| lwb |
| ID: | 1487706696 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 122 (122) | ||
| Sequences: | 172 (96.5) | ||
| Seq/Len: | 1.410 | ||
| Nf(neff/√len): | 8.7 |
HHblits Results: (2016_02)
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: 1.410).
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 |
| 89_Y | 93_K | 2.907 | 1.00 |
| 27_N | 42_T | 2.818 | 1.00 |
| 69_R | 72_K | 2.584 | 1.00 |
| 82_S | 86_S | 2.475 | 1.00 |
| 51_N | 56_P | 1.749 | 0.94 |
| 92_M | 110_T | 1.716 | 0.93 |
| 44_L | 58_N | 1.660 | 0.92 |
| 46_T | 72_K | 1.653 | 0.91 |
| 48_A | 75_G | 1.653 | 0.91 |
| 24_L | 62_A | 1.583 | 0.89 |
| 82_S | 119_K | 1.553 | 0.87 |
| 37_E | 92_M | 1.512 | 0.86 |
| 48_A | 117_A | 1.510 | 0.85 |
| 93_K | 112_W | 1.477 | 0.84 |
| 56_P | 110_T | 1.453 | 0.82 |
| 41_S | 100_T | 1.425 | 0.81 |
| 46_T | 69_R | 1.394 | 0.79 |
| 63_R | 91_D | 1.379 | 0.77 |
| 20_Q | 60_A | 1.358 | 0.76 |
| 39_D | 73_A | 1.338 | 0.74 |
| 6_P | 16_S | 1.326 | 0.73 |
| 53_F | 106_A | 1.313 | 0.72 |
| 12_F | 88_F | 1.304 | 0.72 |
| 81_K | 119_K | 1.301 | 0.71 |
| 81_K | 113_T | 1.293 | 0.71 |
| 56_P | 92_M | 1.278 | 0.70 |
| 86_S | 119_K | 1.270 | 0.69 |
| 32_A | 78_D | 1.242 | 0.66 |
| 26_A | 34_A | 1.240 | 0.66 |
| 25_A | 29_N | 1.211 | 0.63 |
| 117_A | 122_G | 1.209 | 0.63 |
| 6_P | 74_A | 1.208 | 0.63 |
| 71_Y | 80_N | 1.206 | 0.63 |
| 60_A | 94_R | 1.200 | 0.62 |
| 41_S | 79_A | 1.189 | 0.61 |
| 17_A | 84_I | 1.183 | 0.61 |
| 20_Q | 113_T | 1.181 | 0.61 |
| 89_Y | 112_W | 1.179 | 0.60 |
| 25_A | 34_A | 1.156 | 0.58 |
| 51_N | 110_T | 1.116 | 0.54 |
| 38_F | 71_Y | 1.108 | 0.53 |
| 46_T | 60_A | 1.099 | 0.52 |
| 64_H | 122_G | 1.097 | 0.52 |
| 94_R | 110_T | 1.093 | 0.52 |
| 50_D | 114_Y | 1.084 | 0.51 |
| 93_K | 108_N | 1.083 | 0.51 |
| 16_S | 63_R | 1.076 | 0.50 |
| 19_S | 50_D | 1.075 | 0.50 |
| 26_A | 97_T | 1.074 | 0.50 |
| 20_Q | 24_L | 1.069 | 0.49 |
| 36_Y | 83_R | 1.049 | 0.47 |
| 56_P | 90_E | 1.049 | 0.47 |
| 49_P | 92_M | 1.048 | 0.47 |
| 86_S | 90_E | 1.045 | 0.47 |
| 8_V | 13_T | 1.041 | 0.47 |
| 72_K | 91_D | 1.028 | 0.45 |
| 21_N | 94_R | 1.028 | 0.45 |
| 11_S | 119_K | 1.022 | 0.45 |
| 1_A | 12_F | 1.017 | 0.44 |
| 19_S | 49_P | 1.012 | 0.44 |
| 9_L | 13_T | 1.008 | 0.43 |
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 | |
| 1lwbA | 1 | 1 | 100 | 0.215 | Contact Map |
| 4aupA | 2 | 0.9344 | 100 | 0.388 | Contact Map |
| 4g0rA | 1 | 0 | 49.8 | 0.933 | Contact Map |
| 4iovA | 1 | 0 | 40.5 | 0.937 | Contact Map |
| 3ng9A | 10 | 0 | 23.4 | 0.944 | Contact Map |
| 3nttA | 1 | 0 | 8.7 | 0.954 | Contact Map |
| 1vdaA | 1 | 0.1803 | 4.5 | 0.96 | Contact Map |
| 1vd8A | 1 | 0.1803 | 4.2 | 0.96 | Contact Map |
| 1vd7A | 1 | 0.1803 | 3.1 | 0.963 | Contact Map |
| 2e26A | 1 | 0.2787 | 1.9 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)