| Nidovirus_Jackhmmer_E1-06 |
| ID: | 1496241703 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (135) | ||
| Sequences: | 4152 (3230.6) | ||
| Seq/Len: | 30.756 | ||
| Nf(neff/√len): | 278.0 |
Jackhmmer Results: (2016_04)
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: 30.756).
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 |
| 35_A | 38_S | 3.060 | 1.00 |
| 24_K | 27_V | 2.786 | 1.00 |
| 27_V | 30_K | 2.696 | 1.00 |
| 127_V | 130_F | 2.623 | 1.00 |
| 23_L | 27_V | 2.209 | 1.00 |
| 98_L | 101_P | 2.048 | 1.00 |
| 96_T | 99_D | 1.843 | 1.00 |
| 55_K | 59_A | 1.819 | 1.00 |
| 53_L | 77_C | 1.697 | 1.00 |
| 28_V | 32_L | 1.648 | 1.00 |
| 114_Q | 140_T | 1.614 | 1.00 |
| 130_F | 135_L | 1.591 | 1.00 |
| 112_L | 116_G | 1.559 | 1.00 |
| 76_D | 79_N | 1.556 | 1.00 |
| 27_V | 32_L | 1.554 | 1.00 |
| 53_L | 147_Y | 1.527 | 1.00 |
| 87_D | 90_F | 1.498 | 1.00 |
| 97_V | 101_P | 1.495 | 1.00 |
| 87_D | 91_V | 1.492 | 1.00 |
| 136_A | 140_T | 1.491 | 1.00 |
| 26_V | 29_N | 1.490 | 1.00 |
| 24_K | 28_V | 1.485 | 1.00 |
| 96_T | 101_P | 1.467 | 1.00 |
| 71_H | 74_M | 1.463 | 1.00 |
| 101_P | 104_G | 1.456 | 1.00 |
| 64_A | 121_E | 1.449 | 1.00 |
| 127_V | 146_G | 1.404 | 0.99 |
| 28_V | 31_A | 1.379 | 0.99 |
| 30_K | 34_N | 1.365 | 0.99 |
| 25_G | 28_V | 1.365 | 0.99 |
| 21_D | 24_K | 1.352 | 0.99 |
| 124_V | 138_I | 1.339 | 0.99 |
| 96_T | 100_F | 1.338 | 0.99 |
| 102_R | 105_S | 1.327 | 0.99 |
| 110_V | 113_P | 1.326 | 0.99 |
| 95_Y | 99_D | 1.309 | 0.99 |
| 29_N | 33_K | 1.275 | 0.99 |
| 42_E | 150_L | 1.265 | 0.99 |
| 95_Y | 98_L | 1.264 | 0.99 |
| 88_P | 91_V | 1.227 | 0.98 |
| 25_G | 29_N | 1.210 | 0.98 |
| 41_V | 145_K | 1.190 | 0.98 |
| 41_V | 147_Y | 1.187 | 0.98 |
| 122_T | 142_G | 1.180 | 0.98 |
| 23_L | 30_K | 1.178 | 0.98 |
| 88_P | 92_V | 1.172 | 0.98 |
| 27_V | 31_A | 1.160 | 0.97 |
| 97_V | 102_R | 1.144 | 0.97 |
| 41_V | 52_H | 1.136 | 0.97 |
| 112_L | 117_T | 1.136 | 0.97 |
| 94_K | 98_L | 1.134 | 0.97 |
| 135_L | 139_L | 1.131 | 0.97 |
| 29_N | 32_L | 1.122 | 0.97 |
| 72_A | 76_D | 1.119 | 0.96 |
| 20_Q | 23_L | 1.119 | 0.96 |
| 54_V | 57_V | 1.095 | 0.96 |
| 24_K | 32_L | 1.095 | 0.96 |
| 133_V | 137_R | 1.087 | 0.96 |
| 37_A | 143_R | 1.086 | 0.96 |
| 23_L | 26_V | 1.085 | 0.96 |
| 89_Y | 92_V | 1.079 | 0.95 |
| 90_F | 93_P | 1.070 | 0.95 |
| 20_Q | 24_K | 1.068 | 0.95 |
| 45_P | 151_N | 1.066 | 0.95 |
| 97_V | 100_F | 1.065 | 0.95 |
| 23_L | 31_A | 1.060 | 0.95 |
| 54_V | 58_L | 1.056 | 0.95 |
| 132_P | 135_L | 1.054 | 0.95 |
| 131_S | 134_D | 1.043 | 0.94 |
| 91_V | 97_V | 1.042 | 0.94 |
| 112_L | 115_V | 1.027 | 0.94 |
| 98_L | 102_R | 1.018 | 0.93 |
| 124_V | 146_G | 1.000 | 0.92 |
| 96_T | 105_S | 1.000 | 0.92 |
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 | |
| 4n0nA | 1 | 1 | 99.9 | 0.409 | Contact Map |
| 4b3fX | 1 | 0.9936 | 99.8 | 0.488 | Contact Map |
| 2xzlA | 1 | 0.9872 | 99.8 | 0.49 | Contact Map |
| 2zpaA | 2 | 0.8782 | 99.8 | 0.498 | Contact Map |
| 1w36D | 2 | 0.9167 | 99.8 | 0.5 | Contact Map |
| 2wjyA | 1 | 0.9872 | 99.8 | 0.507 | Contact Map |
| 2gk6A | 2 | 0.9872 | 99.8 | 0.512 | Contact Map |
| 3e1sA | 1 | 0.9167 | 99.8 | 0.514 | Contact Map |
| 3vkwA | 1 | 0.9423 | 99.7 | 0.542 | Contact Map |
| 3upuA | 3 | 0.8782 | 99.7 | 0.548 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)