| HMGCR 55-230 |
| ID: | 1441694070 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (170) | ||
| Sequences: | 2824 (1894.6) | ||
| Seq/Len: | 16.612 | ||
| Nf(neff/√len): | 145.3 |
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: 16.612).
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 |
| 52_F | 153_V | 3.244 | 1.00 |
| 82_R | 117_D | 3.209 | 1.00 |
| 126_G | 144_C | 3.119 | 1.00 |
| 115_T | 151_Y | 3.059 | 1.00 |
| 122_C | 148_L | 2.687 | 1.00 |
| 56_V | 149_A | 2.532 | 1.00 |
| 82_R | 118_A | 2.473 | 1.00 |
| 98_E | 101_E | 2.443 | 1.00 |
| 53_S | 146_S | 2.093 | 1.00 |
| 77_L | 81_S | 1.904 | 1.00 |
| 49_S | 150_N | 1.792 | 1.00 |
| 156_T | 160_A | 1.778 | 1.00 |
| 151_Y | 155_M | 1.707 | 1.00 |
| 128_G | 140_C | 1.701 | 1.00 |
| 129_T | 141_C | 1.684 | 1.00 |
| 16_C | 20_L | 1.596 | 1.00 |
| 71_L | 143_G | 1.539 | 1.00 |
| 160_A | 163_S | 1.524 | 1.00 |
| 89_F | 92_S | 1.510 | 1.00 |
| 75_L | 146_S | 1.504 | 1.00 |
| 57_I | 62_K | 1.496 | 1.00 |
| 22_I | 84_S | 1.462 | 1.00 |
| 115_T | 119_L | 1.460 | 1.00 |
| 93_S | 105_R | 1.442 | 1.00 |
| 45_T | 49_S | 1.427 | 1.00 |
| 46_I | 49_S | 1.425 | 1.00 |
| 110_L | 113_T | 1.423 | 1.00 |
| 52_F | 149_A | 1.420 | 1.00 |
| 12_T | 16_C | 1.387 | 0.99 |
| 60_L | 145_M | 1.335 | 0.99 |
| 67_L | 139_M | 1.325 | 0.99 |
| 55_V | 58_H | 1.266 | 0.99 |
| 38_L | 42_G | 1.264 | 0.99 |
| 152_F | 156_T | 1.252 | 0.99 |
| 56_V | 60_L | 1.245 | 0.98 |
| 82_R | 121_E | 1.233 | 0.98 |
| 149_A | 153_V | 1.230 | 0.98 |
| 90_A | 166_L | 1.224 | 0.98 |
| 160_A | 164_L | 1.224 | 0.98 |
| 85_T | 110_L | 1.220 | 0.98 |
| 163_S | 166_L | 1.216 | 0.98 |
| 89_F | 110_L | 1.207 | 0.98 |
| 34_S | 37_I | 1.204 | 0.98 |
| 46_I | 79_D | 1.198 | 0.98 |
| 65_T | 138_I | 1.190 | 0.98 |
| 76_L | 81_S | 1.178 | 0.98 |
| 77_L | 82_R | 1.172 | 0.98 |
| 136_L | 139_M | 1.157 | 0.97 |
| 32_L | 37_I | 1.151 | 0.97 |
| 100_R | 104_A | 1.133 | 0.97 |
| 128_G | 131_S | 1.129 | 0.97 |
| 23_Y | 39_G | 1.121 | 0.97 |
| 15_R | 47_F | 1.117 | 0.96 |
| 153_V | 156_T | 1.113 | 0.96 |
| 48_S | 157_F | 1.112 | 0.96 |
| 41_A | 161_C | 1.112 | 0.96 |
| 126_G | 129_T | 1.112 | 0.96 |
| 94_N | 102_N | 1.110 | 0.96 |
| 54_T | 58_H | 1.104 | 0.96 |
| 103_I | 162_V | 1.098 | 0.96 |
| 105_R | 123_L | 1.091 | 0.96 |
| 165_V | 168_L | 1.089 | 0.96 |
| 82_R | 114_F | 1.082 | 0.96 |
| 65_T | 68_N | 1.070 | 0.95 |
| 33_G | 37_I | 1.058 | 0.95 |
| 45_T | 80_L | 1.058 | 0.95 |
| 101_E | 104_A | 1.055 | 0.95 |
| 42_G | 83_A | 1.055 | 0.95 |
| 117_D | 146_S | 1.046 | 0.94 |
| 7_D | 10_I | 1.034 | 0.94 |
| 52_F | 152_F | 1.032 | 0.94 |
| 114_F | 121_E | 1.032 | 0.94 |
| 23_Y | 27_Q | 1.029 | 0.94 |
| 20_L | 24_F | 1.021 | 0.93 |
| 86_L | 106_G | 1.016 | 0.93 |
| 81_S | 85_T | 1.016 | 0.93 |
| 103_I | 163_S | 1.016 | 0.93 |
| 74_F | 139_M | 1.015 | 0.93 |
| 116_L | 120_V | 1.012 | 0.93 |
| 107_M | 159_P | 1.009 | 0.93 |
| 28_N | 38_L | 1.006 | 0.93 |
| 89_F | 109_I | 1.005 | 0.93 |
| 164_L | 167_E | 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
- 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 | |
| 3w9iA | 6 | 0.9602 | 99.8 | 0.368 | Contact Map |
| 4mt1A | 1 | 0.8977 | 99.8 | 0.369 | Contact Map |
| 4k0jA | 6 | 0.8409 | 99.8 | 0.37 | Contact Map |
| 3aqpA | 2 | 0.9545 | 99.8 | 0.379 | Contact Map |
| 3ne5A | 1 | 0.8977 | 99.8 | 0.379 | Contact Map |
| 4dx5A | 3 | 0.9602 | 99.8 | 0.38 | Contact Map |
| 3w4tA | 1 | 0.4943 | 4.2 | 0.933 | Contact Map |
| 2kluA | 1 | 0.2443 | 2.8 | 0.939 | Contact Map |
| 4xnjA | 1 | 0 | 2.7 | 0.939 | Contact Map |
| 4ikvA | 1 | 0.8864 | 2.3 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)