| scEMC6 |
| ID: | 1504851534 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (105) | ||
| Sequences: | 368 (261.4) | ||
| Seq/Len: | 3.505 | ||
| Nf(neff/√len): | 25.5 |
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: 3.505).
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 |
| 31_S | 60_I | 2.098 | 1.00 |
| 98_M | 101_T | 1.992 | 1.00 |
| 96_F | 100_W | 1.950 | 1.00 |
| 50_F | 93_I | 1.924 | 1.00 |
| 52_W | 96_F | 1.766 | 0.99 |
| 102_F | 106_L | 1.754 | 0.99 |
| 97_V | 101_T | 1.663 | 0.99 |
| 12_N | 17_V | 1.594 | 0.98 |
| 101_T | 104_Y | 1.580 | 0.98 |
| 44_I | 50_F | 1.540 | 0.97 |
| 95_G | 101_T | 1.480 | 0.96 |
| 43_Q | 98_M | 1.346 | 0.93 |
| 102_F | 108_G | 1.342 | 0.93 |
| 53_F | 69_C | 1.338 | 0.93 |
| 95_G | 99_A | 1.303 | 0.92 |
| 28_Q | 64_Y | 1.279 | 0.91 |
| 98_M | 105_A | 1.269 | 0.90 |
| 51_I | 58_N | 1.267 | 0.90 |
| 69_C | 73_P | 1.256 | 0.90 |
| 67_W | 71_L | 1.252 | 0.89 |
| 100_W | 104_Y | 1.239 | 0.89 |
| 28_Q | 95_G | 1.237 | 0.89 |
| 19_D | 23_R | 1.230 | 0.88 |
| 15_A | 22_K | 1.223 | 0.88 |
| 22_K | 87_E | 1.212 | 0.87 |
| 28_Q | 61_N | 1.208 | 0.87 |
| 75_K | 97_V | 1.196 | 0.86 |
| 102_F | 107_I | 1.176 | 0.85 |
| 95_G | 106_L | 1.168 | 0.84 |
| 104_Y | 107_I | 1.149 | 0.83 |
| 68_I | 92_E | 1.146 | 0.83 |
| 54_L | 75_K | 1.145 | 0.83 |
| 95_G | 98_M | 1.142 | 0.83 |
| 83_D | 97_V | 1.141 | 0.82 |
| 72_Q | 76_F | 1.139 | 0.82 |
| 43_Q | 91_R | 1.119 | 0.81 |
| 96_F | 101_T | 1.117 | 0.81 |
| 24_L | 107_I | 1.100 | 0.79 |
| 32_A | 48_H | 1.097 | 0.79 |
| 49_G | 76_F | 1.095 | 0.79 |
| 7_V | 13_A | 1.094 | 0.79 |
| 9_T | 14_T | 1.090 | 0.78 |
| 99_A | 102_F | 1.080 | 0.77 |
| 45_E | 104_Y | 1.078 | 0.77 |
| 18_V | 87_E | 1.073 | 0.77 |
| 20_N | 36_G | 1.072 | 0.77 |
| 105_A | 108_G | 1.055 | 0.75 |
| 19_D | 42_L | 1.046 | 0.74 |
| 38_V | 96_F | 1.043 | 0.74 |
| 27_V | 30_S | 1.034 | 0.73 |
| 59_L | 89_F | 1.033 | 0.73 |
| 60_I | 88_S | 1.033 | 0.73 |
| 95_G | 100_W | 1.027 | 0.72 |
| 33_L | 99_A | 1.021 | 0.72 |
| 29_D | 98_M | 1.016 | 0.71 |
| 98_M | 108_G | 1.014 | 0.71 |
| 41_F | 46_S | 1.014 | 0.71 |
| 22_K | 69_C | 1.013 | 0.71 |
| 39_A | 43_Q | 1.011 | 0.71 |
| 31_S | 90_F | 1.010 | 0.70 |
| 54_L | 93_I | 1.009 | 0.70 |
| 16_N | 32_A | 1.008 | 0.70 |
| 21_K | 45_E | 1.000 | 0.69 |
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 | |
| 4ev6A | 5 | 0.6759 | 14.3 | 0.914 | Contact Map |
| 4djkA | 2 | 0.7407 | 9.8 | 0.92 | Contact Map |
| 4i0uA | 10 | 0.6574 | 7.9 | 0.924 | Contact Map |
| 2l2tA | 2 | 0.4074 | 6.1 | 0.928 | Contact Map |
| 2ww8A | 1 | 0.3611 | 3.6 | 0.935 | Contact Map |
| 4ycsA | 6 | 0.3981 | 3 | 0.938 | Contact Map |
| 3l1lA | 1 | 0.7778 | 2.8 | 0.939 | Contact Map |
| 4xnjA | 1 | 0 | 2.6 | 0.94 | Contact Map |
| 4u4vA | 1 | 0 | 2.5 | 0.94 | Contact Map |
| 2gfpA | 2 | 0.6204 | 2.5 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)