| z15-seqchecked |
| ID: | 1487809870 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (116) | ||
| Sequences: | 338 (223.9) | ||
| Seq/Len: | 2.914 | ||
| Nf(neff/√len): | 20.8 |
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: 2.914).
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 |
| 3_M | 6_E | 2.167 | 1.00 |
| 10_A | 96_I | 2.164 | 1.00 |
| 46_W | 58_R | 1.826 | 0.99 |
| 7_I | 11_L | 1.544 | 0.96 |
| 14_I | 33_E | 1.532 | 0.96 |
| 24_R | 27_V | 1.494 | 0.95 |
| 95_W | 104_Q | 1.456 | 0.94 |
| 54_G | 58_R | 1.444 | 0.94 |
| 14_I | 66_V | 1.439 | 0.94 |
| 97_D | 102_S | 1.426 | 0.94 |
| 8_Q | 12_N | 1.420 | 0.93 |
| 46_W | 54_G | 1.414 | 0.93 |
| 45_H | 57_F | 1.366 | 0.91 |
| 61_H | 91_D | 1.320 | 0.90 |
| 61_H | 100_E | 1.297 | 0.88 |
| 7_I | 83_D | 1.296 | 0.88 |
| 30_F | 67_D | 1.295 | 0.88 |
| 97_D | 104_Q | 1.283 | 0.88 |
| 45_H | 48_P | 1.283 | 0.88 |
| 59_C | 91_D | 1.279 | 0.87 |
| 46_W | 98_P | 1.277 | 0.87 |
| 6_E | 67_D | 1.253 | 0.86 |
| 54_G | 95_W | 1.250 | 0.86 |
| 55_S | 103_Y | 1.245 | 0.86 |
| 112_K | 115_Y | 1.228 | 0.84 |
| 46_W | 97_D | 1.227 | 0.84 |
| 56_G | 95_W | 1.224 | 0.84 |
| 61_H | 93_S | 1.210 | 0.83 |
| 57_F | 95_W | 1.190 | 0.82 |
| 51_P | 58_R | 1.175 | 0.81 |
| 89_P | 103_Y | 1.172 | 0.80 |
| 63_G | 91_D | 1.155 | 0.79 |
| 67_D | 84_V | 1.153 | 0.79 |
| 45_H | 54_G | 1.140 | 0.78 |
| 14_I | 69_V | 1.139 | 0.78 |
| 42_Y | 78_G | 1.126 | 0.77 |
| 83_D | 96_I | 1.125 | 0.77 |
| 104_Q | 107_E | 1.122 | 0.76 |
| 12_N | 77_S | 1.121 | 0.76 |
| 50_K | 53_K | 1.120 | 0.76 |
| 71_E | 74_S | 1.103 | 0.75 |
| 47_Y | 116_V | 1.103 | 0.75 |
| 41_K | 45_H | 1.093 | 0.74 |
| 109_G | 114_L | 1.092 | 0.73 |
| 20_N | 76_E | 1.086 | 0.73 |
| 6_E | 89_P | 1.084 | 0.73 |
| 83_D | 88_L | 1.079 | 0.72 |
| 34_L | 73_A | 1.070 | 0.71 |
| 8_Q | 36_R | 1.070 | 0.71 |
| 10_A | 53_K | 1.063 | 0.71 |
| 4_Q | 117_D | 1.063 | 0.71 |
| 47_Y | 53_K | 1.054 | 0.70 |
| 41_K | 62_I | 1.048 | 0.69 |
| 98_P | 104_Q | 1.047 | 0.69 |
| 55_S | 97_D | 1.045 | 0.69 |
| 77_S | 81_I | 1.035 | 0.68 |
| 41_K | 76_E | 1.030 | 0.67 |
| 109_G | 113_V | 1.026 | 0.67 |
| 25_R | 70_I | 1.026 | 0.67 |
| 20_N | 81_I | 1.023 | 0.66 |
| 18_L | 78_G | 1.020 | 0.66 |
| 46_W | 51_P | 1.019 | 0.66 |
| 10_A | 92_L | 1.015 | 0.65 |
| 3_M | 30_F | 1.011 | 0.65 |
| 45_H | 67_D | 1.011 | 0.65 |
| 40_K | 96_I | 1.009 | 0.65 |
| 18_L | 87_N | 1.001 | 0.64 |
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 | |
| 2z15A | 4 | 1 | 100 | 0.012 | Contact Map |
| 3e9vA | 1 | 0.9916 | 100 | 0.014 | Contact Map |
| 3shrA | 2 | 0.521 | 17.7 | 0.928 | Contact Map |
| 2kmfA | 1 | 0.3782 | 15.7 | 0.929 | Contact Map |
| 2x1dA | 4 | 0.7731 | 14.7 | 0.93 | Contact Map |
| 4ds1A | 2 | 0.6639 | 14.1 | 0.931 | Contact Map |
| 2j0pA | 1 | 0.563 | 13.8 | 0.931 | Contact Map |
| 1lngA | 1 | 0.6303 | 13.5 | 0.931 | Contact Map |
| 1ghhA | 1 | 0.6555 | 13.1 | 0.932 | Contact Map |
| 1e5eA | 2 | 0.3613 | 12.9 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)