| LYSC_CHICK |
| ID: | 1418935695 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 147 (147) | ||
| Sequences: | 643 (387.3) | ||
| Seq/Len: | 4.374 | ||
| Nf(neff/√len): | 31.9 |
Jackhmmer Results: (2014_04_16)
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: 4.374).
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 |
| 103_S | 109_S | 3.352 | 1.00 |
| 103_S | 108_A | 2.644 | 1.00 |
| 96_I | 101_L | 2.424 | 1.00 |
| 21_F | 26_L | 2.224 | 1.00 |
| 66_D | 79_R | 2.105 | 1.00 |
| 53_E | 70_D | 2.036 | 1.00 |
| 33_H | 110_V | 1.976 | 1.00 |
| 71_Y | 102_L | 1.911 | 1.00 |
| 100_A | 103_S | 1.859 | 1.00 |
| 26_L | 106_I | 1.845 | 1.00 |
| 20_V | 57_N | 1.831 | 1.00 |
| 50_A | 56_F | 1.717 | 0.99 |
| 57_N | 60_A | 1.594 | 0.99 |
| 45_N | 49_A | 1.588 | 0.99 |
| 96_I | 109_S | 1.523 | 0.98 |
| 64_N | 70_D | 1.515 | 0.98 |
| 36_D | 42_S | 1.512 | 0.98 |
| 23_R | 144_G | 1.493 | 0.98 |
| 8_V | 11_F | 1.479 | 0.98 |
| 117_V | 123_M | 1.478 | 0.98 |
| 50_A | 73_I | 1.474 | 0.98 |
| 68_S | 77_N | 1.436 | 0.97 |
| 49_A | 129_W | 1.432 | 0.97 |
| 45_N | 129_W | 1.429 | 0.97 |
| 76_I | 116_I | 1.419 | 0.97 |
| 51_K | 55_N | 1.415 | 0.97 |
| 29_A | 110_V | 1.400 | 0.97 |
| 52_F | 132_R | 1.398 | 0.97 |
| 41_Y | 123_M | 1.361 | 0.96 |
| 42_S | 117_V | 1.356 | 0.96 |
| 81_W | 125_A | 1.345 | 0.95 |
| 129_W | 135_G | 1.323 | 0.95 |
| 31_K | 37_N | 1.304 | 0.94 |
| 115_K | 119_D | 1.299 | 0.94 |
| 116_I | 126_W | 1.285 | 0.94 |
| 30_M | 74_L | 1.283 | 0.94 |
| 26_L | 50_A | 1.278 | 0.93 |
| 61_T | 102_L | 1.255 | 0.93 |
| 116_I | 119_D | 1.253 | 0.93 |
| 13_P | 16_A | 1.253 | 0.93 |
| 23_R | 51_K | 1.213 | 0.91 |
| 46_W | 68_S | 1.212 | 0.91 |
| 96_I | 108_A | 1.205 | 0.91 |
| 53_E | 68_S | 1.203 | 0.90 |
| 23_R | 130_R | 1.176 | 0.89 |
| 78_S | 84_D | 1.170 | 0.89 |
| 78_S | 87_T | 1.169 | 0.89 |
| 30_M | 47_V | 1.162 | 0.88 |
| 46_W | 53_E | 1.142 | 0.87 |
| 71_Y | 78_S | 1.141 | 0.87 |
| 52_F | 128_A | 1.130 | 0.86 |
| 111_N | 118_S | 1.120 | 0.86 |
| 49_A | 123_M | 1.120 | 0.86 |
| 70_D | 77_N | 1.116 | 0.85 |
| 100_A | 108_A | 1.112 | 0.85 |
| 10_C | 13_P | 1.111 | 0.85 |
| 70_D | 127_V | 1.102 | 0.84 |
| 61_T | 69_T | 1.090 | 0.84 |
| 32_R | 105_D | 1.089 | 0.83 |
| 8_V | 18_G | 1.078 | 0.83 |
| 85_G | 97_P | 1.069 | 0.82 |
| 93_L | 120_G | 1.060 | 0.81 |
| 88_P | 92_N | 1.059 | 0.81 |
| 27_A | 31_K | 1.057 | 0.81 |
| 96_I | 100_A | 1.054 | 0.81 |
| 8_V | 13_P | 1.042 | 0.80 |
| 63_R | 69_T | 1.037 | 0.79 |
| 121_N | 127_V | 1.032 | 0.79 |
| 36_D | 123_M | 1.031 | 0.79 |
| 100_A | 109_S | 1.020 | 0.78 |
| 117_V | 120_G | 1.006 | 0.76 |
| 18_G | 30_M | 1.004 | 0.76 |
| 101_L | 109_S | 1.002 | 0.76 |
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 | |
| 3b72A | 1 | 0.8776 | 100 | 0.186 | Contact Map |
| 2nwdX | 1 | 0.8776 | 100 | 0.195 | Contact Map |
| 2goiA | 3 | 0.8707 | 100 | 0.201 | Contact Map |
| 2z2fA | 1 | 0.8707 | 100 | 0.204 | Contact Map |
| 1hmlA | 1 | 0.8299 | 100 | 0.218 | Contact Map |
| 1lsgA | 1 | 0.8844 | 100 | 0.238 | Contact Map |
| 1yroA | 2 | 0.8367 | 100 | 0.239 | Contact Map |
| 2vb1A | 1 | 0.8776 | 100 | 0.245 | Contact Map |
| 1b9oA | 1 | 0.8367 | 100 | 0.246 | Contact Map |
| 1qqyA | 1 | 0.8776 | 100 | 0.254 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)