| 1CVJ |
| ID: | 1381530274 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (173) | ||
| Sequences: | 8253 (5588) | ||
| Seq/Len: | 47.705 | ||
| Nf(neff/√len): | 424.8 |
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: 47.705).
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 |
| 36_P | 60_Q | 3.007 | 1.00 |
| 147_T | 150_A | 2.989 | 1.00 |
| 61_Q | 64_D | 2.758 | 1.00 |
| 124_N | 146_E | 2.697 | 1.00 |
| 26_M | 78_K | 2.309 | 1.00 |
| 111_D | 114_A | 2.230 | 1.00 |
| 67_R | 71_T | 2.177 | 1.00 |
| 20_P | 80_K | 2.163 | 1.00 |
| 34_A | 71_T | 2.108 | 1.00 |
| 13_L | 69_L | 1.996 | 1.00 |
| 122_F | 157_K | 1.959 | 1.00 |
| 23_T | 26_M | 1.954 | 1.00 |
| 101_I | 155_I | 1.940 | 1.00 |
| 153_R | 157_K | 1.892 | 1.00 |
| 114_A | 164_N | 1.863 | 1.00 |
| 115_L | 141_G | 1.839 | 1.00 |
| 27_L | 55_A | 1.778 | 1.00 |
| 116_Y | 120_S | 1.773 | 1.00 |
| 126_L | 146_E | 1.755 | 1.00 |
| 15_V | 31_F | 1.710 | 1.00 |
| 162_L | 165_D | 1.699 | 1.00 |
| 28_Y | 32_S | 1.668 | 1.00 |
| 108_K | 166_R | 1.663 | 1.00 |
| 76_V | 81_P | 1.650 | 1.00 |
| 67_R | 70_D | 1.649 | 1.00 |
| 146_E | 150_A | 1.635 | 1.00 |
| 77_I | 82_V | 1.634 | 1.00 |
| 38_L | 60_Q | 1.629 | 1.00 |
| 112_N | 116_Y | 1.596 | 1.00 |
| 60_Q | 64_D | 1.578 | 1.00 |
| 66_E | 86_W | 1.553 | 1.00 |
| 131_V | 140_Y | 1.529 | 1.00 |
| 16_G | 83_R | 1.502 | 1.00 |
| 31_F | 57_V | 1.498 | 1.00 |
| 103_I | 119_F | 1.481 | 1.00 |
| 148_Q | 152_E | 1.466 | 1.00 |
| 62_P | 66_E | 1.454 | 1.00 |
| 24_E | 28_Y | 1.450 | 1.00 |
| 25_A | 29_E | 1.434 | 1.00 |
| 104_K | 169_F | 1.433 | 1.00 |
| 119_F | 143_V | 1.421 | 1.00 |
| 21_D | 78_K | 1.401 | 0.99 |
| 29_E | 32_S | 1.391 | 0.99 |
| 152_E | 156_E | 1.380 | 0.99 |
| 152_E | 172_R | 1.358 | 0.99 |
| 153_R | 156_E | 1.358 | 0.99 |
| 118_T | 161_M | 1.348 | 0.99 |
| 65_A | 86_W | 1.344 | 0.99 |
| 128_C | 141_G | 1.337 | 0.99 |
| 16_G | 54_Y | 1.299 | 0.99 |
| 125_I | 143_V | 1.287 | 0.99 |
| 76_V | 79_G | 1.286 | 0.99 |
| 43_C | 54_Y | 1.284 | 0.99 |
| 162_L | 167_K | 1.284 | 0.99 |
| 107_D | 110_I | 1.278 | 0.99 |
| 40_I | 55_A | 1.269 | 0.99 |
| 34_A | 72_M | 1.268 | 0.99 |
| 36_P | 64_D | 1.263 | 0.99 |
| 126_L | 144_H | 1.262 | 0.99 |
| 38_L | 58_N | 1.253 | 0.99 |
| 30_K | 75_D | 1.251 | 0.99 |
| 42_V | 51_S | 1.245 | 0.98 |
| 63_A | 67_R | 1.241 | 0.98 |
| 113_K | 117_D | 1.219 | 0.98 |
| 66_E | 70_D | 1.213 | 0.98 |
| 45_D | 48_T | 1.209 | 0.98 |
| 16_G | 104_K | 1.207 | 0.98 |
| 163_L | 168_V | 1.207 | 0.98 |
| 117_D | 120_S | 1.206 | 0.98 |
| 11_A | 38_L | 1.204 | 0.98 |
| 124_N | 150_A | 1.183 | 0.98 |
| 118_T | 158_M | 1.174 | 0.98 |
| 62_P | 86_W | 1.168 | 0.97 |
| 151_A | 172_R | 1.156 | 0.97 |
| 145_F | 154_A | 1.154 | 0.97 |
| 11_A | 65_A | 1.141 | 0.97 |
| 158_M | 161_M | 1.132 | 0.97 |
| 24_E | 44_R | 1.119 | 0.96 |
| 112_N | 130_V | 1.098 | 0.96 |
| 114_A | 117_D | 1.091 | 0.96 |
| 130_V | 137_S | 1.080 | 0.95 |
| 104_K | 140_Y | 1.076 | 0.95 |
| 26_M | 29_E | 1.058 | 0.95 |
| 59_F | 68_A | 1.058 | 0.95 |
| 30_K | 77_I | 1.051 | 0.94 |
| 100_N | 144_H | 1.050 | 0.94 |
| 131_V | 142_F | 1.041 | 0.94 |
| 30_K | 82_V | 1.038 | 0.94 |
| 42_V | 55_A | 1.033 | 0.94 |
| 99_G | 144_H | 1.025 | 0.93 |
| 30_K | 33_P | 1.023 | 0.93 |
| 74_F | 81_P | 1.021 | 0.93 |
| 103_I | 143_V | 1.018 | 0.93 |
| 102_F | 142_F | 1.016 | 0.93 |
| 85_M | 88_Q | 1.013 | 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 | |
| 4f02A | 2 | 0.9211 | 100 | 0.185 | Contact Map |
| 2qfjA | 2 | 0.9632 | 100 | 0.269 | Contact Map |
| 1l3kA | 1 | 0.8474 | 100 | 0.29 | Contact Map |
| 3md3A | 1 | 0.8579 | 100 | 0.293 | Contact Map |
| 1b7fA | 2 | 0.8579 | 100 | 0.298 | Contact Map |
| 3nmrA | 1 | 0.8737 | 100 | 0.299 | Contact Map |
| 3smzA | 1 | 0.9947 | 100 | 0.3 | Contact Map |
| 1fxlA | 1 | 0.8579 | 100 | 0.302 | Contact Map |
| 4bs2A | 1 | 0.9105 | 100 | 0.303 | Contact Map |
| 2cjkA | 1 | 0.8684 | 100 | 0.308 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)