| Gremlin results |
| ID: | 1490466521 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 158 (144) | ||
| Sequences: | 1705 (991.9) | ||
| Seq/Len: | 11.840 | ||
| Nf(neff/√len): | 82.7 |
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: 11.840).
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 |
| 34_W | 38_F | 2.835 | 1.00 |
| 130_C | 136_V | 2.283 | 1.00 |
| 25_W | 36_L | 2.271 | 1.00 |
| 94_F | 114_D | 2.240 | 1.00 |
| 36_L | 40_V | 2.079 | 1.00 |
| 53_R | 56_R | 2.042 | 1.00 |
| 47_N | 88_G | 1.976 | 1.00 |
| 123_L | 127_V | 1.834 | 1.00 |
| 49_L | 53_R | 1.830 | 1.00 |
| 9_D | 12_K | 1.825 | 1.00 |
| 134_K | 138_G | 1.622 | 1.00 |
| 56_R | 60_A | 1.606 | 1.00 |
| 54_V | 58_L | 1.527 | 1.00 |
| 91_E | 118_S | 1.482 | 1.00 |
| 88_G | 122_G | 1.472 | 1.00 |
| 36_L | 39_P | 1.462 | 1.00 |
| 70_T | 73_K | 1.450 | 1.00 |
| 127_V | 132_L | 1.444 | 1.00 |
| 88_G | 121_Q | 1.440 | 1.00 |
| 118_S | 125_V | 1.386 | 0.99 |
| 33_W | 36_L | 1.381 | 0.99 |
| 113_F | 117_L | 1.373 | 0.99 |
| 120_F | 123_L | 1.361 | 0.99 |
| 24_Q | 39_P | 1.359 | 0.99 |
| 139_E | 142_D | 1.348 | 0.99 |
| 76_L | 79_S | 1.346 | 0.99 |
| 149_R | 152_E | 1.328 | 0.99 |
| 51_F | 76_L | 1.327 | 0.99 |
| 48_L | 52_T | 1.322 | 0.99 |
| 11_S | 14_L | 1.320 | 0.99 |
| 10_Y | 14_L | 1.308 | 0.99 |
| 122_G | 125_V | 1.265 | 0.99 |
| 82_T | 85_P | 1.262 | 0.99 |
| 90_H | 94_F | 1.261 | 0.99 |
| 51_F | 58_L | 1.256 | 0.99 |
| 57_V | 133_N | 1.251 | 0.99 |
| 7_T | 11_S | 1.230 | 0.98 |
| 10_Y | 15_D | 1.225 | 0.98 |
| 90_H | 118_S | 1.220 | 0.98 |
| 150_R | 153_L | 1.220 | 0.98 |
| 91_E | 114_D | 1.213 | 0.98 |
| 50_I | 54_V | 1.205 | 0.98 |
| 140_V | 143_P | 1.197 | 0.98 |
| 114_D | 118_S | 1.195 | 0.98 |
| 12_K | 15_D | 1.181 | 0.98 |
| 109_A | 112_F | 1.170 | 0.97 |
| 126_A | 131_F | 1.156 | 0.97 |
| 55_L | 85_P | 1.150 | 0.97 |
| 91_E | 94_F | 1.123 | 0.97 |
| 39_P | 44_I | 1.112 | 0.96 |
| 38_F | 42_L | 1.108 | 0.96 |
| 122_G | 126_A | 1.107 | 0.96 |
| 47_N | 121_Q | 1.103 | 0.96 |
| 136_V | 139_E | 1.103 | 0.96 |
| 47_N | 51_F | 1.102 | 0.96 |
| 116_F | 124_L | 1.101 | 0.96 |
| 127_V | 131_F | 1.081 | 0.95 |
| 111_L | 115_L | 1.079 | 0.95 |
| 93_V | 110_K | 1.078 | 0.95 |
| 76_L | 115_L | 1.076 | 0.95 |
| 130_C | 133_N | 1.072 | 0.95 |
| 57_V | 78_K | 1.070 | 0.95 |
| 80_T | 84_I | 1.064 | 0.95 |
| 9_D | 14_L | 1.062 | 0.95 |
| 91_E | 126_A | 1.061 | 0.95 |
| 110_K | 113_F | 1.045 | 0.94 |
| 58_L | 62_L | 1.028 | 0.94 |
| 53_R | 80_T | 1.017 | 0.93 |
| 9_D | 15_D | 1.012 | 0.93 |
| 79_S | 132_L | 1.006 | 0.93 |
| 7_T | 12_K | 1.003 | 0.93 |
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 | |
| 4k5yA | 3 | 0.7975 | 99.9 | 0.295 | Contact Map |
| 4l6rA | 1 | 0.9557 | 99.8 | 0.462 | Contact Map |
| 4jkvA | 2 | 0.8987 | 98.3 | 0.737 | Contact Map |
| 4qinA | 1 | 0.8734 | 97.7 | 0.772 | Contact Map |
| 4zwjA | 4 | 0 | 96.5 | 0.81 | Contact Map |
| 4pxzA | 1 | 0.8354 | 96.2 | 0.814 | Contact Map |
| 4mqsA | 1 | 0.8481 | 95.7 | 0.822 | Contact Map |
| 4ea3A | 2 | 0.8544 | 95.4 | 0.826 | Contact Map |
| 2z73A | 2 | 0.981 | 95.2 | 0.828 | Contact Map |
| 4xnvA | 1 | 0.8481 | 95.2 | 0.828 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)