| bmp4_mature_only |
| ID: | 1494388775 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (109) | ||
| Sequences: | 1161 (714.2) | ||
| Seq/Len: | 10.651 | ||
| Nf(neff/√len): | 68.4 |
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: 10.651).
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 | 39_G | 7.135 | 1.00 |
| 18_R | 43_F | 3.551 | 1.00 |
| 87_S | 111_E | 3.006 | 1.00 |
| 30_W | 33_W | 2.569 | 1.00 |
| 18_R | 110_V | 2.123 | 1.00 |
| 84_T | 114_G | 2.052 | 1.00 |
| 20_S | 41_Q | 2.044 | 1.00 |
| 58_N | 64_I | 2.014 | 1.00 |
| 82_V | 116_R | 1.990 | 1.00 |
| 85_E | 112_G | 1.967 | 1.00 |
| 110_V | 113_C | 1.827 | 1.00 |
| 40_Y | 108_M | 1.765 | 1.00 |
| 26_S | 38_P | 1.734 | 1.00 |
| 62_H | 66_Q | 1.721 | 1.00 |
| 85_E | 111_E | 1.605 | 1.00 |
| 95_D | 99_K | 1.539 | 1.00 |
| 84_T | 112_G | 1.472 | 1.00 |
| 63_A | 66_Q | 1.428 | 1.00 |
| 23_V | 42_A | 1.419 | 1.00 |
| 92_L | 102_L | 1.414 | 1.00 |
| 53_L | 63_A | 1.397 | 0.99 |
| 110_V | 115_C | 1.344 | 0.99 |
| 22_Y | 41_Q | 1.294 | 0.99 |
| 86_L | 92_L | 1.257 | 0.99 |
| 23_V | 55_D | 1.235 | 0.98 |
| 108_M | 113_C | 1.197 | 0.98 |
| 64_I | 67_T | 1.165 | 0.97 |
| 21_L | 43_F | 1.155 | 0.97 |
| 50_P | 57_L | 1.150 | 0.97 |
| 66_Q | 77_P | 1.140 | 0.97 |
| 24_D | 39_G | 1.115 | 0.96 |
| 19_H | 46_H | 1.114 | 0.96 |
| 90_S | 104_N | 1.109 | 0.96 |
| 42_A | 108_M | 1.105 | 0.96 |
| 93_Y | 103_K | 1.102 | 0.96 |
| 17_R | 116_R | 1.093 | 0.96 |
| 48_D | 78_K | 1.073 | 0.95 |
| 16_C | 25_F | 1.057 | 0.95 |
| 15_N | 85_E | 1.055 | 0.95 |
| 24_D | 27_D | 1.053 | 0.95 |
| 35_V | 100_V | 1.038 | 0.94 |
| 45_C | 49_C | 1.025 | 0.93 |
| 68_L | 110_V | 1.021 | 0.93 |
| 36_A | 40_Y | 1.013 | 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 | |
| 2h62A | 2 | 0.8966 | 100 | 0.033 | Contact Map |
| 4n1dA | 1 | 0.8966 | 100 | 0.037 | Contact Map |
| 3evsB | 1 | 0.8879 | 100 | 0.047 | Contact Map |
| 2r52A | 2 | 0.8966 | 100 | 0.058 | Contact Map |
| 1lxiA | 1 | 0.8879 | 100 | 0.061 | Contact Map |
| 2qcqA | 2 | 0.9138 | 100 | 0.076 | Contact Map |
| 4mplA | 1 | 0.9052 | 100 | 0.077 | Contact Map |
| 3rjrA | 4 | 0.8966 | 100 | 0.079 | Contact Map |
| 2arpA | 1 | 0.8793 | 100 | 0.107 | Contact Map |
| 3hh2A | 2 | 0.9224 | 100 | 0.163 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)