| Kdf1 |
| ID: | 1441342142 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 262 (243) | ||
| Sequences: | 2249 (2112.8) | ||
| Seq/Len: | 9.255 | ||
| Nf(neff/√len): | 135.5 |
Jackhmmer Results: (2015_08)
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: 9.255).
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 |
| 197_E | 201_R | 1.840 | 1.00 |
| 75_K | 78_K | 1.826 | 1.00 |
| 231_I | 235_R | 1.674 | 1.00 |
| 131_A | 135_E | 1.657 | 1.00 |
| 99_R | 103_N | 1.641 | 1.00 |
| 122_S | 125_K | 1.599 | 1.00 |
| 26_F | 30_N | 1.557 | 1.00 |
| 235_R | 239_E | 1.557 | 1.00 |
| 140_D | 143_K | 1.515 | 1.00 |
| 209_K | 212_Q | 1.504 | 1.00 |
| 28_R | 50_L | 1.494 | 1.00 |
| 23_Q | 27_D | 1.491 | 1.00 |
| 198_I | 203_R | 1.488 | 1.00 |
| 129_R | 132_Q | 1.487 | 1.00 |
| 52_L | 56_Q | 1.483 | 1.00 |
| 215_V | 218_K | 1.469 | 1.00 |
| 10_S | 13_I | 1.465 | 1.00 |
| 96_D | 100_E | 1.460 | 1.00 |
| 202_E | 206_R | 1.457 | 1.00 |
| 102_I | 106_K | 1.451 | 1.00 |
| 186_S | 190_D | 1.449 | 1.00 |
| 81_E | 85_E | 1.441 | 1.00 |
| 225_Q | 229_V | 1.437 | 0.99 |
| 11_T | 14_T | 1.428 | 0.99 |
| 232_K | 236_E | 1.426 | 0.99 |
| 162_D | 165_R | 1.422 | 0.99 |
| 226_D | 230_R | 1.399 | 0.99 |
| 146_Q | 150_T | 1.398 | 0.99 |
| 56_Q | 60_E | 1.392 | 0.99 |
| 219_E | 223_R | 1.382 | 0.99 |
| 221_S | 225_Q | 1.381 | 0.99 |
| 237_R | 241_Q | 1.372 | 0.99 |
| 28_R | 31_N | 1.362 | 0.99 |
| 88_E | 92_T | 1.347 | 0.99 |
| 42_S | 45_T | 1.341 | 0.99 |
| 57_T | 62_S | 1.341 | 0.99 |
| 212_Q | 216_F | 1.336 | 0.99 |
| 215_V | 219_E | 1.331 | 0.99 |
| 117_K | 121_E | 1.318 | 0.99 |
| 101_L | 104_L | 1.313 | 0.99 |
| 79_L | 83_I | 1.290 | 0.99 |
| 228_L | 236_E | 1.288 | 0.99 |
| 101_L | 105_E | 1.275 | 0.99 |
| 191_R | 194_E | 1.274 | 0.99 |
| 64_R | 67_E | 1.272 | 0.98 |
| 147_A | 150_T | 1.265 | 0.98 |
| 230_R | 234_D | 1.265 | 0.98 |
| 18_Q | 21_R | 1.247 | 0.98 |
| 210_E | 220_L | 1.244 | 0.98 |
| 68_K | 71_N | 1.243 | 0.98 |
| 47_I | 54_F | 1.242 | 0.98 |
| 243_V | 246_I | 1.241 | 0.98 |
| 125_K | 129_R | 1.234 | 0.98 |
| 216_F | 221_S | 1.231 | 0.98 |
| 147_A | 151_S | 1.231 | 0.98 |
| 171_S | 174_I | 1.226 | 0.98 |
| 70_E | 73_A | 1.224 | 0.98 |
| 216_F | 220_L | 1.221 | 0.98 |
| 161_E | 165_R | 1.220 | 0.98 |
| 11_T | 15_N | 1.220 | 0.98 |
| 239_E | 245_L | 1.210 | 0.98 |
| 124_K | 128_Q | 1.205 | 0.98 |
| 236_E | 239_E | 1.205 | 0.98 |
| 111_L | 115_N | 1.204 | 0.98 |
| 190_D | 194_E | 1.196 | 0.98 |
| 133_Q | 136_A | 1.194 | 0.97 |
| 179_E | 183_K | 1.194 | 0.97 |
| 192_I | 195_L | 1.193 | 0.97 |
| 121_E | 125_K | 1.191 | 0.97 |
| 128_Q | 186_S | 1.191 | 0.97 |
| 91_E | 95_N | 1.185 | 0.97 |
| 135_E | 139_V | 1.180 | 0.97 |
| 90_S | 93_Q | 1.178 | 0.97 |
| 175_Q | 178_Q | 1.171 | 0.97 |
| 87_S | 90_S | 1.169 | 0.97 |
| 172_Y | 175_Q | 1.169 | 0.97 |
| 77_R | 81_E | 1.163 | 0.97 |
| 225_Q | 231_I | 1.161 | 0.97 |
| 129_R | 133_Q | 1.151 | 0.97 |
| 150_T | 154_Y | 1.147 | 0.97 |
| 51_I | 54_F | 1.142 | 0.96 |
| 9_N | 12_Q | 1.142 | 0.96 |
| 135_E | 138_T | 1.142 | 0.96 |
| 33_Q | 37_E | 1.139 | 0.96 |
| 44_F | 48_T | 1.138 | 0.96 |
| 238_N | 242_I | 1.129 | 0.96 |
| 227_N | 230_R | 1.120 | 0.96 |
| 21_R | 24_K | 1.117 | 0.96 |
| 238_N | 241_Q | 1.114 | 0.96 |
| 235_R | 238_N | 1.112 | 0.96 |
| 28_R | 32_I | 1.110 | 0.96 |
| 10_S | 14_T | 1.106 | 0.96 |
| 13_I | 16_Q | 1.104 | 0.95 |
| 245_L | 249_V | 1.104 | 0.95 |
| 14_T | 22_V | 1.104 | 0.95 |
| 201_R | 204_K | 1.103 | 0.95 |
| 200_E | 203_R | 1.097 | 0.95 |
| 19_I | 22_V | 1.095 | 0.95 |
| 125_K | 128_Q | 1.094 | 0.95 |
| 31_N | 35_S | 1.093 | 0.95 |
| 127_A | 131_A | 1.085 | 0.95 |
| 27_D | 31_N | 1.084 | 0.95 |
| 15_N | 19_I | 1.083 | 0.95 |
| 187_Q | 190_D | 1.083 | 0.95 |
| 18_Q | 22_V | 1.082 | 0.95 |
| 175_Q | 179_E | 1.076 | 0.95 |
| 113_E | 117_K | 1.075 | 0.95 |
| 22_V | 25_V | 1.072 | 0.94 |
| 40_K | 43_R | 1.071 | 0.94 |
| 56_Q | 59_N | 1.071 | 0.94 |
| 76_L | 79_L | 1.070 | 0.94 |
| 200_E | 204_K | 1.069 | 0.94 |
| 34_N | 38_G | 1.063 | 0.94 |
| 114_L | 117_K | 1.063 | 0.94 |
| 173_E | 181_E | 1.060 | 0.94 |
| 14_T | 19_I | 1.058 | 0.94 |
| 103_N | 107_N | 1.057 | 0.94 |
| 16_Q | 19_I | 1.054 | 0.94 |
| 107_N | 111_L | 1.054 | 0.94 |
| 60_E | 64_R | 1.040 | 0.93 |
| 71_N | 74_E | 1.037 | 0.93 |
| 28_R | 33_Q | 1.035 | 0.93 |
| 171_S | 175_Q | 1.033 | 0.93 |
| 154_Y | 157_T | 1.030 | 0.93 |
| 243_V | 247_E | 1.025 | 0.93 |
| 93_Q | 96_D | 1.024 | 0.93 |
| 13_I | 17_S | 1.021 | 0.92 |
| 95_N | 99_R | 1.016 | 0.92 |
| 144_E | 147_A | 1.010 | 0.92 |
| 20_D | 24_K | 1.009 | 0.92 |
| 127_A | 185_H | 1.005 | 0.92 |
| 59_N | 63_A | 1.003 | 0.91 |
| 235_R | 245_L | 1.003 | 0.91 |
| 7_I | 11_T | 1.001 | 0.91 |
| 166_L | 169_E | 1.001 | 0.91 |
| 234_D | 237_R | 1.001 | 0.91 |
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 | |
| 3s84A | 2 | 0.874 | 97.9 | 0.633 | Contact Map |
| 2a01A | 3 | 0.9046 | 97.5 | 0.666 | Contact Map |
| 2l7bA | 1 | 0.9504 | 97.5 | 0.667 | Contact Map |
| 2lemA | 1 | 0.8244 | 96.3 | 0.718 | Contact Map |
| 1i84S | 2 | 0.1336 | 95.6 | 0.733 | Contact Map |
| 3r2pA | 1 | 0.6832 | 92.6 | 0.768 | Contact Map |
| 1eq1A | 1 | 0.6336 | 92.5 | 0.768 | Contact Map |
| 4uxvA | 1 | 0.9351 | 92.4 | 0.769 | Contact Map |
| 1c1gA | 4 | 0.9504 | 86 | 0.797 | Contact Map |
| 1nfnA | 1 | 0.4962 | 80.7 | 0.809 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)