| PF16998_2 |
| ID: | 1487846723 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 116 (113) | ||
| Sequences: | 128 (80.3) | ||
| Seq/Len: | 1.133 | ||
| Nf(neff/√len): | 7.6 |
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: 1.133).
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 |
| 64_R | 88_V | 1.833 | 0.93 |
| 81_R | 108_W | 1.712 | 0.90 |
| 33_D | 58_N | 1.674 | 0.89 |
| 17_T | 61_T | 1.644 | 0.87 |
| 18_G | 112_S | 1.563 | 0.84 |
| 34_L | 114_K | 1.525 | 0.81 |
| 70_L | 77_G | 1.498 | 0.80 |
| 45_L | 57_E | 1.452 | 0.77 |
| 17_T | 20_I | 1.437 | 0.76 |
| 40_A | 44_A | 1.418 | 0.74 |
| 36_F | 39_A | 1.412 | 0.74 |
| 15_D | 96_L | 1.391 | 0.72 |
| 57_E | 93_E | 1.382 | 0.72 |
| 67_V | 91_G | 1.369 | 0.71 |
| 12_D | 92_G | 1.312 | 0.66 |
| 12_D | 87_Y | 1.301 | 0.65 |
| 82_D | 102_R | 1.266 | 0.62 |
| 66_T | 85_A | 1.261 | 0.61 |
| 90_G | 93_E | 1.261 | 0.61 |
| 37_A | 93_E | 1.252 | 0.61 |
| 12_D | 113_L | 1.251 | 0.60 |
| 16_V | 60_D | 1.238 | 0.59 |
| 112_S | 115_P | 1.222 | 0.58 |
| 32_S | 36_F | 1.216 | 0.57 |
| 68_T | 99_E | 1.215 | 0.57 |
| 58_N | 61_T | 1.205 | 0.56 |
| 26_A | 92_G | 1.199 | 0.56 |
| 44_A | 57_E | 1.199 | 0.56 |
| 58_N | 83_F | 1.196 | 0.55 |
| 6_D | 79_T | 1.192 | 0.55 |
| 53_S | 93_E | 1.178 | 0.54 |
| 36_F | 57_E | 1.171 | 0.53 |
| 69_P | 84_L | 1.159 | 0.52 |
| 15_D | 107_R | 1.150 | 0.51 |
| 76_D | 107_R | 1.147 | 0.51 |
| 90_G | 96_L | 1.139 | 0.50 |
| 88_V | 93_E | 1.128 | 0.49 |
| 66_T | 110_V | 1.128 | 0.49 |
| 15_D | 61_T | 1.127 | 0.49 |
| 14_S | 21_A | 1.119 | 0.48 |
| 66_T | 93_E | 1.103 | 0.46 |
| 15_D | 23_A | 1.093 | 0.45 |
| 37_A | 45_L | 1.092 | 0.45 |
| 63_A | 89_R | 1.075 | 0.44 |
| 24_A | 71_A | 1.048 | 0.41 |
| 94_S | 110_V | 1.044 | 0.41 |
| 53_S | 97_Q | 1.044 | 0.41 |
| 42_S | 78_R | 1.043 | 0.41 |
| 84_L | 116_W | 1.036 | 0.40 |
| 60_D | 92_G | 1.034 | 0.40 |
| 1_G | 5_L | 1.033 | 0.40 |
| 82_D | 114_K | 1.025 | 0.39 |
| 63_A | 100_A | 1.019 | 0.39 |
| 39_A | 72_S | 1.018 | 0.38 |
| 37_A | 58_N | 1.008 | 0.38 |
| 64_R | 96_L | 1.006 | 0.37 |
| 35_A | 51_D | 1.004 | 0.37 |
| 36_F | 61_T | 1.004 | 0.37 |
| 21_A | 27_A | 1.002 | 0.37 |
| 68_T | 97_Q | 1.000 | 0.37 |
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 | |
| 2p6vA | 1 | 0.3707 | 10.8 | 0.933 | Contact Map |
| 2n2hA | 1 | 0 | 3.4 | 0.947 | Contact Map |
| 2l25A | 1 | 0.6207 | 2.9 | 0.949 | Contact Map |
| 2rppA | 1 | 0.4052 | 2.9 | 0.949 | Contact Map |
| 4bkwA | 1 | 0.7931 | 2.5 | 0.95 | Contact Map |
| 1eerA | 1 | 0.8017 | 2.5 | 0.95 | Contact Map |
| 3snoA | 1 | 0.5 | 2.3 | 0.951 | Contact Map |
| 4txaA | 1 | 0.4741 | 2.3 | 0.951 | Contact Map |
| 4mb7A | 1 | 0.7672 | 2.3 | 0.951 | Contact Map |
| 2p5zX | 1 | 0.1638 | 2.2 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)