| 1K4C |
| ID: | 1461694890 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (120) | ||
| Sequences: | 3083 (2013) | ||
| Seq/Len: | 25.692 | ||
| Nf(neff/√len): | 183.8 |
HHblits Results: (2016_02)
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: 25.692).
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 |
| 71_E | 96_M | 3.126 | 1.00 |
| 74_T | 96_M | 2.712 | 1.00 |
| 50_A | 91_V | 2.671 | 1.00 |
| 72_T | 78_Y | 2.293 | 1.00 |
| 64_R | 89_R | 2.001 | 1.00 |
| 85_T | 88_G | 1.949 | 1.00 |
| 76_V | 96_M | 1.912 | 1.00 |
| 68_W | 92_A | 1.812 | 1.00 |
| 61_T | 64_R | 1.793 | 1.00 |
| 50_A | 87_W | 1.776 | 1.00 |
| 46_L | 91_V | 1.742 | 1.00 |
| 51_E | 88_G | 1.662 | 1.00 |
| 45_Y | 62_Y | 1.636 | 1.00 |
| 44_S | 65_A | 1.499 | 1.00 |
| 46_L | 50_A | 1.497 | 1.00 |
| 43_G | 91_V | 1.481 | 1.00 |
| 43_G | 95_V | 1.479 | 1.00 |
| 11_R | 14_K | 1.457 | 1.00 |
| 108_A | 111_A | 1.456 | 1.00 |
| 41_L | 45_Y | 1.453 | 1.00 |
| 72_T | 79_G | 1.430 | 1.00 |
| 75_T | 78_Y | 1.427 | 1.00 |
| 47_A | 59_L | 1.425 | 1.00 |
| 9_L | 13_V | 1.377 | 0.99 |
| 63_P | 93_V | 1.366 | 0.99 |
| 76_V | 79_G | 1.327 | 0.99 |
| 73_A | 108_A | 1.238 | 0.98 |
| 54_A | 85_T | 1.232 | 0.98 |
| 15_L | 20_H | 1.231 | 0.98 |
| 60_I | 64_R | 1.230 | 0.98 |
| 95_V | 101_T | 1.227 | 0.98 |
| 67_W | 82_Y | 1.226 | 0.98 |
| 44_S | 66_L | 1.217 | 0.98 |
| 86_L | 90_C | 1.211 | 0.98 |
| 17_L | 20_H | 1.211 | 0.98 |
| 7_G | 10_A | 1.211 | 0.98 |
| 107_T | 112_T | 1.210 | 0.98 |
| 72_T | 80_D | 1.201 | 0.98 |
| 44_S | 69_S | 1.187 | 0.98 |
| 67_W | 92_A | 1.182 | 0.98 |
| 36_L | 102_S | 1.159 | 0.97 |
| 11_R | 15_L | 1.129 | 0.97 |
| 83_P | 92_A | 1.119 | 0.96 |
| 116_G | 119_Q | 1.106 | 0.96 |
| 75_T | 80_D | 1.094 | 0.96 |
| 75_T | 79_G | 1.087 | 0.96 |
| 103_F | 107_T | 1.064 | 0.95 |
| 45_Y | 49_L | 1.062 | 0.95 |
| 71_E | 78_Y | 1.056 | 0.95 |
| 80_D | 89_R | 1.052 | 0.95 |
| 48_V | 61_T | 1.043 | 0.94 |
| 62_Y | 66_L | 1.030 | 0.94 |
| 24_L | 120_E | 1.024 | 0.93 |
| 92_A | 96_M | 1.016 | 0.93 |
| 51_E | 61_T | 1.009 | 0.93 |
| 34_V | 41_L | 1.009 | 0.93 |
| 106_V | 109_A | 1.008 | 0.93 |
| 106_V | 113_W | 1.005 | 0.93 |
| 41_L | 62_Y | 1.003 | 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 | |
| 2a9hA | 4 | 0.7823 | 99.8 | 0.248 | Contact Map |
| 2ih3C | 1 | 0.7823 | 99.8 | 0.258 | Contact Map |
| 3pjsK | 4 | 0.8306 | 99.8 | 0.264 | Contact Map |
| 2k1eA | 4 | 0.8306 | 99.7 | 0.317 | Contact Map |
| 1orqC | 1 | 0.9597 | 99.7 | 0.317 | Contact Map |
| 3effK | 4 | 0.8306 | 99.7 | 0.317 | Contact Map |
| 2r9rB | 2 | 0.9839 | 99.7 | 0.322 | Contact Map |
| 3behA | 4 | 0.9839 | 99.7 | 0.365 | Contact Map |
| 3syaA | 1 | 0.9758 | 99.7 | 0.367 | Contact Map |
| 3spcA | 1 | 0.9516 | 99.7 | 0.369 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)