| 1Nti |
| ID: | 1453816432 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (86) | ||
| Sequences: | 1565 (1024.1) | ||
| Seq/Len: | 18.198 | ||
| Nf(neff/√len): | 110.4 |
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: 18.198).
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 |
| 48_D | 51_G | 3.668 | 1.00 |
| 59_N | 62_K | 3.616 | 1.00 |
| 2_Q | 70_M | 3.501 | 1.00 |
| 38_D | 63_G | 3.044 | 1.00 |
| 43_R | 56_D | 2.678 | 1.00 |
| 64_T | 72_A | 2.393 | 1.00 |
| 20_A | 23_E | 2.200 | 1.00 |
| 29_S | 61_L | 2.189 | 1.00 |
| 27_I | 77_V | 2.082 | 1.00 |
| 1_S | 70_M | 2.076 | 1.00 |
| 38_D | 62_K | 1.917 | 1.00 |
| 26_F | 76_K | 1.904 | 1.00 |
| 2_Q | 6_D | 1.836 | 1.00 |
| 7_K | 11_E | 1.825 | 1.00 |
| 68_D | 71_K | 1.757 | 1.00 |
| 71_K | 75_D | 1.578 | 1.00 |
| 65_S | 68_D | 1.567 | 1.00 |
| 68_D | 72_A | 1.553 | 1.00 |
| 23_E | 76_K | 1.510 | 1.00 |
| 33_Q | 37_G | 1.464 | 1.00 |
| 66_K | 70_M | 1.453 | 1.00 |
| 41_T | 55_W | 1.447 | 1.00 |
| 21_D | 24_M | 1.434 | 1.00 |
| 52_K | 56_D | 1.431 | 1.00 |
| 55_W | 59_N | 1.425 | 1.00 |
| 75_D | 79_E | 1.423 | 1.00 |
| 78_E | 81_K | 1.397 | 0.99 |
| 61_L | 64_T | 1.348 | 0.99 |
| 26_F | 30_H | 1.279 | 0.99 |
| 23_E | 84_Y | 1.257 | 0.99 |
| 46_M | 52_K | 1.213 | 0.98 |
| 76_K | 79_E | 1.210 | 0.98 |
| 19_P | 24_M | 1.191 | 0.98 |
| 72_A | 75_D | 1.177 | 0.98 |
| 36_V | 40_N | 1.117 | 0.96 |
| 6_D | 10_E | 1.073 | 0.95 |
| 4_E | 78_E | 1.041 | 0.94 |
| 10_E | 13_K | 1.037 | 0.94 |
| 25_L | 28_Y | 1.037 | 0.94 |
| 2_Q | 66_K | 1.001 | 0.92 |
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 | |
| 3epyA | 2 | 1 | 100 | -0.029 | Contact Map |
| 1st7A | 1 | 1 | 100 | -0.029 | Contact Map |
| 2copA | 1 | 1 | 100 | -0.023 | Contact Map |
| 2lbbA | 1 | 1 | 100 | -0.012 | Contact Map |
| 2cb8A | 2 | 1 | 100 | -0.012 | Contact Map |
| 2cquA | 1 | 1 | 100 | -0.012 | Contact Map |
| 3flvA | 2 | 1 | 100 | -0.011 | Contact Map |
| 1hbkA | 1 | 1 | 100 | -0.009 | Contact Map |
| 3fp5A | 1 | 1 | 100 | 0.002 | Contact Map |
| 2wh5A | 6 | 0.9884 | 99.9 | 0.009 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)