| HD1 |
| ID: | 1495544903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 195 (186) | ||
| Sequences: | 805 (683.9) | ||
| Seq/Len: | 4.328 | ||
| Nf(neff/√len): | 50.1 |
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: 4.328).
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 |
| 21_C | 31_C | 4.414 | 1.00 |
| 81_E | 84_K | 3.729 | 1.00 |
| 51_V | 54_S | 3.169 | 1.00 |
| 37_M | 59_F | 3.127 | 1.00 |
| 18_D | 35_Q | 2.969 | 1.00 |
| 40_A | 55_L | 2.753 | 1.00 |
| 60_G | 73_N | 2.736 | 1.00 |
| 83_I | 91_I | 2.718 | 1.00 |
| 62_S | 73_N | 2.341 | 1.00 |
| 106_H | 110_D | 2.337 | 1.00 |
| 101_N | 110_D | 2.243 | 1.00 |
| 59_F | 82_I | 2.108 | 1.00 |
| 140_T | 153_A | 2.093 | 1.00 |
| 133_N | 138_L | 2.087 | 1.00 |
| 36_R | 58_I | 2.000 | 1.00 |
| 152_L | 172_I | 1.937 | 1.00 |
| 132_S | 135_G | 1.930 | 1.00 |
| 34_A | 90_S | 1.804 | 1.00 |
| 131_M | 136_L | 1.698 | 0.99 |
| 33_V | 82_I | 1.683 | 0.99 |
| 129_F | 133_N | 1.609 | 0.99 |
| 63_M | 66_L | 1.606 | 0.99 |
| 11_I | 17_I | 1.588 | 0.99 |
| 80_E | 84_K | 1.562 | 0.99 |
| 92_L | 136_L | 1.555 | 0.98 |
| 16_G | 42_R | 1.528 | 0.98 |
| 62_S | 66_L | 1.518 | 0.98 |
| 10_L | 14_I | 1.485 | 0.98 |
| 2_G | 7_L | 1.437 | 0.97 |
| 83_I | 129_F | 1.422 | 0.97 |
| 79_Q | 105_A | 1.395 | 0.96 |
| 64_P | 81_E | 1.394 | 0.96 |
| 69_E | 77_R | 1.389 | 0.96 |
| 90_S | 117_V | 1.389 | 0.96 |
| 86_S | 133_N | 1.386 | 0.96 |
| 93_A | 157_C | 1.373 | 0.96 |
| 61_I | 81_E | 1.346 | 0.95 |
| 142_L | 151_V | 1.344 | 0.95 |
| 116_G | 159_E | 1.336 | 0.95 |
| 33_V | 86_S | 1.325 | 0.95 |
| 32_S | 117_V | 1.325 | 0.95 |
| 178_L | 185_M | 1.316 | 0.95 |
| 116_G | 160_L | 1.303 | 0.94 |
| 9_V | 19_E | 1.302 | 0.94 |
| 48_E | 72_Q | 1.299 | 0.94 |
| 87_D | 128_P | 1.258 | 0.93 |
| 28_V | 31_C | 1.257 | 0.93 |
| 51_V | 109_S | 1.256 | 0.93 |
| 72_Q | 106_H | 1.255 | 0.93 |
| 92_L | 129_F | 1.255 | 0.93 |
| 28_V | 80_E | 1.235 | 0.92 |
| 34_A | 117_V | 1.223 | 0.91 |
| 89_Q | 153_A | 1.201 | 0.90 |
| 61_I | 157_C | 1.194 | 0.90 |
| 56_L | 65_L | 1.178 | 0.89 |
| 79_Q | 88_D | 1.167 | 0.88 |
| 129_F | 138_L | 1.165 | 0.88 |
| 4_K | 14_I | 1.146 | 0.87 |
| 4_K | 21_C | 1.144 | 0.87 |
| 174_C | 177_L | 1.132 | 0.86 |
| 37_M | 108_P | 1.130 | 0.86 |
| 45_T | 54_S | 1.126 | 0.86 |
| 1_M | 89_Q | 1.121 | 0.86 |
| 92_L | 103_L | 1.119 | 0.85 |
| 56_L | 61_I | 1.115 | 0.85 |
| 63_M | 69_E | 1.114 | 0.85 |
| 1_M | 153_A | 1.104 | 0.84 |
| 89_Q | 140_T | 1.104 | 0.84 |
| 38_S | 90_S | 1.103 | 0.84 |
| 42_R | 112_A | 1.099 | 0.84 |
| 32_S | 89_Q | 1.088 | 0.83 |
| 28_V | 36_R | 1.087 | 0.83 |
| 128_P | 137_S | 1.086 | 0.83 |
| 40_A | 157_C | 1.049 | 0.80 |
| 22_L | 58_I | 1.040 | 0.79 |
| 4_K | 22_L | 1.039 | 0.79 |
| 3_T | 7_L | 1.037 | 0.79 |
| 128_P | 132_S | 1.034 | 0.79 |
| 87_D | 134_A | 1.032 | 0.78 |
| 87_D | 103_L | 1.026 | 0.78 |
| 142_L | 184_F | 1.008 | 0.76 |
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 | |
| 4klzA | 1 | 0.3795 | 5.7 | 0.965 | Contact Map |
| 2a5jA | 1 | 0.4103 | 5.7 | 0.965 | Contact Map |
| 3bc1A | 2 | 0.4 | 4.7 | 0.966 | Contact Map |
| 2bmeA | 4 | 0.4051 | 3.9 | 0.968 | Contact Map |
| 1x6iA | 2 | 0.4564 | 3.9 | 0.968 | Contact Map |
| 3ihwA | 1 | 0.3846 | 3.7 | 0.968 | Contact Map |
| 3dvoA | 4 | 0.3282 | 3.7 | 0.968 | Contact Map |
| 1m7bA | 1 | 0.3436 | 3.4 | 0.969 | Contact Map |
| 1gwnA | 2 | 0.3436 | 3.3 | 0.969 | Contact Map |
| 2gcoA | 1 | 0.4205 | 3.3 | 0.969 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)