| T0846 |
| ID: | 1404841774 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (143) | ||
| Sequences: | 205 (186) | ||
| Seq/Len: | 1.434 | ||
| Nf(neff/√len): | 15.6 |
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: 1.434).
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 |
| 94_K | 102_E | 2.850 | 1.00 |
| 47_V | 86_A | 2.076 | 0.98 |
| 31_H | 40_I | 2.070 | 0.98 |
| 43_L | 104_N | 1.951 | 0.97 |
| 39_E | 91_F | 1.893 | 0.97 |
| 40_I | 43_L | 1.822 | 0.96 |
| 58_L | 111_A | 1.665 | 0.92 |
| 48_F | 56_N | 1.621 | 0.90 |
| 6_H | 44_S | 1.580 | 0.89 |
| 22_E | 126_I | 1.575 | 0.89 |
| 98_R | 101_A | 1.560 | 0.88 |
| 44_S | 54_L | 1.519 | 0.86 |
| 22_E | 130_H | 1.457 | 0.83 |
| 133_E | 136_R | 1.449 | 0.82 |
| 23_F | 123_M | 1.409 | 0.80 |
| 56_N | 95_N | 1.363 | 0.77 |
| 46_I | 86_A | 1.340 | 0.75 |
| 10_I | 141_V | 1.328 | 0.74 |
| 56_N | 135_K | 1.319 | 0.73 |
| 3_H | 6_H | 1.301 | 0.72 |
| 59_S | 105_I | 1.299 | 0.72 |
| 126_I | 130_H | 1.287 | 0.71 |
| 61_I | 112_I | 1.287 | 0.71 |
| 22_E | 51_Q | 1.273 | 0.70 |
| 68_T | 119_V | 1.257 | 0.68 |
| 78_S | 95_N | 1.239 | 0.67 |
| 30_D | 138_A | 1.236 | 0.66 |
| 96_S | 119_V | 1.202 | 0.63 |
| 83_A | 118_A | 1.198 | 0.63 |
| 27_V | 84_K | 1.194 | 0.62 |
| 35_E | 39_E | 1.192 | 0.62 |
| 13_Q | 45_Q | 1.188 | 0.62 |
| 47_V | 93_I | 1.186 | 0.62 |
| 59_S | 71_I | 1.185 | 0.61 |
| 87_G | 101_A | 1.181 | 0.61 |
| 34_Q | 107_K | 1.178 | 0.61 |
| 20_Y | 123_M | 1.178 | 0.61 |
| 27_V | 53_Q | 1.177 | 0.61 |
| 9_F | 141_V | 1.170 | 0.60 |
| 60_Q | 63_E | 1.162 | 0.59 |
| 23_F | 95_N | 1.154 | 0.58 |
| 119_V | 126_I | 1.143 | 0.57 |
| 46_I | 100_Q | 1.132 | 0.56 |
| 18_L | 126_I | 1.123 | 0.55 |
| 41_R | 52_N | 1.101 | 0.53 |
| 17_P | 24_I | 1.081 | 0.51 |
| 26_K | 136_R | 1.081 | 0.51 |
| 9_F | 13_Q | 1.081 | 0.51 |
| 5_H | 74_T | 1.080 | 0.51 |
| 38_K | 125_N | 1.080 | 0.51 |
| 65_P | 116_A | 1.068 | 0.50 |
| 127_I | 138_A | 1.060 | 0.49 |
| 74_T | 131_N | 1.059 | 0.49 |
| 68_T | 116_A | 1.053 | 0.48 |
| 84_K | 127_I | 1.048 | 0.48 |
| 51_Q | 63_E | 1.039 | 0.47 |
| 43_L | 141_V | 1.037 | 0.47 |
| 23_F | 71_I | 1.036 | 0.46 |
| 54_L | 60_Q | 1.034 | 0.46 |
| 3_H | 14_K | 1.029 | 0.46 |
| 15_I | 62_H | 1.028 | 0.46 |
| 96_S | 114_K | 1.025 | 0.45 |
| 89_K | 99_K | 1.025 | 0.45 |
| 56_N | 81_S | 1.024 | 0.45 |
| 37_E | 40_I | 1.021 | 0.45 |
| 9_F | 15_I | 1.012 | 0.44 |
| 13_Q | 77_N | 1.008 | 0.44 |
| 10_I | 144_P | 1.005 | 0.43 |
| 43_L | 67_F | 1.002 | 0.43 |
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 | |
| 2lnmA | 1 | 0.4041 | 36.9 | 0.929 | Contact Map |
| 2llwA | 1 | 0.4863 | 14.3 | 0.942 | Contact Map |
| 2zbcA | 8 | 0.5274 | 11.6 | 0.944 | Contact Map |
| 2llvA | 1 | 0.4863 | 11.3 | 0.944 | Contact Map |
| 2a2fX | 1 | 0.8014 | 10.8 | 0.945 | Contact Map |
| 2f4mB | 1 | 0.411 | 8 | 0.948 | Contact Map |
| 2djwA | 10 | 0.5205 | 7.5 | 0.949 | Contact Map |
| 3hwsA | 6 | 0.637 | 7.5 | 0.949 | Contact Map |
| 2oeqA | 4 | 0.4658 | 5.3 | 0.952 | Contact Map |
| 3k8pC | 1 | 0.4658 | 4.9 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)