| T0826 1-200 |
| ID: | 1403941927 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (194) | ||
| Sequences: | 475 (377.6) | ||
| Seq/Len: | 2.448 | ||
| Nf(neff/√len): | 27.1 |
Jackhmmer Results: (2014_04_16)
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: 2.448).
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 |
| 62_N | 162_S | 3.245 | 1.00 |
| 131_G | 135_A | 3.008 | 1.00 |
| 82_L | 138_Y | 2.710 | 1.00 |
| 52_T | 177_Y | 2.438 | 1.00 |
| 87_A | 127_I | 2.308 | 1.00 |
| 23_S | 65_F | 2.152 | 1.00 |
| 79_P | 139_I | 2.135 | 1.00 |
| 91_Q | 118_L | 2.120 | 1.00 |
| 79_P | 138_Y | 2.079 | 1.00 |
| 79_P | 135_A | 1.987 | 0.99 |
| 59_F | 165_C | 1.961 | 0.99 |
| 173_Q | 177_Y | 1.942 | 0.99 |
| 91_Q | 99_F | 1.868 | 0.99 |
| 15_L | 138_Y | 1.780 | 0.98 |
| 92_E | 99_F | 1.752 | 0.98 |
| 151_E | 155_R | 1.718 | 0.98 |
| 49_F | 177_Y | 1.715 | 0.98 |
| 152_L | 160_A | 1.691 | 0.97 |
| 22_Y | 27_L | 1.667 | 0.97 |
| 63_F | 159_A | 1.616 | 0.96 |
| 71_P | 75_K | 1.608 | 0.96 |
| 94_F | 138_Y | 1.531 | 0.95 |
| 31_F | 185_K | 1.526 | 0.94 |
| 62_N | 158_L | 1.496 | 0.94 |
| 95_F | 153_L | 1.461 | 0.93 |
| 68_I | 77_L | 1.412 | 0.91 |
| 19_L | 78_I | 1.411 | 0.91 |
| 63_F | 166_A | 1.402 | 0.90 |
| 24_S | 58_F | 1.398 | 0.90 |
| 63_F | 163_F | 1.397 | 0.90 |
| 31_F | 192_V | 1.367 | 0.89 |
| 11_G | 84_I | 1.332 | 0.87 |
| 15_L | 78_I | 1.331 | 0.87 |
| 188_T | 198_G | 1.321 | 0.86 |
| 99_F | 118_L | 1.298 | 0.85 |
| 75_K | 81_I | 1.286 | 0.84 |
| 170_A | 183_N | 1.258 | 0.83 |
| 175_Q | 183_N | 1.251 | 0.82 |
| 59_F | 169_I | 1.228 | 0.80 |
| 23_S | 172_L | 1.208 | 0.79 |
| 161_V | 164_L | 1.204 | 0.79 |
| 156_L | 160_A | 1.202 | 0.78 |
| 20_S | 27_L | 1.197 | 0.78 |
| 128_V | 132_V | 1.179 | 0.77 |
| 24_S | 27_L | 1.176 | 0.76 |
| 31_F | 35_V | 1.176 | 0.76 |
| 71_P | 190_L | 1.174 | 0.76 |
| 136_L | 140_A | 1.164 | 0.75 |
| 129_C | 136_L | 1.161 | 0.75 |
| 60_L | 199_A | 1.158 | 0.75 |
| 31_F | 57_L | 1.157 | 0.75 |
| 100_N | 103_M | 1.138 | 0.73 |
| 68_I | 178_A | 1.123 | 0.72 |
| 140_A | 144_K | 1.117 | 0.71 |
| 127_I | 132_V | 1.116 | 0.71 |
| 31_F | 92_E | 1.114 | 0.71 |
| 165_C | 168_G | 1.111 | 0.70 |
| 192_V | 198_G | 1.103 | 0.70 |
| 174_Y | 191_I | 1.101 | 0.69 |
| 104_L | 175_Q | 1.095 | 0.69 |
| 22_Y | 92_E | 1.094 | 0.69 |
| 179_S | 183_N | 1.088 | 0.68 |
| 119_I | 124_V | 1.085 | 0.68 |
| 16_I | 155_R | 1.076 | 0.67 |
| 94_F | 122_G | 1.071 | 0.66 |
| 80_L | 84_I | 1.065 | 0.66 |
| 86_A | 131_G | 1.062 | 0.65 |
| 31_F | 198_G | 1.060 | 0.65 |
| 163_F | 167_L | 1.058 | 0.65 |
| 7_R | 140_A | 1.056 | 0.65 |
| 63_F | 155_R | 1.055 | 0.65 |
| 145_Y | 151_E | 1.053 | 0.64 |
| 169_I | 183_N | 1.052 | 0.64 |
| 48_I | 173_Q | 1.046 | 0.64 |
| 52_T | 57_L | 1.044 | 0.63 |
| 185_K | 194_S | 1.042 | 0.63 |
| 23_S | 81_I | 1.040 | 0.63 |
| 30_A | 93_I | 1.037 | 0.63 |
| 103_M | 106_N | 1.037 | 0.63 |
| 190_L | 195_N | 1.027 | 0.61 |
| 143_V | 159_A | 1.026 | 0.61 |
| 83_V | 160_A | 1.020 | 0.61 |
| 180_F | 195_N | 1.018 | 0.60 |
| 168_G | 172_L | 1.018 | 0.60 |
| 85_S | 196_F | 1.015 | 0.60 |
| 118_L | 123_Y | 1.014 | 0.60 |
| 32_F | 192_V | 1.009 | 0.59 |
| 75_K | 79_P | 1.006 | 0.59 |
| 101_K | 113_A | 1.002 | 0.59 |
| 15_L | 75_K | 1.000 | 0.58 |
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 | |
| 4humA | 1 | 0.83 | 4.5 | 0.966 | Contact Map |
| 4httA | 2 | 0.27 | 4.2 | 0.966 | Contact Map |
| 2ww9C | 1 | 0.105 | 4.1 | 0.966 | Contact Map |
| 4lz6A | 1 | 0.835 | 4.1 | 0.966 | Contact Map |
| 1fmeA | 1 | 0.115 | 4 | 0.967 | Contact Map |
| 3wajA | 1 | 0.755 | 3.9 | 0.967 | Contact Map |
| 2wwbC | 1 | 0.18 | 3.5 | 0.967 | Contact Map |
| 3buaE | 4 | 0.08 | 3.3 | 0.968 | Contact Map |
| 3mktA | 2 | 0.82 | 3 | 0.969 | Contact Map |
| 2a65A | 1 | 0.615 | 3 | 0.969 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)