| T0767 39-312 -force run |
| ID: | 1405630090 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 274 (267) | ||
| Sequences: | 71 (61) | ||
| Seq/Len: | 0.266 | ||
| Nf(neff/√len): | 3.7 |
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: 0.266).
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 |
| 59_S | 80_I | 2.105 | 0.75 |
| 27_F | 31_H | 1.941 | 0.66 |
| 230_E | 233_K | 1.664 | 0.49 |
| 126_T | 159_Y | 1.601 | 0.45 |
| 86_I | 89_S | 1.533 | 0.41 |
| 161_L | 211_S | 1.520 | 0.40 |
| 22_K | 33_D | 1.498 | 0.38 |
| 124_N | 246_L | 1.468 | 0.37 |
| 34_K | 44_M | 1.455 | 0.36 |
| 158_Y | 233_K | 1.428 | 0.34 |
| 62_G | 71_D | 1.412 | 0.33 |
| 209_L | 253_I | 1.399 | 0.33 |
| 209_L | 215_N | 1.378 | 0.31 |
| 85_S | 89_S | 1.370 | 0.31 |
| 248_I | 258_P | 1.363 | 0.30 |
| 30_K | 52_K | 1.360 | 0.30 |
| 211_S | 218_K | 1.357 | 0.30 |
| 14_Q | 149_T | 1.335 | 0.29 |
| 54_T | 70_D | 1.323 | 0.28 |
| 78_A | 81_P | 1.318 | 0.28 |
| 126_T | 147_M | 1.315 | 0.28 |
| 102_M | 106_V | 1.314 | 0.28 |
| 10_K | 31_H | 1.313 | 0.28 |
| 129_L | 138_Y | 1.310 | 0.28 |
| 107_G | 213_K | 1.290 | 0.27 |
| 33_D | 69_C | 1.287 | 0.26 |
| 151_N | 156_N | 1.277 | 0.26 |
| 35_I | 38_R | 1.270 | 0.26 |
| 156_N | 209_L | 1.264 | 0.25 |
| 49_L | 73_D | 1.263 | 0.25 |
| 135_K | 162_T | 1.259 | 0.25 |
| 117_A | 149_T | 1.258 | 0.25 |
| 60_G | 80_I | 1.252 | 0.25 |
| 244_V | 251_K | 1.242 | 0.24 |
| 120_E | 202_R | 1.233 | 0.24 |
| 126_T | 156_N | 1.224 | 0.23 |
| 16_F | 111_S | 1.224 | 0.23 |
| 30_K | 34_K | 1.219 | 0.23 |
| 232_L | 242_L | 1.217 | 0.23 |
| 63_V | 68_H | 1.217 | 0.23 |
| 26_E | 31_H | 1.215 | 0.23 |
| 69_C | 91_S | 1.215 | 0.23 |
| 107_G | 150_Q | 1.208 | 0.23 |
| 25_I | 31_H | 1.204 | 0.22 |
| 82_F | 85_S | 1.203 | 0.22 |
| 176_Q | 179_I | 1.196 | 0.22 |
| 69_C | 87_I | 1.196 | 0.22 |
| 52_K | 70_D | 1.193 | 0.22 |
| 45_D | 150_Q | 1.190 | 0.22 |
| 150_Q | 163_A | 1.185 | 0.22 |
| 89_S | 98_K | 1.185 | 0.22 |
| 128_V | 233_K | 1.175 | 0.21 |
| 86_I | 98_K | 1.173 | 0.21 |
| 127_E | 143_E | 1.166 | 0.21 |
| 64_E | 81_P | 1.164 | 0.21 |
| 33_D | 41_Q | 1.162 | 0.21 |
| 12_V | 52_K | 1.161 | 0.21 |
| 162_T | 202_R | 1.160 | 0.21 |
| 132_Y | 145_A | 1.144 | 0.20 |
| 19_P | 23_D | 1.143 | 0.20 |
| 42_F | 81_P | 1.141 | 0.20 |
| 38_R | 86_I | 1.138 | 0.20 |
| 104_T | 134_S | 1.136 | 0.20 |
| 158_Y | 173_R | 1.134 | 0.19 |
| 49_L | 68_H | 1.133 | 0.19 |
| 69_C | 77_N | 1.131 | 0.19 |
| 37_K | 45_D | 1.130 | 0.19 |
| 18_P | 21_E | 1.129 | 0.19 |
| 33_D | 130_K | 1.126 | 0.19 |
| 135_K | 195_K | 1.123 | 0.19 |
| 61_D | 90_D | 1.116 | 0.19 |
| 222_I | 236_K | 1.112 | 0.19 |
| 59_S | 82_F | 1.107 | 0.18 |
| 28_S | 58_G | 1.105 | 0.18 |
| 80_I | 83_D | 1.104 | 0.18 |
| 224_E | 263_K | 1.102 | 0.18 |
| 9_S | 253_I | 1.102 | 0.18 |
| 54_T | 58_G | 1.102 | 0.18 |
| 44_M | 52_K | 1.101 | 0.18 |
| 20_A | 28_S | 1.096 | 0.18 |
| 138_Y | 240_H | 1.093 | 0.18 |
| 47_F | 178_L | 1.093 | 0.18 |
| 101_D | 174_Y | 1.093 | 0.18 |
| 124_N | 130_K | 1.090 | 0.18 |
| 141_Y | 210_F | 1.087 | 0.18 |
| 202_R | 242_L | 1.086 | 0.18 |
| 152_S | 187_R | 1.086 | 0.18 |
| 251_K | 265_V | 1.082 | 0.17 |
| 42_F | 78_A | 1.081 | 0.17 |
| 64_E | 78_A | 1.080 | 0.17 |
| 252_Y | 261_S | 1.079 | 0.17 |
| 68_H | 109_V | 1.078 | 0.17 |
| 62_G | 81_P | 1.078 | 0.17 |
| 2_V | 6_M | 1.078 | 0.17 |
| 183_D | 224_E | 1.077 | 0.17 |
| 73_D | 160_Y | 1.076 | 0.17 |
| 16_F | 95_S | 1.074 | 0.17 |
| 50_K | 61_D | 1.074 | 0.17 |
| 53_A | 68_H | 1.070 | 0.17 |
| 62_G | 66_F | 1.070 | 0.17 |
| 33_D | 253_I | 1.070 | 0.17 |
| 158_Y | 161_L | 1.067 | 0.17 |
| 63_V | 187_R | 1.066 | 0.17 |
| 53_A | 63_V | 1.066 | 0.17 |
| 10_K | 26_E | 1.066 | 0.17 |
| 250_N | 261_S | 1.064 | 0.17 |
| 143_E | 162_T | 1.063 | 0.17 |
| 20_A | 23_D | 1.063 | 0.17 |
| 165_P | 221_T | 1.063 | 0.17 |
| 46_N | 52_K | 1.061 | 0.17 |
| 241_D | 251_K | 1.060 | 0.17 |
| 179_I | 204_Y | 1.059 | 0.17 |
| 220_N | 242_L | 1.058 | 0.17 |
| 130_K | 133_K | 1.055 | 0.16 |
| 143_E | 157_E | 1.054 | 0.16 |
| 213_K | 224_E | 1.053 | 0.16 |
| 46_N | 80_I | 1.050 | 0.16 |
| 31_H | 45_D | 1.047 | 0.16 |
| 222_I | 226_I | 1.047 | 0.16 |
| 214_D | 250_N | 1.044 | 0.16 |
| 37_K | 44_M | 1.043 | 0.16 |
| 62_G | 65_V | 1.042 | 0.16 |
| 108_T | 217_T | 1.042 | 0.16 |
| 45_D | 50_K | 1.039 | 0.16 |
| 215_N | 266_I | 1.035 | 0.16 |
| 73_D | 82_F | 1.034 | 0.16 |
| 42_F | 62_G | 1.033 | 0.16 |
| 212_T | 220_N | 1.032 | 0.16 |
| 229_S | 233_K | 1.032 | 0.16 |
| 250_N | 263_K | 1.028 | 0.15 |
| 183_D | 238_I | 1.028 | 0.15 |
| 48_G | 106_V | 1.025 | 0.15 |
| 158_Y | 224_E | 1.024 | 0.15 |
| 133_K | 158_Y | 1.022 | 0.15 |
| 220_N | 224_E | 1.022 | 0.15 |
| 172_K | 176_Q | 1.020 | 0.15 |
| 179_I | 254_N | 1.019 | 0.15 |
| 249_S | 258_P | 1.018 | 0.15 |
| 204_Y | 237_N | 1.017 | 0.15 |
| 114_E | 175_F | 1.015 | 0.15 |
| 54_T | 68_H | 1.015 | 0.15 |
| 7_E | 120_E | 1.014 | 0.15 |
| 156_N | 210_F | 1.014 | 0.15 |
| 33_D | 85_S | 1.011 | 0.15 |
| 60_G | 82_F | 1.009 | 0.15 |
| 5_E | 20_A | 1.009 | 0.15 |
| 173_R | 213_K | 1.008 | 0.15 |
| 180_K | 224_E | 1.007 | 0.15 |
| 10_K | 29_K | 1.005 | 0.15 |
| 128_V | 195_K | 1.001 | 0.15 |
| 135_K | 238_I | 1.000 | 0.15 |
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 | |
| 2kvoA | 1 | 0.4161 | 8.6 | 0.975 | Contact Map |
| 2wgoA | 1 | 0.3577 | 5.1 | 0.977 | Contact Map |
| 4k95A | 12 | 0.2263 | 5 | 0.977 | Contact Map |
| 3j39U | 1 | 0.3905 | 4.9 | 0.977 | Contact Map |
| 3u5cf | 1 | 0 | 4.6 | 0.978 | Contact Map |
| 2xzm9 | 1 | 0 | 4.4 | 0.978 | Contact Map |
| 4fjvB | 2 | 0.2518 | 4.4 | 0.978 | Contact Map |
| 4bpe9 | 1 | 0 | 4.1 | 0.978 | Contact Map |
| 1wy8A | 1 | 0.2518 | 4.1 | 0.978 | Contact Map |
| 3n3kB | 1 | 0.2263 | 4.1 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)