| ctr1 |
| ID: | 1483841206 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (153) | ||
| Sequences: | 268 (204.1) | ||
| Seq/Len: | 1.752 | ||
| Nf(neff/√len): | 16.5 |
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: 1.752).
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 |
| 77_F | 170_T | 2.838 | 1.00 |
| 49_F | 158_G | 2.422 | 1.00 |
| 172_Y | 176_S | 2.118 | 0.99 |
| 146_S | 153_F | 2.114 | 0.99 |
| 57_L | 156_Y | 1.948 | 0.98 |
| 56_L | 72_A | 1.918 | 0.98 |
| 76_V | 152_I | 1.764 | 0.96 |
| 153_F | 161_C | 1.746 | 0.96 |
| 67_G | 71_G | 1.653 | 0.94 |
| 69_M | 159_Y | 1.634 | 0.94 |
| 76_V | 84_E | 1.604 | 0.93 |
| 91_E | 94_L | 1.600 | 0.93 |
| 79_L | 145_I | 1.528 | 0.90 |
| 48_Y | 54_V | 1.510 | 0.89 |
| 84_E | 87_K | 1.486 | 0.88 |
| 47_F | 158_G | 1.475 | 0.88 |
| 47_F | 161_C | 1.456 | 0.87 |
| 84_E | 139_H | 1.455 | 0.87 |
| 61_L | 72_A | 1.453 | 0.87 |
| 56_L | 155_T | 1.431 | 0.86 |
| 132_H | 146_S | 1.431 | 0.86 |
| 143_V | 153_F | 1.425 | 0.85 |
| 71_G | 127_M | 1.409 | 0.85 |
| 38_S | 109_P | 1.407 | 0.84 |
| 152_I | 155_T | 1.368 | 0.82 |
| 136_T | 173_F | 1.361 | 0.82 |
| 49_F | 162_I | 1.347 | 0.81 |
| 150_M | 154_M | 1.346 | 0.81 |
| 67_G | 74_V | 1.332 | 0.80 |
| 152_I | 160_L | 1.331 | 0.80 |
| 47_F | 80_A | 1.305 | 0.78 |
| 77_F | 166_A | 1.304 | 0.78 |
| 73_F | 163_A | 1.300 | 0.77 |
| 140_I | 169_G | 1.293 | 0.77 |
| 132_H | 136_T | 1.271 | 0.75 |
| 144_V | 148_F | 1.244 | 0.73 |
| 86_L | 93_L | 1.244 | 0.73 |
| 184_D | 187_E | 1.236 | 0.72 |
| 125_Q | 131_P | 1.231 | 0.72 |
| 132_H | 177_W | 1.219 | 0.71 |
| 41_M | 44_P | 1.217 | 0.71 |
| 81_M | 170_T | 1.199 | 0.69 |
| 71_G | 175_F | 1.192 | 0.68 |
| 83_Y | 87_K | 1.186 | 0.68 |
| 112_N | 117_M | 1.184 | 0.67 |
| 88_I | 92_S | 1.176 | 0.67 |
| 64_N | 68_E | 1.175 | 0.67 |
| 77_F | 163_A | 1.157 | 0.65 |
| 156_Y | 160_L | 1.152 | 0.64 |
| 177_W | 186_T | 1.141 | 0.63 |
| 61_L | 157_N | 1.137 | 0.63 |
| 173_F | 177_W | 1.133 | 0.62 |
| 73_F | 162_I | 1.131 | 0.62 |
| 43_M | 155_T | 1.127 | 0.62 |
| 153_F | 164_V | 1.109 | 0.60 |
| 57_L | 160_L | 1.106 | 0.60 |
| 65_T | 175_F | 1.101 | 0.59 |
| 55_E | 63_I | 1.099 | 0.59 |
| 91_E | 177_W | 1.098 | 0.59 |
| 96_K | 138_L | 1.090 | 0.58 |
| 141_I | 147_Y | 1.080 | 0.57 |
| 73_F | 159_Y | 1.080 | 0.57 |
| 144_V | 165_A | 1.079 | 0.57 |
| 92_S | 95_R | 1.073 | 0.56 |
| 70_A | 145_I | 1.070 | 0.56 |
| 80_A | 149_L | 1.066 | 0.56 |
| 186_T | 190_H | 1.062 | 0.55 |
| 187_E | 190_H | 1.046 | 0.53 |
| 88_I | 94_L | 1.044 | 0.53 |
| 72_A | 160_L | 1.042 | 0.53 |
| 49_F | 60_G | 1.034 | 0.52 |
| 54_V | 156_Y | 1.017 | 0.50 |
| 183_V | 187_E | 1.014 | 0.50 |
| 136_T | 139_H | 1.013 | 0.50 |
| 65_T | 68_E | 1.010 | 0.49 |
| 95_R | 102_R | 1.009 | 0.49 |
| 128_L | 174_L | 1.008 | 0.49 |
| 141_I | 182_V | 1.005 | 0.49 |
| 156_Y | 190_H | 1.002 | 0.49 |
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 | |
| 2ls3A | 1 | 0.1526 | 98.6 | 0.829 | Contact Map |
| 2ls4A | 1 | 0.1263 | 97.9 | 0.859 | Contact Map |
| 2ls2A | 1 | 0.1316 | 96.3 | 0.891 | Contact Map |
| 4hw9A | 7 | 0.4947 | 34.8 | 0.946 | Contact Map |
| 1pp9J | 2 | 0.2632 | 4.9 | 0.964 | Contact Map |
| 3nk4C | 2 | 0.0526 | 4.7 | 0.964 | Contact Map |
| 4zw9A | 1 | 0 | 4.3 | 0.964 | Contact Map |
| 3tj1A | 2 | 0.5789 | 4.2 | 0.965 | Contact Map |
| 2k21A | 1 | 0.5684 | 3.5 | 0.966 | Contact Map |
| 3zfwX | 2 | 0.0316 | 3.3 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)