| mmm_stuff |
| ID: | 1401421284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (101) | ||
| Sequences: | 258 (229.8) | ||
| Seq/Len: | 2.554 | ||
| Nf(neff/√len): | 22.9 |
HHblits Results: (2013_03)
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: 2.554).
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 |
| 22_Y | 43_H | 2.831 | 1.00 |
| 64_P | 67_G | 2.319 | 1.00 |
| 42_F | 96_K | 2.194 | 1.00 |
| 96_K | 102_N | 2.119 | 1.00 |
| 26_L | 30_P | 2.100 | 1.00 |
| 43_H | 85_G | 2.099 | 1.00 |
| 14_S | 37_D | 2.059 | 1.00 |
| 22_Y | 85_G | 1.946 | 0.99 |
| 18_G | 39_F | 1.666 | 0.97 |
| 27_C | 30_P | 1.646 | 0.97 |
| 63_M | 66_L | 1.507 | 0.94 |
| 13_H | 18_G | 1.481 | 0.94 |
| 10_S | 17_M | 1.412 | 0.91 |
| 63_M | 67_G | 1.357 | 0.89 |
| 20_L | 47_G | 1.352 | 0.89 |
| 27_C | 47_G | 1.346 | 0.89 |
| 34_N | 40_I | 1.330 | 0.88 |
| 47_G | 82_S | 1.322 | 0.87 |
| 30_P | 47_G | 1.311 | 0.87 |
| 76_M | 80_L | 1.303 | 0.86 |
| 49_V | 104_S | 1.280 | 0.85 |
| 40_I | 103_I | 1.255 | 0.83 |
| 27_C | 97_L | 1.241 | 0.82 |
| 19_I | 99_V | 1.240 | 0.82 |
| 57_A | 78_I | 1.236 | 0.82 |
| 59_M | 77_L | 1.234 | 0.82 |
| 37_D | 40_I | 1.228 | 0.81 |
| 88_S | 93_R | 1.223 | 0.81 |
| 83_V | 91_F | 1.222 | 0.81 |
| 13_H | 79_V | 1.219 | 0.81 |
| 28_L | 79_V | 1.212 | 0.80 |
| 38_E | 94_A | 1.182 | 0.78 |
| 16_A | 20_L | 1.173 | 0.77 |
| 71_F | 92_S | 1.170 | 0.77 |
| 15_Y | 92_S | 1.135 | 0.74 |
| 50_I | 97_L | 1.122 | 0.73 |
| 18_G | 79_V | 1.122 | 0.73 |
| 16_A | 87_V | 1.092 | 0.70 |
| 13_H | 29_V | 1.091 | 0.70 |
| 20_L | 24_G | 1.088 | 0.69 |
| 21_S | 29_V | 1.077 | 0.68 |
| 63_M | 69_F | 1.069 | 0.67 |
| 71_F | 76_M | 1.056 | 0.66 |
| 34_N | 45_K | 1.053 | 0.66 |
| 73_S | 93_R | 1.048 | 0.65 |
| 18_G | 40_I | 1.043 | 0.65 |
| 60_A | 70_F | 1.040 | 0.64 |
| 11_G | 15_Y | 1.038 | 0.64 |
| 40_I | 44_A | 1.032 | 0.63 |
| 85_G | 97_L | 1.030 | 0.63 |
| 45_K | 85_G | 1.013 | 0.61 |
| 31_L | 44_A | 1.006 | 0.60 |
| 82_S | 86_I | 1.005 | 0.60 |
| 74_S | 79_V | 1.001 | 0.60 |
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 | |
| 2nwlA | 3 | 0.8224 | 2.7 | 0.94 | Contact Map |
| 2uzhA | 3 | 0.2804 | 2.3 | 0.942 | Contact Map |
| 4i0uA | 10 | 0.7009 | 2.3 | 0.942 | Contact Map |
| 1ho8A | 1 | 0.514 | 2.2 | 0.942 | Contact Map |
| 4apsA | 2 | 0.5888 | 2.2 | 0.942 | Contact Map |
| 4ev6A | 5 | 0.7196 | 1.9 | 0.944 | Contact Map |
| 4bbjA | 1 | 0.7944 | 1.6 | 0.947 | Contact Map |
| 1te4A | 1 | 0.4766 | 1.3 | 0.949 | Contact Map |
| 4jw3C | 2 | 0.2243 | 1.3 | 0.95 | Contact Map |
| 1b3uA | 2 | 0.5047 | 1.3 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)