| 4lmiA |
| ID: | 1456171211 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 135 (135) | ||
| Sequences: | 3215 (3215) | ||
| Seq/Len: | 23.815 | ||
| Nf(neff/√len): | 276.7 |
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: 23.815).
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 |
| 84_V | 89_W | 3.397 | 1.00 |
| 1_D | 7_R | 3.374 | 1.00 |
| 13_L | 17_S | 3.311 | 1.00 |
| 23_N | 26_A | 3.198 | 1.00 |
| 54_A | 58_Q | 3.067 | 1.00 |
| 59_D | 63_K | 2.953 | 1.00 |
| 4_D | 75_K | 2.738 | 1.00 |
| 92_L | 110_K | 2.699 | 1.00 |
| 80_T | 132_N | 2.673 | 1.00 |
| 68_T | 82_I | 2.650 | 1.00 |
| 76_W | 97_Y | 2.563 | 1.00 |
| 69_Y | 131_K | 2.552 | 1.00 |
| 28_A | 53_L | 2.507 | 1.00 |
| 35_A | 52_I | 2.489 | 1.00 |
| 10_S | 14_K | 2.440 | 1.00 |
| 24_F | 57_A | 2.395 | 1.00 |
| 37_L | 52_I | 2.367 | 1.00 |
| 99_K | 104_Q | 2.346 | 1.00 |
| 89_W | 133_I | 2.265 | 1.00 |
| 34_N | 104_Q | 2.222 | 1.00 |
| 16_F | 81_C | 2.182 | 1.00 |
| 17_S | 21_S | 2.111 | 1.00 |
| 38_C | 45_K | 2.108 | 1.00 |
| 18_Y | 26_A | 2.031 | 1.00 |
| 6_E | 9_Y | 1.915 | 1.00 |
| 63_K | 85_D | 1.847 | 1.00 |
| 31_L | 35_A | 1.802 | 1.00 |
| 28_A | 49_A | 1.775 | 1.00 |
| 97_Y | 105_V | 1.769 | 1.00 |
| 83_E | 92_L | 1.745 | 1.00 |
| 33_E | 49_A | 1.726 | 1.00 |
| 39_F | 44_L | 1.716 | 1.00 |
| 9_Y | 70_L | 1.707 | 1.00 |
| 32_A | 104_Q | 1.681 | 1.00 |
| 88_Q | 135_S | 1.656 | 1.00 |
| 4_D | 7_R | 1.632 | 1.00 |
| 16_F | 79_V | 1.629 | 1.00 |
| 46_I | 55_F | 1.626 | 1.00 |
| 39_F | 108_V | 1.581 | 1.00 |
| 98_V | 103_I | 1.536 | 1.00 |
| 65_L | 81_C | 1.481 | 1.00 |
| 28_A | 50_E | 1.466 | 1.00 |
| 90_H | 110_K | 1.463 | 1.00 |
| 11_T | 98_V | 1.447 | 1.00 |
| 37_L | 108_V | 1.433 | 1.00 |
| 19_L | 56_W | 1.427 | 1.00 |
| 14_K | 26_A | 1.398 | 0.99 |
| 94_I | 108_V | 1.380 | 0.99 |
| 18_Y | 30_L | 1.379 | 0.99 |
| 16_F | 67_V | 1.373 | 0.99 |
| 15_F | 106_I | 1.362 | 0.99 |
| 13_L | 70_L | 1.341 | 0.99 |
| 7_R | 101_G | 1.309 | 0.99 |
| 8_T | 98_V | 1.306 | 0.99 |
| 46_I | 51_N | 1.277 | 0.99 |
| 56_W | 108_V | 1.274 | 0.99 |
| 91_V | 132_N | 1.272 | 0.99 |
| 4_D | 101_G | 1.258 | 0.99 |
| 81_C | 94_I | 1.245 | 0.98 |
| 90_H | 112_P | 1.215 | 0.98 |
| 40_P | 107_I | 1.210 | 0.98 |
| 20_N | 64_S | 1.206 | 0.98 |
| 27_F | 56_W | 1.200 | 0.98 |
| 27_F | 31_L | 1.187 | 0.98 |
| 36_V | 45_K | 1.186 | 0.98 |
| 67_V | 70_L | 1.181 | 0.98 |
| 24_F | 53_L | 1.142 | 0.97 |
| 32_A | 102_L | 1.139 | 0.97 |
| 9_Y | 13_L | 1.137 | 0.97 |
| 78_A | 95_F | 1.134 | 0.97 |
| 92_L | 108_V | 1.116 | 0.96 |
| 15_F | 96_L | 1.113 | 0.96 |
| 39_F | 42_T | 1.113 | 0.96 |
| 18_Y | 23_N | 1.107 | 0.96 |
| 121_D | 126_H | 1.105 | 0.96 |
| 50_E | 54_A | 1.082 | 0.96 |
| 68_T | 80_T | 1.076 | 0.95 |
| 39_F | 110_K | 1.074 | 0.95 |
| 80_T | 93_I | 1.052 | 0.95 |
| 82_I | 133_I | 1.052 | 0.95 |
| 36_V | 47_V | 1.044 | 0.94 |
| 22_N | 64_S | 1.034 | 0.94 |
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 | |
| 4lmiA | 2 | 1 | 99.2 | 0.786 | Contact Map |
| 3en8A | 1 | 0.9407 | 99 | 0.796 | Contact Map |
| 4mjdA | 2 | 0.8 | 99 | 0.803 | Contact Map |
| 3g0kA | 1 | 0.8815 | 98.6 | 0.827 | Contact Map |
| 3h3hA | 2 | 0.8074 | 98.6 | 0.827 | Contact Map |
| 3hk4A | 4 | 0.7852 | 98.6 | 0.828 | Contact Map |
| 3fh1A | 1 | 0.8296 | 98.5 | 0.83 | Contact Map |
| 3ff2A | 1 | 0.7852 | 98.4 | 0.835 | Contact Map |
| 3wmdA | 2 | 0.8815 | 98.4 | 0.835 | Contact Map |
| 3f40A | 1 | 0.8222 | 98.4 | 0.837 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)