| BI_test -force run |
| ID: | 1483806980 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (140) | ||
| Sequences: | 70 (48.1) | ||
| Seq/Len: | 0.500 | ||
| Nf(neff/√len): | 4.1 |
Jackhmmer Results: (2016_04)
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: 0.500).
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 |
| 14_G | 39_Q | 1.893 | 0.81 |
| 12_R | 81_V | 1.810 | 0.77 |
| 32_C | 44_E | 1.750 | 0.74 |
| 32_C | 36_Y | 1.729 | 0.72 |
| 36_Y | 39_Q | 1.729 | 0.72 |
| 90_M | 110_F | 1.679 | 0.69 |
| 32_C | 42_T | 1.627 | 0.66 |
| 98_E | 125_K | 1.612 | 0.64 |
| 34_F | 42_T | 1.556 | 0.60 |
| 11_V | 14_G | 1.541 | 0.59 |
| 34_F | 77_F | 1.518 | 0.58 |
| 86_I | 131_L | 1.501 | 0.56 |
| 10_D | 15_G | 1.483 | 0.55 |
| 97_F | 114_K | 1.471 | 0.54 |
| 34_F | 44_E | 1.446 | 0.52 |
| 16_V | 21_S | 1.439 | 0.52 |
| 103_V | 112_V | 1.430 | 0.51 |
| 81_V | 135_A | 1.412 | 0.49 |
| 32_C | 46_W | 1.410 | 0.49 |
| 30_Y | 49_S | 1.406 | 0.49 |
| 36_Y | 44_E | 1.365 | 0.46 |
| 137_A | 140_T | 1.359 | 0.45 |
| 132_V | 135_A | 1.351 | 0.45 |
| 17_V | 35_T | 1.347 | 0.45 |
| 122_G | 130_K | 1.346 | 0.44 |
| 81_V | 119_H | 1.344 | 0.44 |
| 104_P | 110_F | 1.328 | 0.43 |
| 110_F | 115_T | 1.324 | 0.43 |
| 75_T | 79_A | 1.320 | 0.42 |
| 39_Q | 42_T | 1.290 | 0.40 |
| 57_Q | 112_V | 1.216 | 0.35 |
| 32_C | 40_G | 1.208 | 0.34 |
| 32_C | 41_G | 1.208 | 0.34 |
| 63_I | 79_A | 1.183 | 0.33 |
| 32_C | 61_C | 1.182 | 0.33 |
| 49_S | 139_R | 1.177 | 0.32 |
| 34_F | 39_Q | 1.176 | 0.32 |
| 46_W | 50_L | 1.171 | 0.32 |
| 4_P | 25_G | 1.166 | 0.31 |
| 36_Y | 42_T | 1.164 | 0.31 |
| 136_K | 139_R | 1.163 | 0.31 |
| 82_R | 123_A | 1.154 | 0.31 |
| 97_F | 100_E | 1.152 | 0.31 |
| 44_E | 61_C | 1.125 | 0.29 |
| 107_T | 121_P | 1.109 | 0.28 |
| 109_E | 122_G | 1.107 | 0.28 |
| 50_L | 137_A | 1.106 | 0.28 |
| 11_V | 129_S | 1.096 | 0.27 |
| 40_G | 71_Y | 1.096 | 0.27 |
| 41_G | 71_Y | 1.096 | 0.27 |
| 46_W | 65_R | 1.086 | 0.26 |
| 15_G | 66_P | 1.085 | 0.26 |
| 59_F | 89_A | 1.080 | 0.26 |
| 81_V | 133_I | 1.079 | 0.26 |
| 85_E | 114_K | 1.078 | 0.26 |
| 114_K | 140_T | 1.078 | 0.26 |
| 97_F | 107_T | 1.073 | 0.26 |
| 124_F | 128_L | 1.069 | 0.25 |
| 105_L | 124_F | 1.068 | 0.25 |
| 53_S | 60_T | 1.065 | 0.25 |
| 24_V | 38_S | 1.060 | 0.25 |
| 117_V | 124_F | 1.049 | 0.24 |
| 5_T | 22_H | 1.031 | 0.23 |
| 48_M | 55_D | 1.019 | 0.23 |
| 34_F | 46_W | 1.016 | 0.22 |
| 32_C | 39_Q | 1.016 | 0.22 |
| 114_K | 125_K | 1.015 | 0.22 |
| 11_V | 18_H | 1.011 | 0.22 |
| 111_E | 115_T | 1.010 | 0.22 |
| 7_V | 24_V | 1.010 | 0.22 |
| 14_G | 36_Y | 1.009 | 0.22 |
| 7_V | 16_V | 1.005 | 0.22 |
| 34_F | 61_C | 1.002 | 0.22 |
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 | |
| 1qfoA | 3 | 0.507 | 14.4 | 0.954 | Contact Map |
| 1vcbB | 4 | 0.2324 | 9.7 | 0.957 | Contact Map |
| 1mfaH | 1 | 0.4859 | 5.2 | 0.962 | Contact Map |
| 4rwhA | 1 | 0.4577 | 4.3 | 0.964 | Contact Map |
| 4kkiA | 1 | 0.6479 | 3.9 | 0.964 | Contact Map |
| 1sr4A | 1 | 0.4155 | 3.9 | 0.964 | Contact Map |
| 2pw0A | 2 | 0.5141 | 3.4 | 0.966 | Contact Map |
| 2pmvA | 4 | 0.6408 | 3.2 | 0.966 | Contact Map |
| 3bp6A | 1 | 0.493 | 3 | 0.966 | Contact Map |
| 1f32A | 1 | 0.331 | 2.9 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)