| tm2 |
| ID: | 1507728746 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (218) | ||
| Sequences: | 1078 (779.2) | ||
| Seq/Len: | 4.945 | ||
| Nf(neff/√len): | 52.8 |
Jackhmmer Results: (2016_04)
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: 4.945).
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 |
| 110_L | 137_A | 3.655 | 1.00 |
| 117_A | 137_A | 3.176 | 1.00 |
| 117_A | 134_S | 2.674 | 1.00 |
| 94_L | 109_T | 2.286 | 1.00 |
| 177_L | 203_A | 2.251 | 1.00 |
| 5_V | 9_L | 2.206 | 1.00 |
| 55_S | 123_K | 2.136 | 1.00 |
| 6_L | 10_L | 2.111 | 1.00 |
| 64_R | 128_E | 2.095 | 1.00 |
| 49_G | 88_G | 2.047 | 1.00 |
| 38_A | 101_R | 1.989 | 1.00 |
| 8_L | 12_C | 1.892 | 1.00 |
| 41_L | 98_L | 1.886 | 1.00 |
| 53_L | 88_G | 1.884 | 1.00 |
| 82_L | 209_G | 1.791 | 1.00 |
| 106_W | 141_A | 1.771 | 1.00 |
| 96_Q | 162_Y | 1.753 | 1.00 |
| 55_S | 129_E | 1.715 | 1.00 |
| 123_K | 129_E | 1.714 | 1.00 |
| 56_G | 84_A | 1.686 | 0.99 |
| 110_L | 141_A | 1.664 | 0.99 |
| 184_V | 190_L | 1.633 | 0.99 |
| 45_V | 98_L | 1.617 | 0.99 |
| 137_A | 141_A | 1.566 | 0.99 |
| 123_K | 126_D | 1.530 | 0.99 |
| 111_V | 115_V | 1.518 | 0.99 |
| 48_S | 133_L | 1.500 | 0.98 |
| 114_L | 137_A | 1.459 | 0.98 |
| 41_L | 143_F | 1.401 | 0.97 |
| 46_F | 92_L | 1.363 | 0.97 |
| 109_T | 113_L | 1.350 | 0.96 |
| 186_Y | 189_Q | 1.346 | 0.96 |
| 1_L | 5_V | 1.345 | 0.96 |
| 38_A | 42_A | 1.341 | 0.96 |
| 46_F | 95_A | 1.315 | 0.96 |
| 189_Q | 192_W | 1.297 | 0.95 |
| 23_L | 27_R | 1.294 | 0.95 |
| 9_L | 13_L | 1.288 | 0.95 |
| 21_R | 25_V | 1.265 | 0.94 |
| 58_T | 129_E | 1.260 | 0.94 |
| 42_A | 99_R | 1.250 | 0.94 |
| 188_N | 192_W | 1.245 | 0.94 |
| 55_S | 128_E | 1.244 | 0.94 |
| 127_W | 131_S | 1.230 | 0.93 |
| 13_L | 25_V | 1.227 | 0.93 |
| 173_S | 177_L | 1.222 | 0.93 |
| 56_G | 85_S | 1.214 | 0.93 |
| 83_V | 119_L | 1.209 | 0.92 |
| 98_L | 106_W | 1.190 | 0.92 |
| 24_W | 27_R | 1.186 | 0.91 |
| 188_N | 191_W | 1.184 | 0.91 |
| 95_A | 113_L | 1.178 | 0.91 |
| 83_V | 86_L | 1.175 | 0.91 |
| 103_S | 150_P | 1.167 | 0.91 |
| 12_C | 16_L | 1.167 | 0.91 |
| 56_G | 64_R | 1.161 | 0.90 |
| 87_I | 112_L | 1.159 | 0.90 |
| 172_A | 176_L | 1.158 | 0.90 |
| 124_G | 129_E | 1.154 | 0.90 |
| 53_L | 57_A | 1.149 | 0.90 |
| 167_I | 171_G | 1.139 | 0.89 |
| 10_L | 138_A | 1.137 | 0.89 |
| 199_D | 207_A | 1.134 | 0.89 |
| 103_S | 152_R | 1.123 | 0.88 |
| 12_C | 39_P | 1.122 | 0.88 |
| 186_Y | 194_F | 1.111 | 0.87 |
| 97_G | 105_A | 1.104 | 0.87 |
| 210_S | 213_L | 1.104 | 0.87 |
| 169_V | 215_L | 1.091 | 0.86 |
| 98_L | 140_L | 1.082 | 0.86 |
| 86_L | 91_C | 1.081 | 0.86 |
| 66_E | 144_R | 1.070 | 0.85 |
| 175_W | 190_L | 1.068 | 0.85 |
| 209_G | 213_L | 1.058 | 0.84 |
| 77_I | 196_L | 1.056 | 0.84 |
| 117_A | 212_L | 1.054 | 0.84 |
| 208_L | 211_C | 1.051 | 0.83 |
| 46_F | 165_A | 1.051 | 0.83 |
| 68_L | 73_P | 1.046 | 0.83 |
| 89_V | 93_L | 1.037 | 0.82 |
| 98_L | 109_T | 1.037 | 0.82 |
| 126_D | 129_E | 1.035 | 0.82 |
| 138_A | 142_M | 1.032 | 0.82 |
| 187_S | 191_W | 1.025 | 0.81 |
| 106_W | 110_L | 1.022 | 0.81 |
| 102_L | 106_W | 1.021 | 0.81 |
| 78_D | 202_R | 1.017 | 0.80 |
| 102_L | 149_R | 1.016 | 0.80 |
| 25_V | 218_A | 1.016 | 0.80 |
| 118_L | 178_L | 1.015 | 0.80 |
| 20_A | 26_T | 1.015 | 0.80 |
| 11_A | 42_A | 1.006 | 0.79 |
| 22_R | 27_R | 1.003 | 0.79 |
| 9_L | 16_L | 1.001 | 0.79 |
| 212_L | 215_L | 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 | |
| 4us3A | 1 | 0.9502 | 41.6 | 0.923 | Contact Map |
| 2ostA | 4 | 0.2262 | 6.6 | 0.947 | Contact Map |
| 3nd0A | 2 | 0.2941 | 6.3 | 0.947 | Contact Map |
| 4cadC | 4 | 0.6606 | 5.7 | 0.949 | Contact Map |
| 4yayA | 1 | 0 | 5 | 0.95 | Contact Map |
| 4eneA | 2 | 0.3529 | 4.5 | 0.951 | Contact Map |
| 1lnqA | 8 | 0.2851 | 4.4 | 0.951 | Contact Map |
| 3dh4A | 4 | 0.9638 | 4.2 | 0.952 | Contact Map |
| 2z73A | 2 | 0.9412 | 3 | 0.955 | Contact Map |
| 2xq2A | 1 | 0.9638 | 2.9 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)