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (97) | ||
| Sequences: | 2109 (1693.5) | ||
| Seq/Len: | 21.742 | ||
| Nf(neff/√len): | 171.9 |
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: 21.742).
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 |
| 18_V | 90_I | 2.979 | 1.00 |
| 34_I | 63_M | 2.914 | 1.00 |
| 2_Q | 91_K | 2.740 | 1.00 |
| 6_Y | 76_I | 2.616 | 1.00 |
| 84_S | 87_E | 2.615 | 1.00 |
| 4_K | 82_D | 2.261 | 1.00 |
| 20_V | 34_I | 2.188 | 1.00 |
| 7_T | 80_V | 2.161 | 1.00 |
| 8_Y | 17_F | 1.904 | 1.00 |
| 33_V | 71_V | 1.837 | 1.00 |
| 47_S | 66_T | 1.831 | 1.00 |
| 34_I | 65_T | 1.777 | 1.00 |
| 89_D | 93_A | 1.671 | 1.00 |
| 4_K | 79_E | 1.670 | 1.00 |
| 17_F | 33_V | 1.619 | 1.00 |
| 5_V | 36_L | 1.608 | 1.00 |
| 64_M | 67_D | 1.603 | 1.00 |
| 8_Y | 71_V | 1.583 | 1.00 |
| 34_I | 68_M | 1.544 | 1.00 |
| 72_P | 75_V | 1.542 | 1.00 |
| 38_S | 59_E | 1.510 | 1.00 |
| 63_M | 90_I | 1.502 | 1.00 |
| 32_M | 97_M | 1.425 | 1.00 |
| 40_R | 62_R | 1.389 | 0.99 |
| 32_M | 70_S | 1.346 | 0.99 |
| 36_L | 63_M | 1.345 | 0.99 |
| 20_V | 94_I | 1.325 | 0.99 |
| 21_Q | 26_D | 1.309 | 0.99 |
| 25_I | 97_M | 1.291 | 0.99 |
| 12_S | 15_R | 1.286 | 0.99 |
| 16_L | 61_W | 1.278 | 0.99 |
| 68_M | 94_I | 1.264 | 0.99 |
| 69_A | 75_V | 1.248 | 0.99 |
| 88_N | 95_N | 1.187 | 0.98 |
| 67_D | 72_P | 1.178 | 0.98 |
| 6_Y | 17_F | 1.169 | 0.97 |
| 91_K | 98_F | 1.158 | 0.97 |
| 88_N | 92_N | 1.133 | 0.97 |
| 31_R | 73_V | 1.133 | 0.97 |
| 36_L | 61_W | 1.125 | 0.97 |
| 38_S | 61_W | 1.113 | 0.96 |
| 83_L | 87_E | 1.112 | 0.96 |
| 7_T | 14_Y | 1.094 | 0.96 |
| 18_V | 83_L | 1.091 | 0.96 |
| 47_S | 64_M | 1.083 | 0.96 |
| 48_R | 52_P | 1.064 | 0.95 |
| 86_R | 89_D | 1.054 | 0.95 |
| 21_Q | 30_R | 1.036 | 0.94 |
| 19_D | 31_R | 1.015 | 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 | |
| 3vubA | 1 | 0.9901 | 99.8 | 0.172 | Contact Map |
| 2kmtA | 2 | 0.9604 | 99.7 | 0.227 | Contact Map |
| 4mdxA | 2 | 0.9901 | 99.6 | 0.262 | Contact Map |
| 1m1fA | 2 | 0.9406 | 99.6 | 0.269 | Contact Map |
| 1ub4A | 2 | 0.9208 | 99.6 | 0.271 | Contact Map |
| 1h3zA | 1 | 0.9109 | 36.6 | 0.853 | Contact Map |
| 2l89A | 1 | 0.8911 | 32.8 | 0.857 | Contact Map |
| 3pfsA | 2 | 0.9703 | 12 | 0.883 | Contact Map |
| 3l42A | 1 | 0.9703 | 10.2 | 0.887 | Contact Map |
| 1ri0A | 1 | 0.8416 | 7.9 | 0.892 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)