| 3g0m |
| ID: | 1492603688 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (135) | ||
| Sequences: | 1913 (1029.3) | ||
| Seq/Len: | 14.170 | ||
| Nf(neff/√len): | 88.6 |
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: 14.170).
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 |
| 95_M | 99_D | 3.472 | 1.00 |
| 75_D | 82_K | 3.228 | 1.00 |
| 98_Q | 102_H | 2.985 | 1.00 |
| 110_E | 115_A | 2.751 | 1.00 |
| 71_E | 93_H | 2.354 | 1.00 |
| 46_N | 49_N | 2.337 | 1.00 |
| 96_T | 99_D | 2.325 | 1.00 |
| 71_E | 94_Q | 2.124 | 1.00 |
| 44_D | 61_V | 2.020 | 1.00 |
| 44_D | 73_Q | 2.007 | 1.00 |
| 40_L | 45_R | 1.968 | 1.00 |
| 30_I | 87_V | 1.913 | 1.00 |
| 50_T | 57_Q | 1.911 | 1.00 |
| 45_R | 75_D | 1.897 | 1.00 |
| 16_N | 90_I | 1.835 | 1.00 |
| 41_N | 44_D | 1.829 | 1.00 |
| 14_L | 111_K | 1.827 | 1.00 |
| 42_P | 45_R | 1.814 | 1.00 |
| 74_G | 85_M | 1.786 | 1.00 |
| 29_Y | 32_E | 1.766 | 1.00 |
| 132_A | 136_K | 1.587 | 1.00 |
| 13_L | 90_I | 1.571 | 1.00 |
| 62_M | 136_K | 1.550 | 1.00 |
| 57_Q | 77_D | 1.519 | 1.00 |
| 62_M | 72_L | 1.515 | 1.00 |
| 55_Q | 121_S | 1.511 | 1.00 |
| 91_L | 108_W | 1.389 | 0.99 |
| 63_R | 73_Q | 1.352 | 0.99 |
| 47_P | 52_H | 1.335 | 0.99 |
| 56_S | 78_A | 1.329 | 0.99 |
| 41_N | 73_Q | 1.325 | 0.99 |
| 91_L | 103_F | 1.310 | 0.99 |
| 20_C | 25_E | 1.303 | 0.99 |
| 31_I | 34_G | 1.290 | 0.99 |
| 40_L | 44_D | 1.290 | 0.99 |
| 92_Y | 133_I | 1.279 | 0.99 |
| 29_Y | 33_L | 1.261 | 0.99 |
| 72_L | 133_I | 1.261 | 0.99 |
| 101_V | 138_A | 1.232 | 0.98 |
| 10_K | 91_L | 1.228 | 0.98 |
| 23_W | 117_H | 1.223 | 0.98 |
| 18_T | 111_K | 1.211 | 0.98 |
| 44_D | 49_N | 1.196 | 0.98 |
| 40_L | 73_Q | 1.179 | 0.98 |
| 23_W | 27_Y | 1.167 | 0.97 |
| 38_A | 73_Q | 1.164 | 0.97 |
| 64_R | 97_A | 1.159 | 0.97 |
| 131_R | 138_A | 1.158 | 0.97 |
| 80_I | 117_H | 1.152 | 0.97 |
| 16_N | 29_Y | 1.147 | 0.97 |
| 49_N | 62_M | 1.140 | 0.97 |
| 132_A | 135_A | 1.129 | 0.97 |
| 10_K | 51_I | 1.124 | 0.97 |
| 72_L | 100_I | 1.123 | 0.97 |
| 92_Y | 105_V | 1.122 | 0.97 |
| 131_R | 135_A | 1.085 | 0.96 |
| 53_G | 76_S | 1.081 | 0.95 |
| 85_M | 129_M | 1.073 | 0.95 |
| 88_V | 133_I | 1.066 | 0.95 |
| 27_Y | 117_H | 1.052 | 0.95 |
| 81_V | 84_L | 1.050 | 0.94 |
| 60_I | 72_L | 1.049 | 0.94 |
| 135_A | 139_T | 1.046 | 0.94 |
| 136_K | 140_L | 1.032 | 0.94 |
| 62_M | 70_I | 1.021 | 0.93 |
| 74_G | 89_F | 1.012 | 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 | |
| 3g0mA | 1 | 0.9787 | 100 | -0.017 | Contact Map |
| 4lw4C | 2 | 0.9929 | 100 | -0.009 | Contact Map |
| 1wloA | 1 | 0.9362 | 100 | 0.067 | Contact Map |
| 3lvlA | 1 | 0.7872 | 54.3 | 0.912 | Contact Map |
| 2qq4A | 10 | 0.8227 | 33.5 | 0.922 | Contact Map |
| 2z7eA | 3 | 0.8156 | 31.5 | 0.923 | Contact Map |
| 4eb5C | 2 | 0.7801 | 28 | 0.925 | Contact Map |
| 1xjsA | 1 | 0.8582 | 13.7 | 0.935 | Contact Map |
| 3zidA | 2 | 0.3333 | 11.1 | 0.938 | Contact Map |
| 1su0B | 1 | 0.7801 | 10.6 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)