| hxlr |
| ID: | 1508140749 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (114) | ||
| Sequences: | 13720 (8581.9) | ||
| Seq/Len: | 120.351 | ||
| Nf(neff/√len): | 803.8 |
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: 120.351).
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 |
| 44_K | 52_Q | 2.876 | 1.00 |
| 69_H | 83_S | 2.822 | 1.00 |
| 90_S | 104_G | 2.734 | 1.00 |
| 53_K | 57_N | 2.727 | 1.00 |
| 71_E | 83_S | 2.583 | 1.00 |
| 33_G | 92_M | 2.429 | 1.00 |
| 75_V | 79_K | 2.395 | 1.00 |
| 32_L | 68_V | 2.394 | 1.00 |
| 69_H | 85_T | 2.271 | 1.00 |
| 73_Y | 81_E | 2.061 | 1.00 |
| 31_H | 46_L | 2.049 | 1.00 |
| 32_L | 43_L | 2.009 | 1.00 |
| 87_H | 105_Y | 1.998 | 1.00 |
| 64_Q | 117_K | 1.921 | 1.00 |
| 94_I | 97_A | 1.901 | 1.00 |
| 93_P | 97_A | 1.859 | 1.00 |
| 73_Y | 79_K | 1.736 | 1.00 |
| 38_K | 46_L | 1.705 | 1.00 |
| 37_T | 83_S | 1.703 | 1.00 |
| 97_A | 100_E | 1.672 | 1.00 |
| 28_I | 58_Q | 1.662 | 1.00 |
| 84_L | 88_G | 1.654 | 1.00 |
| 22_G | 61_E | 1.646 | 1.00 |
| 60_R | 63_E | 1.603 | 1.00 |
| 70_R | 80_V | 1.522 | 1.00 |
| 25_K | 58_Q | 1.506 | 1.00 |
| 67_I | 88_G | 1.484 | 1.00 |
| 25_K | 61_E | 1.478 | 1.00 |
| 90_S | 101_W | 1.436 | 1.00 |
| 37_T | 81_E | 1.428 | 1.00 |
| 87_H | 90_S | 1.406 | 0.99 |
| 86_P | 89_E | 1.370 | 0.99 |
| 54_I | 57_N | 1.357 | 0.99 |
| 89_E | 92_M | 1.352 | 0.99 |
| 16_T | 98_M | 1.339 | 0.99 |
| 25_K | 62_L | 1.328 | 0.99 |
| 87_H | 108_L | 1.253 | 0.99 |
| 90_S | 105_Y | 1.227 | 0.98 |
| 19_V | 65_D | 1.212 | 0.98 |
| 99_Y | 103_K | 1.192 | 0.98 |
| 16_T | 102_G | 1.178 | 0.98 |
| 50_I | 55_L | 1.166 | 0.97 |
| 71_E | 81_E | 1.148 | 0.97 |
| 72_V | 80_V | 1.144 | 0.97 |
| 63_E | 68_V | 1.132 | 0.97 |
| 38_K | 42_E | 1.123 | 0.97 |
| 41_N | 45_T | 1.115 | 0.96 |
| 22_G | 58_Q | 1.111 | 0.96 |
| 73_Y | 77_P | 1.087 | 0.96 |
| 15_L | 106_M | 1.086 | 0.96 |
| 29_L | 84_L | 1.083 | 0.96 |
| 52_Q | 56_V | 1.078 | 0.95 |
| 56_V | 60_R | 1.077 | 0.95 |
| 39_R | 81_E | 1.076 | 0.95 |
| 72_V | 77_P | 1.068 | 0.95 |
| 32_L | 38_K | 1.062 | 0.95 |
| 73_Y | 76_V | 1.061 | 0.95 |
| 92_M | 96_E | 1.047 | 0.94 |
| 40_F | 56_V | 1.036 | 0.94 |
| 54_I | 58_Q | 1.029 | 0.94 |
| 91_L | 101_W | 1.026 | 0.94 |
| 67_I | 91_L | 1.020 | 0.93 |
| 64_Q | 116_M | 1.005 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4gcvA | 12 | 0.9 | 99.8 | 0.291 | Contact Map |
| 1yyvA | 2 | 0.925 | 99.7 | 0.406 | Contact Map |
| 4a5nA | 4 | 0.875 | 99.7 | 0.417 | Contact Map |
| 2f2eA | 2 | 0.95 | 99.6 | 0.432 | Contact Map |
| 2hztA | 4 | 0.7917 | 99.6 | 0.433 | Contact Map |
| 1z7uA | 2 | 0.925 | 99.6 | 0.433 | Contact Map |
| 2fswA | 2 | 0.8583 | 99.6 | 0.434 | Contact Map |
| 3df8A | 1 | 0.85 | 99.5 | 0.487 | Contact Map |
| 4hw0A | 3 | 0.8083 | 99.5 | 0.488 | Contact Map |
| 4hqeA | 2 | 0.8917 | 99.3 | 0.532 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)