| tnfn |
| ID: | 1478537901 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (88) | ||
| Sequences: | 37406 (22956.4) | ||
| Seq/Len: | 425.068 | ||
| Nf(neff/√len): | 2447.2 |
Jackhmmer Results: (2016_04)
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: 425.068).
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 |
| 75_R | 80_S | 3.830 | 1.00 |
| 59_I | 70_V | 3.300 | 1.00 |
| 73_I | 83_P | 2.965 | 1.00 |
| 73_I | 80_S | 2.513 | 1.00 |
| 35_T | 71_S | 2.509 | 1.00 |
| 31_G | 75_R | 2.371 | 1.00 |
| 36_Y | 59_I | 2.308 | 1.00 |
| 33_E | 75_R | 2.279 | 1.00 |
| 37_G | 69_E | 2.268 | 1.00 |
| 33_E | 80_S | 2.256 | 1.00 |
| 19_L | 58_S | 2.208 | 1.00 |
| 36_Y | 70_V | 2.166 | 1.00 |
| 19_L | 56_Q | 2.128 | 1.00 |
| 14_T | 17_T | 1.960 | 1.00 |
| 38_I | 66_T | 1.879 | 1.00 |
| 35_T | 73_I | 1.852 | 1.00 |
| 71_S | 83_P | 1.659 | 1.00 |
| 35_T | 83_P | 1.636 | 1.00 |
| 76_R | 79_M | 1.616 | 1.00 |
| 7_Q | 23_F | 1.537 | 1.00 |
| 33_E | 73_I | 1.477 | 1.00 |
| 39_K | 69_E | 1.476 | 1.00 |
| 34_L | 57_Y | 1.450 | 1.00 |
| 11_K | 21_T | 1.409 | 1.00 |
| 9_E | 21_T | 1.389 | 0.99 |
| 74_S | 81_S | 1.372 | 0.99 |
| 63_K | 66_T | 1.368 | 0.99 |
| 18_A | 88_F | 1.329 | 0.99 |
| 38_I | 63_K | 1.270 | 0.99 |
| 39_K | 67_E | 1.268 | 0.99 |
| 8_I | 84_A | 1.253 | 0.99 |
| 25_P | 32_I | 1.239 | 0.98 |
| 24_K | 55_N | 1.238 | 0.98 |
| 63_K | 68_Y | 1.222 | 0.98 |
| 15_D | 64_P | 1.192 | 0.98 |
| 30_D | 77_G | 1.180 | 0.98 |
| 17_T | 58_S | 1.159 | 0.97 |
| 10_V | 18_A | 1.140 | 0.97 |
| 6_S | 23_F | 1.128 | 0.97 |
| 44_D | 47_T | 1.122 | 0.97 |
| 11_K | 19_L | 1.121 | 0.97 |
| 22_W | 72_L | 1.074 | 0.95 |
| 31_G | 49_D | 1.060 | 0.95 |
| 29_I | 74_S | 1.048 | 0.94 |
| 10_V | 20_I | 1.026 | 0.94 |
| 13_V | 18_A | 1.011 | 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 | |
| 1j8kA | 1 | 1 | 99.4 | 0.156 | Contact Map |
| 3b83A | 8 | 1 | 99.4 | 0.164 | Contact Map |
| 2rb8A | 1 | 1 | 99.3 | 0.169 | Contact Map |
| 3teuA | 1 | 1 | 99.3 | 0.17 | Contact Map |
| 3csgA | 1 | 1 | 99.3 | 0.178 | Contact Map |
| 4u3hA | 1 | 0.9778 | 99.3 | 0.185 | Contact Map |
| 4lxoA | 2 | 1 | 99.3 | 0.191 | Contact Map |
| 2ekjA | 1 | 1 | 99.3 | 0.191 | Contact Map |
| 3r8qA | 1 | 1 | 99.3 | 0.192 | Contact Map |
| 1tdqA | 1 | 1 | 99.3 | 0.193 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)