| 4m2p |
| ID: | 1453737597 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 201 (186) | ||
| Sequences: | 2110 (1265.6) | ||
| Seq/Len: | 11.344 | ||
| Nf(neff/√len): | 92.8 |
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: 11.344).
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 |
| 115_T | 165_K | 4.450 | 1.00 |
| 73_D | 78_G | 3.377 | 1.00 |
| 109_D | 114_G | 2.934 | 1.00 |
| 159_G | 163_D | 2.933 | 1.00 |
| 118_K | 152_E | 2.847 | 1.00 |
| 163_D | 170_E | 2.757 | 1.00 |
| 102_E | 168_E | 2.650 | 1.00 |
| 159_G | 164_D | 2.621 | 1.00 |
| 77_D | 84_E | 2.558 | 1.00 |
| 16_L | 20_T | 2.283 | 1.00 |
| 45_R | 66_Q | 2.211 | 1.00 |
| 161_K | 170_E | 2.189 | 1.00 |
| 159_G | 162_D | 2.114 | 1.00 |
| 159_G | 170_E | 1.925 | 1.00 |
| 75_N | 84_E | 1.909 | 1.00 |
| 69_F | 73_D | 1.833 | 1.00 |
| 116_I | 121_V | 1.747 | 1.00 |
| 22_F | 26_E | 1.677 | 1.00 |
| 161_K | 167_T | 1.664 | 1.00 |
| 81_D | 84_E | 1.615 | 1.00 |
| 73_D | 77_D | 1.560 | 1.00 |
| 111_D | 120_E | 1.544 | 1.00 |
| 31_Y | 35_L | 1.520 | 1.00 |
| 168_E | 172_I | 1.499 | 1.00 |
| 73_D | 84_E | 1.499 | 1.00 |
| 31_Y | 82_F | 1.490 | 1.00 |
| 105_F | 109_D | 1.467 | 1.00 |
| 113_N | 120_E | 1.459 | 1.00 |
| 86_V | 89_L | 1.439 | 1.00 |
| 21_K | 99_Q | 1.385 | 0.99 |
| 109_D | 120_E | 1.384 | 0.99 |
| 44_T | 47_E | 1.340 | 0.99 |
| 49_Q | 66_Q | 1.329 | 0.99 |
| 42_R | 79_T | 1.322 | 0.99 |
| 73_D | 80_L | 1.279 | 0.99 |
| 184_L | 188_E | 1.246 | 0.98 |
| 67_H | 70_R | 1.228 | 0.98 |
| 155_W | 159_G | 1.208 | 0.98 |
| 37_E | 43_I | 1.200 | 0.98 |
| 185_I | 189_P | 1.156 | 0.97 |
| 38_D | 41_G | 1.153 | 0.97 |
| 52_Y | 56_F | 1.137 | 0.97 |
| 84_E | 120_E | 1.128 | 0.97 |
| 9_S | 12_I | 1.124 | 0.97 |
| 41_G | 47_E | 1.121 | 0.97 |
| 90_H | 100_K | 1.121 | 0.97 |
| 169_K | 172_I | 1.120 | 0.96 |
| 11_E | 18_L | 1.105 | 0.96 |
| 43_I | 47_E | 1.094 | 0.96 |
| 184_L | 189_P | 1.086 | 0.96 |
| 163_D | 167_T | 1.084 | 0.96 |
| 104_A | 161_K | 1.073 | 0.95 |
| 178_N | 181_I | 1.068 | 0.95 |
| 143_D | 153_K | 1.066 | 0.95 |
| 74_A | 80_L | 1.058 | 0.95 |
| 141_P | 148_E | 1.053 | 0.95 |
| 11_E | 14_E | 1.051 | 0.94 |
| 73_D | 76_S | 1.049 | 0.94 |
| 121_V | 155_W | 1.048 | 0.94 |
| 27_L | 86_V | 1.042 | 0.94 |
| 24_E | 28_S | 1.041 | 0.94 |
| 110_V | 120_E | 1.039 | 0.94 |
| 48_F | 69_F | 1.037 | 0.94 |
| 110_V | 116_I | 1.036 | 0.94 |
| 126_T | 144_E | 1.032 | 0.94 |
| 183_R | 187_F | 1.026 | 0.94 |
| 74_A | 106_S | 1.024 | 0.93 |
| 57_P | 113_N | 1.021 | 0.93 |
| 12_I | 15_E | 1.016 | 0.93 |
| 150_R | 154_I | 1.016 | 0.93 |
| 69_F | 88_A | 1.015 | 0.93 |
| 83_K | 87_I | 1.012 | 0.93 |
| 173_E | 177_A | 1.010 | 0.93 |
| 35_L | 39_P | 1.010 | 0.93 |
| 121_V | 158_F | 1.007 | 0.93 |
| 30_W | 92_T | 1.005 | 0.93 |
| 183_R | 186_Q | 1.002 | 0.92 |
| 100_K | 103_W | 1.000 | 0.92 |
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 | |
| 4m2pA | 1 | 0.9502 | 100 | 0.285 | Contact Map |
| 4gukA | 4 | 0.9104 | 99.9 | 0.337 | Contact Map |
| 3dd4A | 1 | 0.8856 | 99.9 | 0.338 | Contact Map |
| 2l2eA | 1 | 0.9403 | 99.9 | 0.342 | Contact Map |
| 1s6cA | 1 | 0.8209 | 99.9 | 0.344 | Contact Map |
| 2julA | 1 | 0.9005 | 99.9 | 0.348 | Contact Map |
| 1fpwA | 1 | 0.9403 | 99.9 | 0.349 | Contact Map |
| 1bjfA | 2 | 0.9005 | 99.9 | 0.35 | Contact Map |
| 1s1eA | 1 | 0.9005 | 99.9 | 0.35 | Contact Map |
| 2l4hA | 1 | 0.8507 | 99.9 | 0.389 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)