| cd81H |
| ID: | 1446732248 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 236 (227) | ||
| Sequences: | 4887 (3401.5) | ||
| Seq/Len: | 21.529 | ||
| Nf(neff/√len): | 225.8 |
Jackhmmer Results: (2015_08)
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: 21.529).
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 |
| 207_I | 211_V | 4.358 | 1.00 |
| 105_E | 216_M | 3.670 | 1.00 |
| 188_E | 193_K | 3.112 | 1.00 |
| 63_Y | 67_A | 2.928 | 1.00 |
| 107_A | 111_W | 2.834 | 1.00 |
| 33_L | 37_H | 2.796 | 1.00 |
| 32_A | 62_I | 2.613 | 1.00 |
| 30_G | 34_W | 2.509 | 1.00 |
| 11_K | 86_E | 2.457 | 1.00 |
| 89_C | 93_T | 2.334 | 1.00 |
| 26_G | 30_G | 2.322 | 1.00 |
| 113_F | 206_G | 2.315 | 1.00 |
| 95_F | 220_M | 2.191 | 1.00 |
| 151_H | 165_L | 2.186 | 1.00 |
| 148_K | 151_H | 2.175 | 1.00 |
| 110_I | 114_V | 1.957 | 1.00 |
| 18_N | 94_F | 1.932 | 1.00 |
| 32_A | 69_G | 1.909 | 1.00 |
| 224_M | 228_C | 1.825 | 1.00 |
| 25_G | 69_G | 1.816 | 1.00 |
| 29_L | 33_L | 1.809 | 1.00 |
| 79_G | 94_F | 1.781 | 1.00 |
| 135_V | 144_K | 1.729 | 1.00 |
| 25_G | 72_M | 1.684 | 1.00 |
| 154_L | 157_C | 1.683 | 1.00 |
| 92_G | 227_C | 1.645 | 1.00 |
| 92_G | 96_T | 1.618 | 1.00 |
| 9_C | 13_L | 1.613 | 1.00 |
| 171_K | 174_L | 1.593 | 1.00 |
| 147_V | 151_H | 1.584 | 1.00 |
| 150_F | 156_C | 1.580 | 1.00 |
| 22_W | 76_G | 1.558 | 1.00 |
| 23_L | 27_V | 1.534 | 1.00 |
| 12_Y | 15_F | 1.522 | 1.00 |
| 191_H | 195_D | 1.470 | 1.00 |
| 147_V | 159_S | 1.466 | 1.00 |
| 151_H | 158_G | 1.456 | 1.00 |
| 203_Y | 207_I | 1.446 | 1.00 |
| 155_D | 186_F | 1.422 | 1.00 |
| 206_G | 210_I | 1.416 | 1.00 |
| 124_K | 160_S | 1.411 | 1.00 |
| 34_W | 38_D | 1.377 | 0.99 |
| 113_F | 210_I | 1.375 | 0.99 |
| 127_Y | 130_A | 1.369 | 0.99 |
| 148_K | 173_N | 1.358 | 0.99 |
| 127_Y | 159_S | 1.308 | 0.99 |
| 79_G | 82_G | 1.301 | 0.99 |
| 25_G | 76_G | 1.299 | 0.99 |
| 82_G | 91_L | 1.298 | 0.99 |
| 109_G | 213_A | 1.295 | 0.99 |
| 134_A | 148_K | 1.287 | 0.99 |
| 151_H | 173_N | 1.275 | 0.99 |
| 66_I | 70_A | 1.263 | 0.99 |
| 6_C | 9_C | 1.260 | 0.99 |
| 95_F | 99_V | 1.249 | 0.99 |
| 159_S | 191_H | 1.242 | 0.98 |
| 180_N | 183_S | 1.232 | 0.98 |
| 131_L | 159_S | 1.230 | 0.98 |
| 111_W | 115_N | 1.219 | 0.98 |
| 178_G | 183_S | 1.217 | 0.98 |
| 165_L | 171_K | 1.209 | 0.98 |
| 17_F | 219_E | 1.193 | 0.98 |
| 32_A | 66_I | 1.191 | 0.98 |
| 164_A | 171_K | 1.188 | 0.98 |
| 130_A | 134_A | 1.186 | 0.98 |
| 95_F | 224_M | 1.178 | 0.98 |
| 77_F | 81_Y | 1.168 | 0.97 |
| 151_H | 156_C | 1.167 | 0.97 |
| 98_L | 105_E | 1.163 | 0.97 |
| 88_Q | 92_G | 1.161 | 0.97 |
| 22_W | 73_M | 1.160 | 0.97 |
| 153_T | 156_C | 1.149 | 0.97 |
| 88_Q | 231_R | 1.146 | 0.97 |
| 129_Q | 133_Q | 1.138 | 0.97 |
| 221_I | 225_V | 1.135 | 0.97 |
| 162_L | 189_D | 1.130 | 0.97 |
| 170_L | 175_C | 1.128 | 0.97 |
| 210_I | 214_V | 1.116 | 0.96 |
| 29_L | 69_G | 1.110 | 0.96 |
| 82_G | 90_L | 1.107 | 0.96 |
| 151_H | 157_C | 1.107 | 0.96 |
| 78_L | 90_L | 1.101 | 0.96 |
| 95_F | 227_C | 1.098 | 0.96 |
| 179_S | 183_S | 1.087 | 0.96 |
| 83_A | 91_L | 1.084 | 0.96 |
| 108_A | 112_G | 1.082 | 0.96 |
| 134_A | 137_D | 1.080 | 0.95 |
| 164_A | 189_D | 1.077 | 0.95 |
| 155_D | 158_G | 1.074 | 0.95 |
| 154_L | 158_G | 1.074 | 0.95 |
| 136_V | 144_K | 1.074 | 0.95 |
| 99_V | 220_M | 1.073 | 0.95 |
| 224_M | 227_C | 1.069 | 0.95 |
| 148_K | 171_K | 1.062 | 0.95 |
| 143_A | 149_T | 1.042 | 0.94 |
| 81_Y | 90_L | 1.042 | 0.94 |
| 95_F | 223_S | 1.042 | 0.94 |
| 219_E | 223_S | 1.031 | 0.94 |
| 131_L | 147_V | 1.028 | 0.94 |
| 25_G | 73_M | 1.020 | 0.93 |
| 127_Y | 147_V | 1.016 | 0.93 |
| 156_C | 159_S | 1.015 | 0.93 |
| 14_L | 98_L | 1.014 | 0.93 |
| 149_T | 153_T | 1.008 | 0.93 |
| 156_C | 171_K | 1.005 | 0.93 |
| 204_L | 208_A | 1.004 | 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 | |
| 3x0fA | 2 | 0 | 99.2 | 0.635 | Contact Map |
| 2m7zA | 1 | 0.3432 | 99.2 | 0.645 | Contact Map |
| 2ks1B | 1 | 0.1864 | 48.5 | 0.9 | Contact Map |
| 2jwaA | 2 | 0.1864 | 29.8 | 0.911 | Contact Map |
| 2kluA | 1 | 0.1737 | 20.2 | 0.918 | Contact Map |
| 2l2tA | 2 | 0.1822 | 14.7 | 0.923 | Contact Map |
| 2m20A | 2 | 0.1525 | 12.5 | 0.925 | Contact Map |
| 4h33A | 1 | 0.3814 | 12.2 | 0.925 | Contact Map |
| 4l6rA | 1 | 0.4831 | 6.8 | 0.934 | Contact Map |
| 4or2A | 2 | 0.4831 | 6.2 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)