| VbhT |
| ID: | 1434709168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 199 (189) | ||
| Sequences: | 949 (738.2) | ||
| Seq/Len: | 5.021 | ||
| Nf(neff/√len): | 53.7 |
HHblits Results: (2013_03)
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: 5.021).
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 |
| 58_L | 79_T | 3.457 | 1.00 |
| 134_N | 147_L | 2.878 | 1.00 |
| 144_G | 148_R | 2.594 | 1.00 |
| 83_D | 94_Y | 2.343 | 1.00 |
| 111_E | 125_R | 2.266 | 1.00 |
| 80_R | 84_I | 2.139 | 1.00 |
| 137_H | 145_R | 2.060 | 1.00 |
| 79_T | 101_A | 2.028 | 1.00 |
| 130_M | 172_M | 2.028 | 1.00 |
| 43_R | 70_G | 2.019 | 1.00 |
| 137_H | 144_G | 1.974 | 1.00 |
| 104_I | 129_Y | 1.954 | 1.00 |
| 86_K | 141_E | 1.881 | 1.00 |
| 133_L | 147_L | 1.847 | 1.00 |
| 178_E | 186_L | 1.806 | 1.00 |
| 127_G | 188_S | 1.785 | 1.00 |
| 141_E | 145_R | 1.776 | 1.00 |
| 64_I | 146_T | 1.734 | 1.00 |
| 58_L | 101_A | 1.725 | 1.00 |
| 92_A | 100_Y | 1.701 | 1.00 |
| 24_L | 39_F | 1.659 | 0.99 |
| 43_R | 46_E | 1.649 | 0.99 |
| 100_Y | 103_Q | 1.603 | 0.99 |
| 44_S | 149_E | 1.574 | 0.99 |
| 131_G | 179_S | 1.547 | 0.99 |
| 66_K | 70_G | 1.538 | 0.99 |
| 134_N | 144_G | 1.531 | 0.99 |
| 178_E | 183_N | 1.526 | 0.99 |
| 151_I | 191_I | 1.424 | 0.98 |
| 31_R | 34_R | 1.417 | 0.98 |
| 172_M | 176_S | 1.415 | 0.98 |
| 124_Q | 188_S | 1.411 | 0.98 |
| 62_K | 79_T | 1.404 | 0.97 |
| 91_F | 144_G | 1.376 | 0.97 |
| 168_E | 171_E | 1.320 | 0.96 |
| 24_L | 35_V | 1.315 | 0.96 |
| 138_P | 144_G | 1.300 | 0.95 |
| 61_M | 105_T | 1.286 | 0.95 |
| 149_E | 152_W | 1.258 | 0.94 |
| 120_N | 192_R | 1.251 | 0.94 |
| 138_P | 148_R | 1.244 | 0.94 |
| 62_K | 78_K | 1.242 | 0.94 |
| 82_V | 140_R | 1.241 | 0.94 |
| 185_D | 189_A | 1.235 | 0.94 |
| 134_N | 176_S | 1.214 | 0.93 |
| 104_I | 136_L | 1.212 | 0.93 |
| 189_A | 193_R | 1.202 | 0.92 |
| 137_H | 141_E | 1.201 | 0.92 |
| 54_G | 60_H | 1.195 | 0.92 |
| 97_I | 136_L | 1.189 | 0.92 |
| 89_S | 92_A | 1.171 | 0.91 |
| 114_L | 117_L | 1.168 | 0.91 |
| 145_R | 148_R | 1.159 | 0.90 |
| 131_G | 184_S | 1.158 | 0.90 |
| 47_L | 67_K | 1.155 | 0.90 |
| 73_Y | 76_A | 1.149 | 0.90 |
| 122_F | 126_A | 1.147 | 0.90 |
| 64_I | 149_E | 1.145 | 0.90 |
| 14_D | 18_G | 1.134 | 0.89 |
| 122_F | 155_A | 1.134 | 0.89 |
| 38_A | 41_Y | 1.129 | 0.89 |
| 9_N | 13_T | 1.126 | 0.89 |
| 91_F | 134_N | 1.113 | 0.88 |
| 57_D | 60_H | 1.100 | 0.87 |
| 80_R | 97_I | 1.097 | 0.87 |
| 76_A | 80_R | 1.092 | 0.87 |
| 183_N | 186_L | 1.083 | 0.86 |
| 89_S | 180_Y | 1.081 | 0.86 |
| 85_V | 162_I | 1.081 | 0.86 |
| 153_Q | 157_E | 1.081 | 0.86 |
| 13_T | 17_T | 1.080 | 0.86 |
| 58_L | 102_P | 1.063 | 0.85 |
| 130_M | 134_N | 1.060 | 0.84 |
| 67_K | 70_G | 1.059 | 0.84 |
| 187_M | 191_I | 1.057 | 0.84 |
| 112_Q | 115_R | 1.054 | 0.84 |
| 130_M | 147_L | 1.050 | 0.84 |
| 14_D | 17_T | 1.049 | 0.83 |
| 61_M | 150_F | 1.048 | 0.83 |
| 96_Q | 100_Y | 1.041 | 0.83 |
| 30_A | 34_R | 1.036 | 0.82 |
| 137_H | 148_R | 1.032 | 0.82 |
| 147_L | 150_F | 1.009 | 0.80 |
| 163_D | 166_R | 1.007 | 0.80 |
| 22_N | 25_G | 1.004 | 0.80 |
| 69_F | 73_Y | 1.000 | 0.79 |
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 | |
| 3shgA | 1 | 0.995 | 100 | 0.159 | Contact Map |
| 3zc7A | 1 | 0.9598 | 100 | 0.164 | Contact Map |
| 4npsA | 1 | 0.9598 | 100 | 0.237 | Contact Map |
| 2jk8A | 2 | 0.9749 | 100 | 0.247 | Contact Map |
| 4n67A | 1 | 0.9698 | 100 | 0.258 | Contact Map |
| 4m16A | 1 | 0.9648 | 100 | 0.258 | Contact Map |
| 4u04A | 2 | 0.9648 | 100 | 0.391 | Contact Map |
| 3cucA | 2 | 0.9749 | 100 | 0.42 | Contact Map |
| 3zlmA | 1 | 0.7688 | 100 | 0.442 | Contact Map |
| 3se5A | 4 | 0.7739 | 100 | 0.442 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)