| BMP4 |
| ID: | 1494626512 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (109) | ||
| Sequences: | 1163 (715.5) | ||
| Seq/Len: | 10.670 | ||
| Nf(neff/√len): | 68.5 |
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: 10.670).
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 | 7.108 | 1.00 |
| 18_R | 43_F | 3.550 | 1.00 |
| 87_S | 111_E | 3.003 | 1.00 |
| 30_W | 33_W | 2.578 | 1.00 |
| 84_T | 114_G | 2.102 | 1.00 |
| 18_R | 110_V | 2.080 | 1.00 |
| 20_S | 41_Q | 2.040 | 1.00 |
| 58_N | 64_I | 2.004 | 1.00 |
| 85_E | 112_G | 1.949 | 1.00 |
| 82_V | 116_R | 1.875 | 1.00 |
| 110_V | 113_C | 1.846 | 1.00 |
| 40_Y | 108_M | 1.765 | 1.00 |
| 26_S | 38_P | 1.721 | 1.00 |
| 62_H | 66_Q | 1.685 | 1.00 |
| 85_E | 111_E | 1.589 | 1.00 |
| 95_D | 99_K | 1.492 | 1.00 |
| 84_T | 112_G | 1.460 | 1.00 |
| 92_L | 102_L | 1.426 | 1.00 |
| 110_V | 115_C | 1.424 | 1.00 |
| 23_V | 42_A | 1.416 | 1.00 |
| 63_A | 66_Q | 1.410 | 1.00 |
| 53_L | 63_A | 1.391 | 0.99 |
| 22_Y | 41_Q | 1.254 | 0.99 |
| 86_L | 92_L | 1.249 | 0.99 |
| 50_P | 57_L | 1.234 | 0.98 |
| 108_M | 113_C | 1.195 | 0.98 |
| 66_Q | 77_P | 1.170 | 0.97 |
| 21_L | 43_F | 1.164 | 0.97 |
| 42_A | 108_M | 1.158 | 0.97 |
| 19_H | 46_H | 1.141 | 0.97 |
| 93_Y | 103_K | 1.127 | 0.97 |
| 64_I | 67_T | 1.126 | 0.97 |
| 15_N | 85_E | 1.108 | 0.96 |
| 17_R | 116_R | 1.104 | 0.96 |
| 90_S | 104_N | 1.096 | 0.96 |
| 23_V | 55_D | 1.088 | 0.96 |
| 48_D | 78_K | 1.088 | 0.96 |
| 24_D | 39_G | 1.080 | 0.95 |
| 89_I | 109_V | 1.065 | 0.95 |
| 45_C | 49_C | 1.054 | 0.95 |
| 36_A | 40_Y | 1.051 | 0.94 |
| 35_V | 100_V | 1.044 | 0.94 |
| 16_C | 25_F | 1.043 | 0.94 |
| 24_D | 27_D | 1.037 | 0.94 |
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 | 0.036 | Contact Map |
| 4n1dA | 1 | 0.8966 | 100 | 0.038 | Contact Map |
| 3evsB | 1 | 0.8879 | 100 | 0.049 | Contact Map |
| 1lxiA | 1 | 0.8879 | 100 | 0.055 | Contact Map |
| 2r52A | 2 | 0.8966 | 100 | 0.063 | Contact Map |
| 2qcqA | 2 | 0.9138 | 100 | 0.08 | Contact Map |
| 3rjrA | 4 | 0.8966 | 100 | 0.081 | Contact Map |
| 4mplA | 1 | 0.9052 | 100 | 0.081 | Contact Map |
| 2arpA | 1 | 0.8793 | 100 | 0.109 | Contact Map |
| 3hh2A | 2 | 0.9224 | 100 | 0.165 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)