| PF16998 |
| ID: | 1487845893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (113) | ||
| Sequences: | 249 (165) | ||
| Seq/Len: | 2.204 | ||
| Nf(neff/√len): | 15.5 |
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: 2.204).
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 |
| 58_N | 62_G | 2.384 | 1.00 |
| 33_D | 58_N | 2.365 | 1.00 |
| 81_R | 108_W | 1.922 | 0.99 |
| 83_F | 98_G | 1.692 | 0.97 |
| 40_A | 44_A | 1.579 | 0.95 |
| 17_T | 20_I | 1.491 | 0.92 |
| 15_D | 23_A | 1.475 | 0.92 |
| 14_S | 21_A | 1.453 | 0.91 |
| 58_N | 61_T | 1.449 | 0.91 |
| 1_G | 5_L | 1.435 | 0.90 |
| 16_V | 22_A | 1.408 | 0.89 |
| 64_R | 88_V | 1.380 | 0.88 |
| 37_A | 40_A | 1.367 | 0.87 |
| 32_S | 61_T | 1.350 | 0.86 |
| 1_G | 6_D | 1.340 | 0.85 |
| 40_A | 51_D | 1.335 | 0.85 |
| 70_L | 85_A | 1.312 | 0.84 |
| 41_A | 110_V | 1.300 | 0.83 |
| 67_V | 75_Q | 1.285 | 0.82 |
| 41_A | 94_S | 1.276 | 0.81 |
| 1_G | 10_K | 1.266 | 0.81 |
| 58_N | 83_F | 1.217 | 0.77 |
| 41_A | 85_A | 1.213 | 0.77 |
| 65_G | 86_S | 1.213 | 0.77 |
| 34_L | 114_K | 1.213 | 0.77 |
| 66_T | 110_V | 1.207 | 0.76 |
| 5_L | 9_F | 1.197 | 0.75 |
| 36_F | 39_A | 1.194 | 0.75 |
| 11_M | 15_D | 1.191 | 0.75 |
| 10_K | 16_V | 1.182 | 0.74 |
| 104_G | 111_R | 1.167 | 0.73 |
| 6_D | 10_K | 1.165 | 0.72 |
| 6_D | 9_F | 1.160 | 0.72 |
| 7_G | 10_K | 1.154 | 0.71 |
| 2_G | 6_D | 1.148 | 0.71 |
| 40_A | 106_G | 1.143 | 0.70 |
| 65_G | 100_A | 1.134 | 0.69 |
| 1_G | 9_F | 1.127 | 0.69 |
| 112_S | 115_P | 1.125 | 0.69 |
| 16_V | 21_A | 1.123 | 0.68 |
| 1_G | 115_P | 1.123 | 0.68 |
| 67_V | 110_V | 1.099 | 0.66 |
| 47_R | 59_P | 1.091 | 0.65 |
| 2_G | 9_F | 1.088 | 0.65 |
| 37_A | 110_V | 1.087 | 0.65 |
| 100_A | 112_S | 1.079 | 0.64 |
| 65_G | 98_G | 1.077 | 0.64 |
| 86_S | 99_E | 1.059 | 0.62 |
| 41_A | 70_L | 1.057 | 0.62 |
| 26_A | 83_F | 1.055 | 0.61 |
| 63_A | 89_R | 1.050 | 0.61 |
| 49_G | 107_R | 1.049 | 0.61 |
| 46_T | 83_F | 1.046 | 0.60 |
| 63_A | 92_G | 1.043 | 0.60 |
| 2_G | 5_L | 1.038 | 0.59 |
| 32_S | 36_F | 1.037 | 0.59 |
| 61_T | 65_G | 1.037 | 0.59 |
| 12_D | 17_T | 1.036 | 0.59 |
| 19_S | 22_A | 1.035 | 0.59 |
| 15_D | 114_K | 1.030 | 0.59 |
| 48_G | 107_R | 1.027 | 0.58 |
| 41_A | 71_A | 1.017 | 0.57 |
| 5_L | 10_K | 1.017 | 0.57 |
| 25_A | 75_Q | 1.017 | 0.57 |
| 66_T | 88_V | 1.011 | 0.56 |
| 77_G | 103_Q | 1.008 | 0.56 |
| 43_D | 47_R | 1.005 | 0.56 |
| 15_D | 115_P | 1.004 | 0.56 |
| 43_D | 55_P | 1.002 | 0.55 |
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 | |
| 1eerA | 1 | 0.8362 | 10.4 | 0.92 | Contact Map |
| 3u6pA | 1 | 0.6983 | 10.4 | 0.92 | Contact Map |
| 4pd2A | 1 | 0.8534 | 10.2 | 0.92 | Contact Map |
| 3vk8A | 2 | 0.8707 | 5.9 | 0.929 | Contact Map |
| 1k82A | 4 | 0.7845 | 5.5 | 0.929 | Contact Map |
| 2l25A | 1 | 0.6293 | 4.6 | 0.932 | Contact Map |
| 1ee8A | 2 | 0.8793 | 4.4 | 0.933 | Contact Map |
| 4mb7A | 1 | 0.7586 | 4 | 0.934 | Contact Map |
| 1k3xA | 1 | 0.7414 | 3.9 | 0.935 | Contact Map |
| 4w4iA | 1 | 0.4224 | 2.9 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)