| d4g4zc_ |
| ID: | 1451491637 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (113) | ||
| Sequences: | 12849 (9027.6) | ||
| Seq/Len: | 113.708 | ||
| Nf(neff/√len): | 849.2 |
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: 113.708).
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 |
| 47_E | 90_F | 3.453 | 1.00 |
| 17_N | 58_L | 2.754 | 1.00 |
| 63_S | 89_G | 2.736 | 1.00 |
| 61_R | 65_A | 2.548 | 1.00 |
| 90_F | 94_Q | 2.481 | 1.00 |
| 16_T | 53_T | 2.478 | 1.00 |
| 15_D | 22_K | 2.465 | 1.00 |
| 71_K | 87_T | 2.284 | 1.00 |
| 53_T | 105_R | 2.148 | 1.00 |
| 19_S | 65_A | 2.143 | 1.00 |
| 64_L | 68_N | 2.122 | 1.00 |
| 97_A | 104_G | 2.111 | 1.00 |
| 30_A | 77_E | 2.082 | 1.00 |
| 97_A | 107_M | 2.024 | 1.00 |
| 99_N | 104_G | 1.978 | 1.00 |
| 60_E | 64_L | 1.897 | 1.00 |
| 29_I | 73_A | 1.859 | 1.00 |
| 30_A | 73_A | 1.822 | 1.00 |
| 47_E | 114_T | 1.815 | 1.00 |
| 56_R | 92_W | 1.638 | 1.00 |
| 71_K | 75_V | 1.588 | 1.00 |
| 56_R | 93_D | 1.579 | 1.00 |
| 49_H | 94_Q | 1.567 | 1.00 |
| 45_R | 86_S | 1.564 | 1.00 |
| 60_E | 93_D | 1.547 | 1.00 |
| 68_N | 71_K | 1.538 | 1.00 |
| 46_I | 111_V | 1.482 | 1.00 |
| 51_D | 59_N | 1.433 | 1.00 |
| 45_R | 88_Q | 1.405 | 0.99 |
| 73_A | 77_E | 1.372 | 0.99 |
| 52_N | 105_R | 1.338 | 0.99 |
| 21_I | 73_A | 1.337 | 0.99 |
| 75_V | 82_A | 1.303 | 0.99 |
| 28_E | 31_K | 1.293 | 0.99 |
| 45_R | 116_T | 1.291 | 0.99 |
| 98_D | 104_G | 1.282 | 0.99 |
| 58_L | 61_R | 1.279 | 0.99 |
| 54_G | 59_N | 1.278 | 0.99 |
| 71_K | 85_L | 1.210 | 0.98 |
| 15_D | 18_K | 1.191 | 0.98 |
| 26_K | 73_A | 1.175 | 0.98 |
| 68_N | 72_S | 1.168 | 0.97 |
| 68_N | 87_T | 1.164 | 0.97 |
| 47_E | 88_Q | 1.131 | 0.97 |
| 71_K | 82_A | 1.123 | 0.97 |
| 49_H | 112_F | 1.112 | 0.96 |
| 75_V | 85_L | 1.112 | 0.96 |
| 72_S | 76_N | 1.094 | 0.96 |
| 100_K | 104_G | 1.081 | 0.95 |
| 43_T | 86_S | 1.067 | 0.95 |
| 101_T | 104_G | 1.065 | 0.95 |
| 51_D | 109_R | 1.061 | 0.95 |
| 16_T | 51_D | 1.061 | 0.95 |
| 64_L | 89_G | 1.058 | 0.95 |
| 101_T | 105_R | 1.057 | 0.95 |
| 81_D | 84_R | 1.048 | 0.94 |
| 46_I | 71_K | 1.024 | 0.93 |
| 23_D | 26_K | 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 | |
| 2l26A | 1 | 0.9664 | 99.9 | -0.009 | Contact Map |
| 3ldtA | 1 | 0.9664 | 99.9 | -0.009 | Contact Map |
| 2hqsH | 4 | 0.9076 | 99.9 | -0.003 | Contact Map |
| 2k1sA | 1 | 0.9916 | 99.9 | 0.004 | Contact Map |
| 1r1mA | 1 | 0.9916 | 99.9 | 0.005 | Contact Map |
| 3td3A | 8 | 1 | 99.9 | 0.008 | Contact Map |
| 3s0yA | 2 | 0.9916 | 99.9 | 0.011 | Contact Map |
| 3wpwA | 2 | 0.9664 | 99.9 | 0.026 | Contact Map |
| 3s06A | 2 | 0.9916 | 99.9 | 0.029 | Contact Map |
| 3nb3A | 3 | 0 | 99.9 | 0.03 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)