| T0815 |
| ID: | 1402513597 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (105) | ||
| Sequences: | 203 (181.7) | ||
| Seq/Len: | 1.933 | ||
| Nf(neff/√len): | 17.7 |
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: 1.933).
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 |
| 32_V | 48_W | 2.793 | 1.00 |
| 28_P | 42_V | 1.685 | 0.96 |
| 11_F | 74_V | 1.608 | 0.94 |
| 10_Y | 93_F | 1.607 | 0.94 |
| 20_D | 46_L | 1.543 | 0.92 |
| 35_E | 52_A | 1.503 | 0.91 |
| 94_T | 102_R | 1.479 | 0.90 |
| 62_P | 74_V | 1.474 | 0.90 |
| 35_E | 39_H | 1.469 | 0.89 |
| 76_A | 86_P | 1.455 | 0.89 |
| 35_E | 48_W | 1.451 | 0.89 |
| 82_F | 89_L | 1.433 | 0.88 |
| 4_P | 95_I | 1.349 | 0.83 |
| 35_E | 78_V | 1.345 | 0.83 |
| 27_A | 101_A | 1.342 | 0.83 |
| 35_E | 89_L | 1.325 | 0.82 |
| 56_A | 83_P | 1.318 | 0.81 |
| 57_S | 81_R | 1.313 | 0.81 |
| 40_Q | 67_V | 1.304 | 0.80 |
| 49_W | 53_K | 1.289 | 0.79 |
| 78_V | 86_P | 1.281 | 0.79 |
| 56_A | 91_Y | 1.255 | 0.77 |
| 56_A | 82_F | 1.247 | 0.76 |
| 80_G | 83_P | 1.244 | 0.76 |
| 5_D | 81_R | 1.241 | 0.75 |
| 66_T | 99_R | 1.234 | 0.75 |
| 59_V | 63_L | 1.218 | 0.73 |
| 17_N | 105_I | 1.196 | 0.71 |
| 94_T | 101_A | 1.181 | 0.70 |
| 11_F | 85_S | 1.174 | 0.69 |
| 80_G | 86_P | 1.173 | 0.69 |
| 84_G | 103_L | 1.156 | 0.68 |
| 46_L | 50_V | 1.143 | 0.66 |
| 32_V | 35_E | 1.142 | 0.66 |
| 7_V | 23_S | 1.123 | 0.64 |
| 61_E | 77_K | 1.112 | 0.63 |
| 13_A | 101_A | 1.110 | 0.63 |
| 38_R | 59_V | 1.102 | 0.62 |
| 6_I | 43_V | 1.102 | 0.62 |
| 84_G | 87_V | 1.074 | 0.59 |
| 79_S | 85_S | 1.061 | 0.58 |
| 19_T | 74_V | 1.059 | 0.58 |
| 12_D | 27_A | 1.054 | 0.57 |
| 63_L | 98_G | 1.044 | 0.56 |
| 35_E | 84_G | 1.043 | 0.56 |
| 35_E | 82_F | 1.033 | 0.55 |
| 31_V | 44_A | 1.033 | 0.55 |
| 2_D | 106_Q | 1.028 | 0.54 |
| 7_V | 72_A | 1.022 | 0.54 |
| 23_S | 47_R | 1.017 | 0.53 |
| 24_E | 37_A | 1.017 | 0.53 |
| 24_E | 69_G | 1.010 | 0.52 |
| 32_V | 62_P | 1.002 | 0.52 |
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 | |
| 3mg1A | 2 | 1 | 99.3 | 0.627 | Contact Map |
| 4h3uA | 2 | 1 | 99.2 | 0.637 | Contact Map |
| 4mjdA | 2 | 0.9811 | 99.2 | 0.651 | Contact Map |
| 3dm8A | 1 | 1 | 99.1 | 0.658 | Contact Map |
| 3g16A | 2 | 1 | 99.1 | 0.659 | Contact Map |
| 3ff2A | 1 | 1 | 99.1 | 0.659 | Contact Map |
| 2k54A | 1 | 1 | 99.1 | 0.66 | Contact Map |
| 2a15A | 1 | 0.9811 | 99.1 | 0.66 | Contact Map |
| 1ohpA | 4 | 0.9906 | 99.1 | 0.662 | Contact Map |
| 3dmcA | 2 | 1 | 99 | 0.668 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)