| YidC |
| ID: | 1380096497 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (198) | ||
| Sequences: | 2212 (1571.1) | ||
| Seq/Len: | 11.172 | ||
| Nf(neff/√len): | 111.7 |
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: 11.172).
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 |
| 69_A | 73_A | 4.124 | 1.00 |
| 66_E | 69_A | 4.043 | 1.00 |
| 48_K | 51_A | 3.906 | 1.00 |
| 50_Q | 53_R | 3.790 | 1.00 |
| 131_G | 162_T | 3.780 | 1.00 |
| 52_M | 63_I | 3.128 | 1.00 |
| 46_Q | 50_Q | 3.015 | 1.00 |
| 50_Q | 54_E | 2.887 | 1.00 |
| 62_R | 66_E | 2.608 | 1.00 |
| 133_T | 180_N | 2.549 | 1.00 |
| 1_K | 5_W | 2.354 | 1.00 |
| 45_L | 76_V | 2.334 | 1.00 |
| 96_Y | 100_M | 2.276 | 1.00 |
| 129_L | 177_I | 2.226 | 1.00 |
| 10_V | 19_I | 2.210 | 1.00 |
| 62_R | 65_Q | 2.149 | 1.00 |
| 18_I | 178_V | 2.037 | 1.00 |
| 53_R | 57_G | 2.010 | 1.00 |
| 48_K | 73_A | 1.978 | 1.00 |
| 61_Q | 65_Q | 1.925 | 1.00 |
| 113_W | 121_D | 1.913 | 1.00 |
| 33_K | 37_T | 1.782 | 1.00 |
| 89_M | 93_L | 1.772 | 1.00 |
| 51_A | 55_R | 1.750 | 1.00 |
| 160_I | 164_F | 1.745 | 1.00 |
| 26_G | 182_V | 1.730 | 1.00 |
| 185_I | 189_L | 1.721 | 1.00 |
| 6_I | 19_I | 1.717 | 1.00 |
| 93_L | 97_Y | 1.668 | 1.00 |
| 63_I | 67_M | 1.666 | 1.00 |
| 52_M | 70_L | 1.650 | 1.00 |
| 53_R | 63_I | 1.594 | 1.00 |
| 29_Y | 33_K | 1.589 | 1.00 |
| 97_Y | 101_G | 1.586 | 1.00 |
| 124_Y | 127_P | 1.578 | 1.00 |
| 41_K | 44_M | 1.560 | 1.00 |
| 15_F | 18_I | 1.545 | 1.00 |
| 49_I | 67_M | 1.524 | 1.00 |
| 48_K | 74_E | 1.478 | 1.00 |
| 45_L | 70_L | 1.471 | 1.00 |
| 59_D | 62_R | 1.471 | 1.00 |
| 65_Q | 69_A | 1.456 | 1.00 |
| 28_M | 91_I | 1.391 | 0.99 |
| 55_R | 66_E | 1.388 | 0.99 |
| 15_F | 110_F | 1.353 | 0.99 |
| 5_W | 9_F | 1.332 | 0.99 |
| 40_A | 43_R | 1.312 | 0.99 |
| 117_L | 121_D | 1.305 | 0.99 |
| 139_K | 155_T | 1.305 | 0.99 |
| 181_L | 185_I | 1.304 | 0.99 |
| 37_T | 41_K | 1.299 | 0.99 |
| 7_H | 13_W | 1.284 | 0.99 |
| 15_F | 19_I | 1.282 | 0.99 |
| 6_I | 23_I | 1.256 | 0.99 |
| 67_M | 71_Y | 1.255 | 0.99 |
| 6_I | 10_V | 1.254 | 0.99 |
| 97_Y | 100_M | 1.248 | 0.99 |
| 86_L | 90_P | 1.232 | 0.98 |
| 132_V | 136_F | 1.231 | 0.98 |
| 163_V | 167_W | 1.204 | 0.98 |
| 165_F | 173_V | 1.200 | 0.98 |
| 17_I | 171_G | 1.197 | 0.98 |
| 121_D | 124_Y | 1.195 | 0.98 |
| 60_K | 64_S | 1.195 | 0.98 |
| 137_I | 183_T | 1.194 | 0.98 |
| 157_M | 160_I | 1.177 | 0.98 |
| 89_M | 92_F | 1.172 | 0.98 |
| 176_Y | 180_N | 1.166 | 0.97 |
| 6_I | 20_I | 1.164 | 0.97 |
| 137_I | 184_I | 1.163 | 0.97 |
| 147_D | 150_Q | 1.159 | 0.97 |
| 20_I | 95_L | 1.157 | 0.97 |
| 152_K | 155_T | 1.153 | 0.97 |
| 116_D | 119_A | 1.129 | 0.97 |
| 3_L | 16_S | 1.124 | 0.97 |
| 128_I | 132_V | 1.111 | 0.96 |
| 23_I | 27_I | 1.092 | 0.96 |
| 51_A | 54_E | 1.092 | 0.96 |
| 180_N | 183_T | 1.091 | 0.96 |
| 85_L | 89_M | 1.090 | 0.96 |
| 92_F | 183_T | 1.087 | 0.96 |
| 156_F | 160_I | 1.083 | 0.96 |
| 57_G | 60_K | 1.071 | 0.95 |
| 28_M | 88_Q | 1.070 | 0.95 |
| 69_A | 72_K | 1.070 | 0.95 |
| 179_S | 183_T | 1.070 | 0.95 |
| 4_K | 8_S | 1.063 | 0.95 |
| 64_S | 68_M | 1.063 | 0.95 |
| 2_L | 23_I | 1.056 | 0.95 |
| 25_R | 28_M | 1.055 | 0.95 |
| 60_K | 63_I | 1.044 | 0.94 |
| 64_S | 67_M | 1.044 | 0.94 |
| 126_L | 174_L | 1.041 | 0.94 |
| 135_F | 139_K | 1.033 | 0.94 |
| 30_P | 34_A | 1.021 | 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 | |
| 3rvyA | 2 | 0.1739 | 15.2 | 0.952 | Contact Map |
| 4hkrA | 2 | 0.3092 | 8.5 | 0.957 | Contact Map |
| 4h33A | 1 | 0.1787 | 6.2 | 0.96 | Contact Map |
| 4bgnA | 2 | 0.1932 | 6.1 | 0.96 | Contact Map |
| 4ltoA | 4 | 0.3575 | 4.4 | 0.963 | Contact Map |
| 2ywxA | 1 | 0.3237 | 3.8 | 0.963 | Contact Map |
| 3effK | 4 | 0.3671 | 3.8 | 0.964 | Contact Map |
| 2y65A | 4 | 0.3237 | 3.8 | 0.964 | Contact Map |
| 3vouA | 2 | 0.3285 | 3.7 | 0.964 | Contact Map |
| 4n7bA | 1 | 0 | 3.2 | 0.965 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)