| d4nftd2 |
| ID: | 1448470861 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (89) | ||
| Sequences: | 649 (329.2) | ||
| Seq/Len: | 7.292 | ||
| Nf(neff/√len): | 34.9 |
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: 7.292).
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 |
| 59_L | 75_G | 2.485 | 1.00 |
| 22_R | 25_S | 2.043 | 1.00 |
| 67_R | 71_L | 1.827 | 1.00 |
| 24_T | 27_G | 1.652 | 1.00 |
| 15_I | 19_L | 1.609 | 1.00 |
| 25_S | 28_R | 1.592 | 1.00 |
| 16_H | 23_T | 1.591 | 1.00 |
| 15_I | 41_L | 1.583 | 1.00 |
| 54_N | 58_D | 1.578 | 1.00 |
| 3_S | 11_P | 1.551 | 1.00 |
| 69_L | 73_I | 1.517 | 0.99 |
| 35_V | 44_L | 1.511 | 0.99 |
| 43_Y | 47_E | 1.457 | 0.99 |
| 22_R | 26_H | 1.440 | 0.99 |
| 23_T | 89_G | 1.390 | 0.99 |
| 16_H | 20_K | 1.376 | 0.99 |
| 23_T | 26_H | 1.359 | 0.99 |
| 52_A | 64_I | 1.352 | 0.98 |
| 13_G | 16_H | 1.318 | 0.98 |
| 52_A | 81_S | 1.318 | 0.98 |
| 8_L | 12_V | 1.314 | 0.98 |
| 64_I | 68_H | 1.282 | 0.98 |
| 29_V | 32_T | 1.279 | 0.98 |
| 12_V | 17_R | 1.222 | 0.97 |
| 45_T | 48_V | 1.215 | 0.96 |
| 54_N | 59_L | 1.209 | 0.96 |
| 36_Y | 40_I | 1.191 | 0.96 |
| 62_K | 69_L | 1.188 | 0.96 |
| 6_A | 12_V | 1.184 | 0.96 |
| 69_L | 89_G | 1.160 | 0.95 |
| 48_V | 82_L | 1.145 | 0.95 |
| 31_A | 35_V | 1.134 | 0.94 |
| 31_A | 34_A | 1.114 | 0.93 |
| 42_E | 47_E | 1.106 | 0.93 |
| 37_S | 40_I | 1.104 | 0.93 |
| 10_F | 14_R | 1.074 | 0.92 |
| 16_H | 89_G | 1.067 | 0.91 |
| 1_S | 6_A | 1.066 | 0.91 |
| 69_L | 80_D | 1.056 | 0.91 |
| 45_T | 49_L | 1.036 | 0.90 |
| 2_R | 6_A | 1.035 | 0.90 |
| 70_Q | 74_R | 1.031 | 0.89 |
| 53_G | 57_K | 1.030 | 0.89 |
| 84_K | 89_G | 1.023 | 0.89 |
| 80_D | 89_G | 1.007 | 0.88 |
| 78_E | 87_I | 1.001 | 0.87 |
| 54_N | 75_G | 1.000 | 0.87 |
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 | |
| 4m6bA | 2 | 1 | 100 | 0.149 | Contact Map |
| 2f8nK | 1 | 0.9888 | 100 | 0.149 | Contact Map |
| 4cayA | 1 | 0.9551 | 100 | 0.152 | Contact Map |
| 1f66C | 2 | 1 | 100 | 0.159 | Contact Map |
| 1tzyA | 2 | 0.9888 | 100 | 0.168 | Contact Map |
| 3ksyA | 1 | 0.9213 | 100 | 0.173 | Contact Map |
| 2f8nG | 1 | 0.9888 | 100 | 0.177 | Contact Map |
| 2nqbC | 2 | 0.9888 | 100 | 0.178 | Contact Map |
| 4jjnC | 2 | 0.9888 | 100 | 0.208 | Contact Map |
| 1f1eA | 1 | 0.8764 | 100 | 0.239 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)