| het-e het |
| ID: | 1490372407 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (120) | ||
| Sequences: | 4969 (4204) | ||
| Seq/Len: | 41.408 | ||
| Nf(neff/√len): | 383.8 |
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: 41.408).
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 |
| 8_T | 110_K | 4.056 | 1.00 |
| 65_L | 69_I | 3.136 | 1.00 |
| 38_C | 50_F | 3.131 | 1.00 |
| 58_D | 61_N | 2.777 | 1.00 |
| 45_D | 83_Y | 2.698 | 1.00 |
| 1_P | 80_A | 2.652 | 1.00 |
| 3_A | 81_K | 2.520 | 1.00 |
| 111_W | 117_T | 2.471 | 1.00 |
| 4_I | 79_A | 2.452 | 1.00 |
| 3_A | 47_R | 2.425 | 1.00 |
| 3_A | 48_K | 2.207 | 1.00 |
| 79_A | 82_C | 2.202 | 1.00 |
| 58_D | 64_E | 2.138 | 1.00 |
| 72_M | 76_Y | 2.135 | 1.00 |
| 7_H | 54_T | 2.071 | 1.00 |
| 4_I | 82_C | 2.031 | 1.00 |
| 89_V | 109_C | 2.004 | 1.00 |
| 84_V | 111_W | 1.910 | 1.00 |
| 41_Q | 45_D | 1.810 | 1.00 |
| 68_A | 75_W | 1.769 | 1.00 |
| 47_R | 80_A | 1.765 | 1.00 |
| 3_A | 42_A | 1.738 | 1.00 |
| 35_I | 52_V | 1.592 | 1.00 |
| 5_L | 52_V | 1.541 | 1.00 |
| 62_S | 65_L | 1.517 | 1.00 |
| 71_S | 74_R | 1.477 | 1.00 |
| 21_L | 55_C | 1.443 | 1.00 |
| 37_F | 40_D | 1.408 | 1.00 |
| 106_F | 109_C | 1.399 | 0.99 |
| 68_A | 71_S | 1.384 | 0.99 |
| 36_R | 40_D | 1.354 | 0.99 |
| 116_W | 120_E | 1.313 | 0.99 |
| 59_K | 65_L | 1.308 | 0.99 |
| 2_Y | 78_D | 1.304 | 0.99 |
| 39_A | 50_F | 1.269 | 0.99 |
| 61_N | 64_E | 1.254 | 0.99 |
| 31_G | 34_K | 1.250 | 0.99 |
| 10_G | 87_T | 1.248 | 0.99 |
| 110_K | 113_T | 1.247 | 0.99 |
| 36_R | 39_A | 1.221 | 0.98 |
| 74_R | 78_D | 1.203 | 0.98 |
| 33_N | 36_R | 1.196 | 0.98 |
| 114_R | 120_E | 1.164 | 0.97 |
| 62_S | 66_Q | 1.151 | 0.97 |
| 20_D | 24_G | 1.146 | 0.97 |
| 41_Q | 83_Y | 1.144 | 0.97 |
| 1_P | 47_R | 1.119 | 0.96 |
| 63_T | 66_Q | 1.104 | 0.96 |
| 33_N | 37_F | 1.099 | 0.96 |
| 19_K | 60_S | 1.097 | 0.96 |
| 9_W | 59_K | 1.086 | 0.96 |
| 116_W | 119_Q | 1.059 | 0.95 |
| 102_W | 106_F | 1.042 | 0.94 |
| 76_Y | 119_Q | 1.037 | 0.94 |
| 72_M | 119_Q | 1.035 | 0.94 |
| 35_I | 39_A | 1.022 | 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 | |
| 2uw1A | 1 | 0.7333 | 2.6 | 0.935 | Contact Map |
| 4pz1A | 1 | 0.4917 | 2.1 | 0.938 | Contact Map |
| 3h16A | 4 | 0.6167 | 1.9 | 0.94 | Contact Map |
| 4lqcA | 2 | 0.6167 | 1.8 | 0.941 | Contact Map |
| 4x9cA | 6 | 0.4083 | 1.7 | 0.941 | Contact Map |
| 2v0xA | 2 | 0.5833 | 1.7 | 0.941 | Contact Map |
| 4lzpB | 4 | 0.6167 | 1.7 | 0.941 | Contact Map |
| 3fo3A | 2 | 0.3667 | 1.5 | 0.943 | Contact Map |
| 4u4cB | 1 | 0.05 | 1.5 | 0.944 | Contact Map |
| 4c6sA | 1 | 0.6 | 1.4 | 0.944 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)