| d3tdea1 |
| ID: | 1449333586 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (95) | ||
| Sequences: | 2077 (855.9) | ||
| Seq/Len: | 21.863 | ||
| Nf(neff/√len): | 87.8 |
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: 21.863).
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 |
| 74_L | 87_G | 3.889 | 1.00 |
| 28_L | 35_S | 3.540 | 1.00 |
| 27_A | 30_A | 3.242 | 1.00 |
| 42_L | 51_V | 2.823 | 1.00 |
| 21_S | 41_T | 2.811 | 1.00 |
| 16_I | 76_I | 2.549 | 1.00 |
| 67_N | 71_A | 2.473 | 1.00 |
| 79_D | 83_K | 2.350 | 1.00 |
| 39_V | 54_V | 2.231 | 1.00 |
| 74_L | 88_A | 2.215 | 1.00 |
| 19_A | 23_S | 2.147 | 1.00 |
| 50_V | 65_I | 2.006 | 1.00 |
| 19_A | 72_R | 1.985 | 1.00 |
| 50_V | 69_V | 1.943 | 1.00 |
| 28_L | 56_T | 1.922 | 1.00 |
| 47_Q | 91_G | 1.857 | 1.00 |
| 23_S | 72_R | 1.837 | 1.00 |
| 80_S | 83_K | 1.689 | 1.00 |
| 73_I | 85_F | 1.662 | 1.00 |
| 64_D | 67_N | 1.617 | 1.00 |
| 17_C | 43_V | 1.617 | 1.00 |
| 47_Q | 93_N | 1.609 | 1.00 |
| 48_V | 73_I | 1.545 | 1.00 |
| 91_G | 95_G | 1.525 | 1.00 |
| 28_L | 54_V | 1.393 | 0.99 |
| 17_C | 51_V | 1.331 | 0.99 |
| 23_S | 68_T | 1.318 | 0.99 |
| 24_V | 39_V | 1.281 | 0.99 |
| 47_Q | 95_G | 1.277 | 0.99 |
| 35_S | 58_A | 1.218 | 0.98 |
| 46_G | 91_G | 1.211 | 0.98 |
| 36_R | 55_T | 1.191 | 0.98 |
| 27_A | 68_T | 1.165 | 0.97 |
| 79_D | 87_G | 1.157 | 0.97 |
| 71_A | 74_L | 1.135 | 0.97 |
| 28_L | 63_A | 1.131 | 0.97 |
| 27_A | 31_A | 1.109 | 0.96 |
| 72_R | 75_E | 1.099 | 0.96 |
| 73_I | 90_C | 1.098 | 0.96 |
| 46_G | 66_T | 1.083 | 0.96 |
| 17_C | 48_V | 1.075 | 0.95 |
| 65_I | 94_I | 1.056 | 0.95 |
| 9_T | 17_C | 1.050 | 0.94 |
| 24_V | 65_I | 1.015 | 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 | |
| 3so4A | 4 | 0.9694 | 100 | 0.03 | Contact Map |
| 3s82A | 2 | 1 | 100 | 0.037 | Contact Map |
| 3imlA | 4 | 0.8776 | 100 | 0.038 | Contact Map |
| 1p7lA | 4 | 0.9694 | 100 | 0.041 | Contact Map |
| 2p02A | 1 | 0.9694 | 100 | 0.045 | Contact Map |
| 4odjA | 1 | 0.9694 | 100 | 0.047 | Contact Map |
| 4le5A | 2 | 0.9592 | 100 | 0.06 | Contact Map |
| 4l7iA | 2 | 0.9184 | 100 | 0.262 | Contact Map |
| 4l4qA | 4 | 0.9898 | 65 | 0.898 | Contact Map |
| 3lvtA | 1 | 0.9388 | 22 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)