| BaheA17330aB2 |
| ID: | 1453412757 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (132) | ||
| Sequences: | 189 (169.3) | ||
| Seq/Len: | 1.432 | ||
| Nf(neff/√len): | 14.7 |
HHblits Results: (2015_06)
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: 1.432).
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 |
| 94_K | 102_E | 2.690 | 1.00 |
| 47_V | 86_A | 2.348 | 0.99 |
| 98_R | 101_A | 1.898 | 0.97 |
| 48_Y | 56_E | 1.738 | 0.94 |
| 40_V | 43_W | 1.665 | 0.92 |
| 23_I | 123_Q | 1.631 | 0.91 |
| 39_E | 91_C | 1.617 | 0.90 |
| 133_E | 136_R | 1.583 | 0.89 |
| 44_C | 54_L | 1.514 | 0.86 |
| 87_G | 101_A | 1.508 | 0.86 |
| 13_S | 48_Y | 1.459 | 0.83 |
| 43_W | 104_G | 1.458 | 0.83 |
| 16_P | 45_K | 1.430 | 0.81 |
| 22_E | 126_I | 1.376 | 0.78 |
| 86_A | 101_A | 1.347 | 0.76 |
| 56_E | 95_T | 1.335 | 0.75 |
| 119_V | 126_I | 1.333 | 0.74 |
| 87_G | 98_R | 1.325 | 0.74 |
| 59_Q | 105_F | 1.322 | 0.74 |
| 50_N | 117_S | 1.276 | 0.70 |
| 60_E | 63_Q | 1.274 | 0.70 |
| 33_V | 119_V | 1.267 | 0.69 |
| 38_Q | 125_N | 1.265 | 0.69 |
| 56_E | 135_R | 1.263 | 0.69 |
| 22_E | 26_R | 1.233 | 0.66 |
| 55_K | 129_V | 1.227 | 0.65 |
| 65_P | 116_T | 1.226 | 0.65 |
| 44_C | 67_E | 1.209 | 0.64 |
| 13_S | 16_P | 1.201 | 0.63 |
| 23_I | 71_L | 1.195 | 0.62 |
| 57_K | 81_S | 1.179 | 0.61 |
| 47_V | 93_L | 1.166 | 0.60 |
| 78_N | 95_T | 1.147 | 0.58 |
| 31_P | 40_V | 1.138 | 0.57 |
| 129_V | 140_E | 1.124 | 0.55 |
| 13_S | 45_K | 1.114 | 0.54 |
| 58_M | 111_A | 1.113 | 0.54 |
| 61_V | 119_V | 1.110 | 0.54 |
| 127_K | 138_G | 1.110 | 0.54 |
| 18_L | 126_I | 1.110 | 0.54 |
| 18_L | 136_R | 1.094 | 0.52 |
| 85_L | 101_A | 1.085 | 0.51 |
| 22_E | 130_P | 1.074 | 0.50 |
| 43_W | 67_E | 1.070 | 0.50 |
| 61_V | 112_L | 1.054 | 0.48 |
| 41_M | 52_D | 1.053 | 0.48 |
| 83_H | 118_A | 1.047 | 0.48 |
| 78_N | 82_V | 1.043 | 0.47 |
| 20_R | 40_V | 1.043 | 0.47 |
| 15_I | 141_S | 1.043 | 0.47 |
| 34_Q | 107_H | 1.040 | 0.47 |
| 110_Q | 116_T | 1.036 | 0.46 |
| 33_V | 122_A | 1.036 | 0.46 |
| 73_R | 78_N | 1.035 | 0.46 |
| 53_V | 80_T | 1.034 | 0.46 |
| 27_M | 53_V | 1.031 | 0.46 |
| 126_I | 130_P | 1.028 | 0.46 |
| 33_V | 109_C | 1.025 | 0.45 |
| 78_N | 139_Q | 1.022 | 0.45 |
| 103_E | 121_Q | 1.022 | 0.45 |
| 33_V | 121_Q | 1.021 | 0.45 |
| 45_K | 141_S | 1.020 | 0.45 |
| 37_Q | 40_V | 1.020 | 0.45 |
| 30_N | 138_G | 1.017 | 0.45 |
| 115_Y | 127_K | 1.015 | 0.44 |
| 39_E | 114_G | 1.013 | 0.44 |
| 27_M | 84_K | 1.011 | 0.44 |
| 35_A | 83_H | 1.002 | 0.43 |
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 | |
| 4npsA | 1 | 0.0138 | 100 | 0.233 | Contact Map |
| 2lnmA | 1 | 0.4069 | 26.5 | 0.942 | Contact Map |
| 3hgfA | 3 | 0.6345 | 19.1 | 0.946 | Contact Map |
| 4hhjA | 1 | 0.8207 | 12.5 | 0.95 | Contact Map |
| 4n9gC | 4 | 0 | 8.7 | 0.954 | Contact Map |
| 2zbcA | 8 | 0.531 | 8.2 | 0.954 | Contact Map |
| 1t3wA | 2 | 0.8 | 7.5 | 0.955 | Contact Map |
| 4im9A | 3 | 0.7931 | 7.4 | 0.955 | Contact Map |
| 2llwA | 1 | 0.4897 | 6.9 | 0.956 | Contact Map |
| 1tr2A | 2 | 0.9586 | 6.8 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)