| 4cu5A |
| ID: | 1491996671 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (82) | ||
| Sequences: | 2102 (1723.7) | ||
| Seq/Len: | 25.634 | ||
| Nf(neff/√len): | 190.4 |
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: 25.634).
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 |
| 65_I | 82_F | 3.330 | 1.00 |
| 78_K | 81_D | 3.046 | 1.00 |
| 17_A | 48_V | 2.895 | 1.00 |
| 76_L | 80_L | 2.777 | 1.00 |
| 16_S | 76_L | 2.707 | 1.00 |
| 47_V | 54_E | 2.638 | 1.00 |
| 4_H | 46_Y | 2.416 | 1.00 |
| 74_D | 78_K | 2.142 | 1.00 |
| 3_K | 43_Q | 2.032 | 1.00 |
| 71_D | 74_D | 1.947 | 1.00 |
| 4_H | 44_N | 1.919 | 1.00 |
| 5_T | 42_T | 1.849 | 1.00 |
| 12_V | 72_R | 1.768 | 1.00 |
| 44_N | 65_I | 1.673 | 1.00 |
| 68_K | 78_K | 1.586 | 1.00 |
| 32_C | 54_E | 1.490 | 1.00 |
| 20_V | 26_D | 1.413 | 1.00 |
| 32_C | 38_V | 1.380 | 0.99 |
| 45_L | 62_E | 1.348 | 0.99 |
| 49_G | 66_M | 1.344 | 0.99 |
| 11_E | 33_D | 1.322 | 0.99 |
| 44_N | 63_K | 1.316 | 0.99 |
| 45_L | 64_F | 1.297 | 0.99 |
| 77_Y | 81_D | 1.233 | 0.98 |
| 67_I | 78_K | 1.216 | 0.98 |
| 20_V | 24_Y | 1.213 | 0.98 |
| 9_D | 53_C | 1.199 | 0.98 |
| 6_I | 21_G | 1.198 | 0.98 |
| 4_H | 24_Y | 1.183 | 0.98 |
| 70_N | 74_D | 1.179 | 0.98 |
| 50_G | 68_K | 1.177 | 0.98 |
| 13_D | 50_G | 1.152 | 0.97 |
| 72_R | 75_T | 1.151 | 0.97 |
| 33_D | 37_Y | 1.148 | 0.97 |
| 13_D | 72_R | 1.127 | 0.97 |
| 18_T | 22_W | 1.111 | 0.96 |
| 20_V | 79_A | 1.104 | 0.96 |
| 17_A | 20_V | 1.091 | 0.96 |
| 50_G | 72_R | 1.084 | 0.96 |
| 53_C | 75_T | 1.071 | 0.95 |
| 33_D | 39_P | 1.070 | 0.95 |
| 48_V | 79_A | 1.053 | 0.95 |
| 68_K | 75_T | 1.027 | 0.94 |
| 6_I | 46_Y | 1.025 | 0.93 |
| 5_T | 8_Y | 1.012 | 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 | |
| 4cu2A | 1 | 0.9176 | 99.7 | 0.03 | Contact Map |
| 4cu5A | 6 | 1 | 99.3 | 0.243 | Contact Map |
| 2eguA | 1 | 0.8471 | 26.8 | 0.826 | Contact Map |
| 1o58A | 4 | 0.8471 | 23.1 | 0.831 | Contact Map |
| 4ql4A | 1 | 0.8471 | 22.9 | 0.832 | Contact Map |
| 1kl7A | 2 | 0.8588 | 22.9 | 0.832 | Contact Map |
| 3dwgA | 2 | 0.8471 | 22.7 | 0.832 | Contact Map |
| 1y7lA | 1 | 0.8471 | 22.3 | 0.832 | Contact Map |
| 4r2vA | 2 | 0.8471 | 22.1 | 0.832 | Contact Map |
| 2pqmA | 2 | 0.8471 | 21.9 | 0.833 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)