| Q9RP17_NEIME |
| ID: | 1417104424 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 174 (174) | ||
| Sequences: | 12674 (11183.7) | ||
| Seq/Len: | 72.839 | ||
| Nf(neff/√len): | 847.8 |
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: 72.839).
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 |
| 147_Y | 164_G | 4.291 | 1.00 |
| 142_D | 171_R | 3.076 | 1.00 |
| 144_D | 169_G | 2.849 | 1.00 |
| 105_L | 125_I | 2.833 | 1.00 |
| 102_G | 130_L | 2.645 | 1.00 |
| 96_P | 135_Y | 2.599 | 1.00 |
| 97_V | 135_Y | 2.503 | 1.00 |
| 137_V | 143_L | 2.478 | 1.00 |
| 26_Y | 53_G | 2.453 | 1.00 |
| 138_T | 141_V | 2.440 | 1.00 |
| 97_V | 133_V | 2.393 | 1.00 |
| 141_V | 172_V | 2.364 | 1.00 |
| 65_Y | 81_Y | 2.363 | 1.00 |
| 14_P | 18_L | 2.314 | 1.00 |
| 107_L | 123_T | 2.277 | 1.00 |
| 28_Q | 51_S | 2.076 | 1.00 |
| 30_D | 49_R | 2.028 | 1.00 |
| 149_Y | 164_G | 2.002 | 1.00 |
| 25_F | 54_Y | 1.978 | 1.00 |
| 31_A | 46_F | 1.938 | 1.00 |
| 99_P | 103_A | 1.925 | 1.00 |
| 134_S | 144_D | 1.804 | 1.00 |
| 60_R | 88_I | 1.758 | 1.00 |
| 100_Y | 132_G | 1.731 | 1.00 |
| 136_A | 142_D | 1.687 | 1.00 |
| 25_F | 52_A | 1.675 | 1.00 |
| 86_S | 128_G | 1.657 | 1.00 |
| 33_H | 44_K | 1.643 | 1.00 |
| 107_L | 125_I | 1.605 | 1.00 |
| 104_R | 128_G | 1.557 | 1.00 |
| 25_F | 29_A | 1.548 | 1.00 |
| 134_S | 142_D | 1.534 | 1.00 |
| 55_R | 60_R | 1.504 | 1.00 |
| 60_R | 90_D | 1.503 | 1.00 |
| 146_G | 167_S | 1.490 | 1.00 |
| 15_A | 18_L | 1.490 | 1.00 |
| 100_Y | 144_D | 1.460 | 1.00 |
| 129_V | 149_Y | 1.450 | 1.00 |
| 102_G | 148_R | 1.387 | 0.99 |
| 86_S | 102_G | 1.376 | 0.99 |
| 81_Y | 84_G | 1.372 | 0.99 |
| 136_A | 173_K | 1.365 | 0.99 |
| 142_D | 173_K | 1.352 | 0.99 |
| 98_K | 134_S | 1.324 | 0.99 |
| 95_S | 99_P | 1.318 | 0.99 |
| 130_L | 146_G | 1.309 | 0.99 |
| 144_D | 171_R | 1.308 | 0.99 |
| 130_L | 148_R | 1.299 | 0.99 |
| 141_V | 170_V | 1.298 | 0.99 |
| 56_I | 61_F | 1.291 | 0.99 |
| 67_R | 81_Y | 1.276 | 0.99 |
| 98_K | 136_A | 1.272 | 0.99 |
| 106_S | 126_G | 1.250 | 0.99 |
| 64_D | 84_G | 1.247 | 0.99 |
| 141_V | 145_A | 1.247 | 0.99 |
| 99_P | 133_V | 1.230 | 0.98 |
| 63_V | 67_R | 1.218 | 0.98 |
| 108_N | 126_G | 1.218 | 0.98 |
| 100_Y | 146_G | 1.209 | 0.98 |
| 48_P | 52_A | 1.176 | 0.98 |
| 134_S | 171_R | 1.133 | 0.97 |
| 62_A | 88_I | 1.131 | 0.97 |
| 4_A | 8_L | 1.131 | 0.97 |
| 17_A | 20_E | 1.128 | 0.97 |
| 48_P | 67_R | 1.125 | 0.97 |
| 51_S | 171_R | 1.122 | 0.97 |
| 140_N | 172_V | 1.119 | 0.96 |
| 16_A | 19_A | 1.102 | 0.96 |
| 62_A | 86_S | 1.092 | 0.96 |
| 32_A | 47_S | 1.088 | 0.96 |
| 148_R | 167_S | 1.078 | 0.95 |
| 82_S | 86_S | 1.073 | 0.95 |
| 103_A | 107_L | 1.062 | 0.95 |
| 45_G | 48_P | 1.058 | 0.95 |
| 30_D | 51_S | 1.044 | 0.94 |
| 149_Y | 162_R | 1.032 | 0.94 |
| 12_A | 16_A | 1.024 | 0.93 |
| 90_D | 98_K | 1.017 | 0.93 |
| 84_G | 88_I | 1.013 | 0.93 |
| 50_I | 54_Y | 1.012 | 0.93 |
| 127_L | 151_Y | 1.007 | 0.93 |
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 | |
| 3nb3A | 3 | 0.7586 | 99.8 | 0.227 | Contact Map |
| 1p4tA | 1 | 0.8908 | 99.7 | 0.287 | Contact Map |
| 2mlhA | 1 | 0.8966 | 99.7 | 0.311 | Contact Map |
| 2x27X | 1 | 0.9138 | 99.7 | 0.327 | Contact Map |
| 2k0lA | 1 | 0.9655 | 99.6 | 0.356 | Contact Map |
| 2lhfA | 1 | 0.8678 | 99.6 | 0.357 | Contact Map |
| 2f1vA | 6 | 0.8736 | 99.6 | 0.371 | Contact Map |
| 1qjpA | 1 | 0.7759 | 99.6 | 0.377 | Contact Map |
| 2jmmA | 1 | 0.8046 | 99.4 | 0.423 | Contact Map |
| 3qraA | 1 | 0.8448 | 99.4 | 0.438 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)