| 1E4CP |
| ID: | 1411760827 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (203) | ||
| Sequences: | 3188 (2068) | ||
| Seq/Len: | 15.704 | ||
| Nf(neff/√len): | 145.1 |
HHblits Results: (2013_03)
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: 15.704).
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 |
| 59_D | 63_K | 5.309 | 1.00 |
| 97_H | 183_T | 3.341 | 1.00 |
| 179_Q | 183_T | 2.984 | 1.00 |
| 162_V | 166_K | 2.876 | 1.00 |
| 38_M | 78_M | 2.741 | 1.00 |
| 39_L | 55_I | 2.682 | 1.00 |
| 9_Q | 165_E | 2.409 | 1.00 |
| 106_R | 185_L | 2.286 | 1.00 |
| 134_R | 138_E | 2.142 | 1.00 |
| 11_I | 52_E | 2.097 | 1.00 |
| 100_A | 183_T | 2.014 | 1.00 |
| 149_A | 174_V | 2.013 | 1.00 |
| 6_L | 32_V | 2.004 | 1.00 |
| 87_A | 160_C | 1.950 | 1.00 |
| 97_H | 179_Q | 1.930 | 1.00 |
| 39_L | 57_F | 1.886 | 1.00 |
| 8_R | 12_D | 1.854 | 1.00 |
| 97_H | 182_L | 1.845 | 1.00 |
| 163_N | 166_K | 1.823 | 1.00 |
| 195_S | 198_E | 1.758 | 1.00 |
| 88_N | 163_N | 1.755 | 1.00 |
| 96_V | 179_Q | 1.722 | 1.00 |
| 157_L | 174_V | 1.695 | 1.00 |
| 51_T | 54_H | 1.695 | 1.00 |
| 89_A | 164_L | 1.687 | 1.00 |
| 91_V | 167_A | 1.666 | 1.00 |
| 92_H | 155_H | 1.659 | 1.00 |
| 94_H | 155_H | 1.636 | 1.00 |
| 11_I | 15_L | 1.622 | 1.00 |
| 79_A | 138_E | 1.607 | 1.00 |
| 34_Y | 39_L | 1.586 | 1.00 |
| 79_A | 83_S | 1.582 | 1.00 |
| 37_G | 57_F | 1.580 | 1.00 |
| 32_V | 164_L | 1.576 | 1.00 |
| 8_R | 52_E | 1.572 | 1.00 |
| 107_S | 122_S | 1.562 | 1.00 |
| 20_L | 172_H | 1.540 | 1.00 |
| 161_E | 166_K | 1.525 | 1.00 |
| 10_I | 55_I | 1.491 | 1.00 |
| 10_I | 30_V | 1.441 | 1.00 |
| 79_A | 82_Q | 1.412 | 1.00 |
| 61_N | 82_Q | 1.408 | 1.00 |
| 159_A | 171_A | 1.400 | 0.99 |
| 93_N | 171_A | 1.395 | 0.99 |
| 104_L | 187_I | 1.350 | 0.99 |
| 183_T | 186_A | 1.349 | 0.99 |
| 127_P | 142_L | 1.347 | 0.99 |
| 40_I | 71_Q | 1.346 | 0.99 |
| 32_V | 89_A | 1.335 | 0.99 |
| 197_E | 201_V | 1.325 | 0.99 |
| 105_N | 153_Q | 1.324 | 0.99 |
| 54_H | 68_K | 1.322 | 0.99 |
| 108_I | 178_A | 1.319 | 0.99 |
| 101_V | 185_L | 1.314 | 0.99 |
| 76_F | 158_I | 1.314 | 0.99 |
| 15_L | 19_R | 1.304 | 0.99 |
| 181_Y | 185_L | 1.277 | 0.99 |
| 157_L | 171_A | 1.275 | 0.99 |
| 182_L | 186_A | 1.275 | 0.99 |
| 96_V | 100_A | 1.274 | 0.99 |
| 58_I | 74_W | 1.261 | 0.99 |
| 124_P | 147_R | 1.254 | 0.99 |
| 83_S | 141_A | 1.247 | 0.99 |
| 95_A | 98_C | 1.235 | 0.98 |
| 38_M | 60_G | 1.229 | 0.98 |
| 149_A | 159_A | 1.227 | 0.98 |
| 152_L | 158_I | 1.204 | 0.98 |
| 107_S | 125_C | 1.201 | 0.98 |
| 98_C | 157_L | 1.193 | 0.98 |
| 13_T | 168_L | 1.191 | 0.98 |
| 196_D | 200_A | 1.189 | 0.98 |
| 34_Y | 57_F | 1.188 | 0.98 |
| 161_E | 170_L | 1.180 | 0.98 |
| 144_L | 160_C | 1.160 | 0.97 |
| 5_K | 9_Q | 1.158 | 0.97 |
| 16_E | 20_L | 1.152 | 0.97 |
| 84_R | 87_A | 1.152 | 0.97 |
| 139_H | 142_L | 1.128 | 0.97 |
| 43_T | 71_Q | 1.128 | 0.97 |
| 73_E | 136_L | 1.117 | 0.96 |
| 78_M | 82_Q | 1.113 | 0.96 |
| 45_I | 68_K | 1.111 | 0.96 |
| 129_A | 139_H | 1.111 | 0.96 |
| 45_I | 54_H | 1.105 | 0.96 |
| 100_A | 182_L | 1.091 | 0.96 |
| 83_S | 145_K | 1.085 | 0.96 |
| 175_E | 179_Q | 1.084 | 0.96 |
| 80_A | 87_A | 1.077 | 0.95 |
| 42_P | 45_I | 1.076 | 0.95 |
| 76_F | 140_V | 1.075 | 0.95 |
| 80_A | 144_L | 1.074 | 0.95 |
| 99_T | 102_S | 1.074 | 0.95 |
| 148_K | 170_L | 1.070 | 0.95 |
| 42_P | 55_I | 1.063 | 0.95 |
| 17_M | 168_L | 1.058 | 0.95 |
| 113_Y | 116_A | 1.053 | 0.95 |
| 14_C | 30_V | 1.045 | 0.94 |
| 142_L | 145_K | 1.041 | 0.94 |
| 12_D | 49_K | 1.039 | 0.94 |
| 109_P | 181_Y | 1.037 | 0.94 |
| 11_I | 55_I | 1.029 | 0.94 |
| 13_T | 164_L | 1.027 | 0.94 |
| 29_N | 71_Q | 1.020 | 0.93 |
| 140_V | 152_L | 1.019 | 0.93 |
| 81_Y | 90_V | 1.017 | 0.93 |
| 38_M | 74_W | 1.014 | 0.93 |
| 182_L | 187_I | 1.007 | 0.93 |
| 193_V | 196_D | 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 | |
| 1e4cP | 1 | 1 | 100 | 0.035 | Contact Map |
| 4c24A | 1 | 0.9903 | 100 | 0.07 | Contact Map |
| 2opiA | 2 | 0.9806 | 100 | 0.099 | Contact Map |
| 3ocrA | 2 | 0.9903 | 100 | 0.117 | Contact Map |
| 2z7bA | 1 | 0.9806 | 100 | 0.118 | Contact Map |
| 1k0wA | 6 | 0.9903 | 100 | 0.12 | Contact Map |
| 2v9lA | 1 | 0.9903 | 100 | 0.127 | Contact Map |
| 2fk5A | 2 | 0.9126 | 100 | 0.136 | Contact Map |
| 4m6rA | 4 | 0.9709 | 100 | 0.138 | Contact Map |
| 1pvtA | 1 | 0.9175 | 100 | 0.156 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)