| HEWL |
| ID: | 1425141626 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (129) | ||
| Sequences: | 379 (245) | ||
| Seq/Len: | 2.938 | ||
| Nf(neff/√len): | 21.6 |
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: 2.938).
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 |
| 85_S | 91_S | 3.008 | 1.00 |
| 85_S | 90_A | 2.741 | 1.00 |
| 8_L | 88_I | 2.592 | 1.00 |
| 3_F | 8_L | 2.124 | 1.00 |
| 53_Y | 84_L | 1.972 | 1.00 |
| 39_N | 42_A | 1.899 | 0.99 |
| 35_E | 52_D | 1.810 | 0.99 |
| 23_Y | 105_M | 1.740 | 0.99 |
| 32_A | 55_I | 1.738 | 0.99 |
| 2_V | 39_N | 1.713 | 0.98 |
| 78_I | 83_L | 1.623 | 0.97 |
| 8_L | 29_V | 1.585 | 0.97 |
| 48_D | 61_R | 1.576 | 0.97 |
| 12_M | 56_L | 1.566 | 0.97 |
| 31_A | 111_W | 1.477 | 0.95 |
| 82_A | 85_S | 1.435 | 0.94 |
| 32_A | 38_F | 1.414 | 0.93 |
| 99_V | 105_M | 1.379 | 0.92 |
| 4_G | 7_E | 1.366 | 0.92 |
| 32_A | 88_I | 1.355 | 0.91 |
| 53_Y | 60_S | 1.350 | 0.91 |
| 15_H | 92_V | 1.344 | 0.91 |
| 44_N | 52_D | 1.343 | 0.91 |
| 27_N | 111_W | 1.328 | 0.90 |
| 52_D | 59_N | 1.285 | 0.88 |
| 82_A | 91_S | 1.284 | 0.88 |
| 33_K | 37_N | 1.282 | 0.88 |
| 27_N | 31_A | 1.253 | 0.86 |
| 82_A | 90_A | 1.247 | 0.86 |
| 55_I | 60_S | 1.245 | 0.86 |
| 34_F | 114_R | 1.242 | 0.85 |
| 59_N | 111_W | 1.239 | 0.85 |
| 8_L | 32_A | 1.227 | 0.85 |
| 78_I | 91_S | 1.222 | 0.84 |
| 46_N | 51_T | 1.205 | 0.83 |
| 43_T | 51_T | 1.178 | 0.81 |
| 44_N | 47_T | 1.175 | 0.81 |
| 44_N | 109_V | 1.161 | 0.80 |
| 9_A | 13_K | 1.153 | 0.79 |
| 79_P | 82_A | 1.152 | 0.79 |
| 16_G | 25_L | 1.142 | 0.78 |
| 43_T | 84_L | 1.133 | 0.77 |
| 65_N | 72_S | 1.125 | 0.77 |
| 39_N | 116_K | 1.120 | 0.76 |
| 10_A | 41_Q | 1.105 | 0.75 |
| 97_K | 102_G | 1.103 | 0.75 |
| 123_W | 127_C | 1.102 | 0.75 |
| 97_K | 101_D | 1.094 | 0.74 |
| 5_R | 33_K | 1.088 | 0.73 |
| 18_D | 24_S | 1.084 | 0.73 |
| 2_V | 42_A | 1.081 | 0.73 |
| 86_S | 89_T | 1.076 | 0.72 |
| 24_S | 99_V | 1.075 | 0.72 |
| 34_F | 38_F | 1.068 | 0.71 |
| 92_V | 126_G | 1.062 | 0.71 |
| 14_R | 87_D | 1.053 | 0.70 |
| 31_A | 105_M | 1.044 | 0.69 |
| 113_N | 118_T | 1.044 | 0.69 |
| 120_V | 127_C | 1.041 | 0.69 |
| 35_E | 59_N | 1.038 | 0.68 |
| 16_G | 26_G | 1.035 | 0.68 |
| 124_I | 127_C | 1.033 | 0.68 |
| 3_F | 10_A | 1.013 | 0.65 |
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 | |
| 3b72A | 1 | 1 | 100 | 0.038 | Contact Map |
| 2vb1A | 1 | 1 | 100 | 0.049 | Contact Map |
| 2z2fA | 1 | 0.9922 | 100 | 0.092 | Contact Map |
| 2nwdX | 1 | 1 | 100 | 0.14 | Contact Map |
| 1lmqA | 1 | 1 | 100 | 0.149 | Contact Map |
| 2goiA | 3 | 0.9845 | 100 | 0.15 | Contact Map |
| 2gv0A | 1 | 1 | 100 | 0.15 | Contact Map |
| 1qqyA | 1 | 0.9922 | 100 | 0.164 | Contact Map |
| 1yroA | 2 | 0.9457 | 100 | 0.202 | Contact Map |
| 1b9oA | 1 | 0.9457 | 100 | 0.21 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)