| 1CDH |
| ID: | 1515662558 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 178 (173) | ||
| Sequences: | 20880 (14305.8) | ||
| Seq/Len: | 120.694 | ||
| Nf(neff/√len): | 1087.6 |
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: 120.694).
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 |
| 131_R | 160_T | 3.693 | 1.00 |
| 29_K | 85_E | 3.047 | 1.00 |
| 6_G | 74_L | 2.898 | 1.00 |
| 13_E | 70_I | 2.603 | 1.00 |
| 81_T | 94_Q | 2.532 | 1.00 |
| 7_K | 10_D | 2.483 | 1.00 |
| 11_T | 70_I | 2.397 | 1.00 |
| 156_T | 171_K | 2.348 | 1.00 |
| 158_T | 169_E | 2.344 | 1.00 |
| 81_T | 92_E | 2.335 | 1.00 |
| 16_C | 84_C | 2.245 | 1.00 |
| 13_E | 68_P | 2.210 | 1.00 |
| 156_T | 173_D | 2.204 | 1.00 |
| 115_T | 145_S | 2.169 | 1.00 |
| 118_L | 159_C | 2.163 | 1.00 |
| 113_S | 147_S | 2.123 | 1.00 |
| 115_T | 143_T | 2.097 | 1.00 |
| 20_Q | 24_I | 2.079 | 1.00 |
| 109_L | 112_Q | 2.044 | 1.00 |
| 11_T | 72_K | 2.033 | 1.00 |
| 117_T | 143_T | 2.003 | 1.00 |
| 30_N | 80_D | 2.003 | 1.00 |
| 108_L | 149_L | 1.980 | 1.00 |
| 129_Q | 160_T | 1.955 | 1.00 |
| 131_R | 158_T | 1.947 | 1.00 |
| 160_T | 169_E | 1.909 | 1.00 |
| 129_Q | 162_L | 1.905 | 1.00 |
| 29_K | 83_I | 1.901 | 1.00 |
| 15_T | 68_P | 1.895 | 1.00 |
| 113_S | 145_S | 1.886 | 1.00 |
| 132_S | 155_G | 1.851 | 1.00 |
| 122_P | 126_P | 1.850 | 1.00 |
| 162_L | 167_K | 1.820 | 1.00 |
| 133_P | 137_N | 1.814 | 1.00 |
| 27_H | 85_E | 1.774 | 1.00 |
| 158_T | 171_K | 1.732 | 1.00 |
| 27_H | 87_E | 1.680 | 1.00 |
| 120_S | 161_V | 1.605 | 1.00 |
| 12_V | 95_L | 1.602 | 1.00 |
| 54_R | 78_D | 1.592 | 1.00 |
| 108_L | 114_L | 1.588 | 1.00 |
| 8_K | 76_I | 1.561 | 1.00 |
| 116_L | 174_I | 1.552 | 1.00 |
| 6_G | 12_V | 1.544 | 1.00 |
| 30_N | 82_Y | 1.539 | 1.00 |
| 114_L | 174_I | 1.528 | 1.00 |
| 83_I | 92_E | 1.524 | 1.00 |
| 127_S | 162_L | 1.489 | 1.00 |
| 31_S | 83_I | 1.485 | 1.00 |
| 131_R | 136_K | 1.483 | 1.00 |
| 120_S | 128_V | 1.476 | 1.00 |
| 31_S | 35_K | 1.458 | 1.00 |
| 133_P | 158_T | 1.439 | 1.00 |
| 5_L | 96_L | 1.437 | 1.00 |
| 56_D | 72_K | 1.405 | 0.99 |
| 132_S | 157_W | 1.386 | 0.99 |
| 18_A | 86_V | 1.344 | 0.99 |
| 11_T | 73_N | 1.324 | 0.99 |
| 129_Q | 136_K | 1.312 | 0.99 |
| 58_R | 70_I | 1.289 | 0.99 |
| 110_Q | 151_L | 1.283 | 0.99 |
| 114_L | 146_V | 1.282 | 0.99 |
| 18_A | 26_F | 1.278 | 0.99 |
| 107_H | 175_V | 1.265 | 0.99 |
| 113_S | 148_Q | 1.247 | 0.99 |
| 128_V | 142_K | 1.241 | 0.98 |
| 116_L | 172_I | 1.213 | 0.98 |
| 5_L | 98_F | 1.204 | 0.98 |
| 31_S | 81_T | 1.203 | 0.98 |
| 4_V | 12_V | 1.200 | 0.98 |
| 114_L | 149_L | 1.189 | 0.98 |
| 108_L | 112_Q | 1.150 | 0.97 |
| 160_T | 167_K | 1.139 | 0.97 |
| 7_K | 98_F | 1.132 | 0.97 |
| 27_H | 34_I | 1.119 | 0.96 |
| 154_S | 176_V | 1.103 | 0.96 |
| 28_W | 69_L | 1.087 | 0.96 |
| 55_A | 71_I | 1.084 | 0.96 |
| 15_T | 66_N | 1.077 | 0.95 |
| 79_S | 97_V | 1.070 | 0.95 |
| 132_S | 135_G | 1.064 | 0.95 |
| 56_D | 70_I | 1.060 | 0.95 |
| 12_V | 71_I | 1.054 | 0.95 |
| 6_G | 10_D | 1.048 | 0.94 |
| 122_P | 163_Q | 1.045 | 0.94 |
| 128_V | 161_V | 1.032 | 0.94 |
| 29_K | 34_I | 1.029 | 0.94 |
| 14_L | 95_L | 1.017 | 0.93 |
| 130_C | 144_L | 1.009 | 0.93 |
| 108_L | 174_I | 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 | |
| 1wioA | 2 | 1 | 99.9 | 0.028 | Contact Map |
| 4q6iC | 4 | 1 | 99.9 | 0.056 | Contact Map |
| 4h8wC | 1 | 0.9888 | 99.9 | 0.059 | Contact Map |
| 1qz1A | 1 | 0.8989 | 99.8 | 0.12 | Contact Map |
| 1cs6A | 1 | 0.8708 | 99.8 | 0.126 | Contact Map |
| 2rikA | 1 | 0.9045 | 99.8 | 0.129 | Contact Map |
| 3kldA | 1 | 0.882 | 99.8 | 0.13 | Contact Map |
| 3b43A | 1 | 0.9045 | 99.8 | 0.13 | Contact Map |
| 2v5mA | 1 | 0.9101 | 99.8 | 0.135 | Contact Map |
| 2v5tA | 1 | 0.8708 | 99.8 | 0.136 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)