| d2g2pb_ |
| ID: | 1447475932 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 111 (111) | ||
| Sequences: | 1429 (907.7) | ||
| Seq/Len: | 12.874 | ||
| Nf(neff/√len): | 86.2 |
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: 12.874).
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 |
| 7_I | 19_V | 2.881 | 1.00 |
| 60_R | 84_E | 2.501 | 1.00 |
| 16_A | 19_V | 2.388 | 1.00 |
| 22_T | 64_K | 2.348 | 1.00 |
| 24_E | 62_V | 2.331 | 1.00 |
| 40_D | 46_K | 2.305 | 1.00 |
| 31_W | 60_R | 2.138 | 1.00 |
| 64_K | 67_D | 2.105 | 1.00 |
| 42_D | 111_S | 1.996 | 1.00 |
| 37_A | 45_I | 1.974 | 1.00 |
| 22_T | 36_T | 1.915 | 1.00 |
| 10_Q | 104_G | 1.893 | 1.00 |
| 1_N | 4_S | 1.873 | 1.00 |
| 89_K | 92_E | 1.848 | 1.00 |
| 26_K | 31_W | 1.790 | 1.00 |
| 22_T | 62_V | 1.785 | 1.00 |
| 33_Q | 36_T | 1.734 | 1.00 |
| 60_R | 82_P | 1.721 | 1.00 |
| 75_E | 88_N | 1.715 | 1.00 |
| 62_V | 80_E | 1.630 | 1.00 |
| 9_N | 12_T | 1.604 | 1.00 |
| 20_T | 64_K | 1.572 | 1.00 |
| 77_F | 96_V | 1.489 | 1.00 |
| 24_E | 33_Q | 1.448 | 1.00 |
| 18_D | 38_K | 1.356 | 0.99 |
| 21_V | 61_V | 1.351 | 0.99 |
| 22_T | 33_Q | 1.339 | 0.99 |
| 63_F | 98_L | 1.330 | 0.99 |
| 62_V | 82_P | 1.326 | 0.99 |
| 11_Q | 104_G | 1.307 | 0.99 |
| 24_E | 60_R | 1.305 | 0.99 |
| 20_T | 36_T | 1.294 | 0.99 |
| 25_K | 32_L | 1.277 | 0.99 |
| 27_A | 32_L | 1.241 | 0.98 |
| 15_P | 111_S | 1.239 | 0.98 |
| 5_V | 61_V | 1.233 | 0.98 |
| 20_T | 38_K | 1.232 | 0.98 |
| 8_L | 44_R | 1.229 | 0.98 |
| 61_V | 96_V | 1.222 | 0.98 |
| 10_Q | 78_F | 1.191 | 0.98 |
| 42_D | 99_L | 1.141 | 0.97 |
| 87_I | 90_V | 1.136 | 0.97 |
| 65_T | 81_I | 1.127 | 0.97 |
| 6_H | 44_R | 1.116 | 0.96 |
| 58_D | 86_H | 1.108 | 0.96 |
| 98_L | 105_Y | 1.097 | 0.96 |
| 70_K | 76_S | 1.095 | 0.96 |
| 69_F | 100_L | 1.088 | 0.96 |
| 26_K | 60_R | 1.078 | 0.95 |
| 6_H | 95_H | 1.076 | 0.95 |
| 12_T | 72_Q | 1.074 | 0.95 |
| 25_K | 57_G | 1.055 | 0.95 |
| 45_I | 48_L | 1.051 | 0.94 |
| 80_E | 84_E | 1.039 | 0.94 |
| 64_K | 80_E | 1.019 | 0.93 |
| 101_S | 104_G | 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 | |
| 3iwvA | 4 | 1 | 100 | -0.01 | Contact Map |
| 2g2nA | 4 | 1 | 100 | -0.008 | Contact Map |
| 4q14A | 2 | 1 | 100 | 0.005 | Contact Map |
| 2h0eA | 2 | 0.973 | 100 | 0.042 | Contact Map |
| 1f86A | 2 | 1 | 100 | 0.048 | Contact Map |
| 3qvaA | 4 | 0.9369 | 100 | 0.051 | Contact Map |
| 1oo2A | 4 | 1 | 100 | 0.054 | Contact Map |
| 4pweA | 2 | 1 | 100 | 0.07 | Contact Map |
| 4zjhA | 1 | 0 | 98.5 | 0.757 | Contact Map |
| 3e8vA | 1 | 0.7387 | 96 | 0.845 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)