| HemJ 1790 |
| ID: | 1504445104 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 193 (182) | ||
| Sequences: | 393 (209.1) | ||
| Seq/Len: | 2.159 | ||
| Nf(neff/√len): | 15.5 |
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: 2.159).
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 |
| 39_E | 43_T | 3.436 | 1.00 |
| 32_A | 124_F | 2.900 | 1.00 |
| 40_P | 43_T | 2.885 | 1.00 |
| 16_V | 64_G | 2.869 | 1.00 |
| 87_W | 142_A | 2.782 | 1.00 |
| 29_V | 124_F | 2.640 | 1.00 |
| 134_L | 138_I | 2.523 | 1.00 |
| 69_V | 99_L | 2.179 | 1.00 |
| 25_V | 105_C | 2.015 | 0.99 |
| 79_E | 82_I | 1.939 | 0.99 |
| 31_H | 53_E | 1.929 | 0.99 |
| 48_Q | 52_M | 1.920 | 0.99 |
| 29_V | 32_A | 1.859 | 0.98 |
| 76_I | 83_L | 1.844 | 0.98 |
| 86_G | 89_H | 1.838 | 0.98 |
| 25_V | 61_T | 1.788 | 0.98 |
| 89_H | 93_T | 1.736 | 0.97 |
| 15_V | 68_T | 1.734 | 0.97 |
| 50_E | 115_G | 1.716 | 0.97 |
| 37_E | 41_A | 1.657 | 0.96 |
| 29_V | 168_I | 1.626 | 0.95 |
| 76_I | 88_L | 1.619 | 0.95 |
| 73_I | 77_F | 1.606 | 0.95 |
| 120_S | 123_Q | 1.511 | 0.93 |
| 11_L | 124_F | 1.481 | 0.92 |
| 12_I | 135_L | 1.439 | 0.90 |
| 39_E | 148_L | 1.404 | 0.88 |
| 158_V | 162_I | 1.386 | 0.87 |
| 3_Y | 82_I | 1.385 | 0.87 |
| 58_N | 109_M | 1.374 | 0.87 |
| 138_I | 149_P | 1.369 | 0.87 |
| 25_V | 49_Y | 1.367 | 0.87 |
| 14_I | 142_A | 1.306 | 0.83 |
| 35_D | 46_K | 1.299 | 0.82 |
| 96_A | 100_L | 1.288 | 0.82 |
| 139_V | 145_K | 1.282 | 0.81 |
| 160_L | 176_R | 1.273 | 0.81 |
| 52_M | 55_R | 1.268 | 0.80 |
| 18_F | 55_R | 1.266 | 0.80 |
| 40_P | 44_I | 1.258 | 0.80 |
| 119_W | 123_Q | 1.242 | 0.78 |
| 51_L | 55_R | 1.216 | 0.76 |
| 85_S | 88_L | 1.203 | 0.75 |
| 67_V | 126_A | 1.197 | 0.75 |
| 6_F | 74_G | 1.194 | 0.74 |
| 15_V | 135_L | 1.176 | 0.73 |
| 57_Y | 106_G | 1.166 | 0.72 |
| 7_K | 18_F | 1.160 | 0.71 |
| 8_A | 12_I | 1.142 | 0.70 |
| 9_F | 71_M | 1.122 | 0.68 |
| 42_K | 115_G | 1.117 | 0.67 |
| 49_Y | 59_I | 1.111 | 0.67 |
| 164_M | 168_I | 1.108 | 0.66 |
| 174_K | 178_D | 1.105 | 0.66 |
| 80_P | 83_L | 1.103 | 0.66 |
| 155_W | 158_V | 1.100 | 0.65 |
| 29_V | 121_G | 1.097 | 0.65 |
| 94_F | 142_A | 1.092 | 0.65 |
| 173_K | 177_R | 1.086 | 0.64 |
| 158_V | 179_Q | 1.086 | 0.64 |
| 16_V | 164_M | 1.074 | 0.63 |
| 111_K | 118_Q | 1.069 | 0.62 |
| 18_F | 71_M | 1.067 | 0.62 |
| 75_L | 82_I | 1.062 | 0.61 |
| 38_P | 41_A | 1.060 | 0.61 |
| 48_Q | 55_R | 1.060 | 0.61 |
| 169_Q | 172_A | 1.060 | 0.61 |
| 90_I | 159_A | 1.056 | 0.61 |
| 160_L | 168_I | 1.056 | 0.61 |
| 140_L | 144_F | 1.056 | 0.61 |
| 31_H | 46_K | 1.053 | 0.60 |
| 69_V | 72_A | 1.046 | 0.60 |
| 25_V | 161_V | 1.043 | 0.59 |
| 11_L | 139_V | 1.040 | 0.59 |
| 106_G | 109_M | 1.037 | 0.59 |
| 69_V | 73_I | 1.034 | 0.58 |
| 26_R | 128_N | 1.030 | 0.58 |
| 57_Y | 131_P | 1.024 | 0.57 |
| 109_M | 113_A | 1.023 | 0.57 |
| 105_C | 144_F | 1.023 | 0.57 |
| 100_L | 103_F | 1.019 | 0.57 |
| 38_P | 173_K | 1.017 | 0.57 |
| 13_G | 144_F | 1.017 | 0.57 |
| 18_F | 141_L | 1.011 | 0.56 |
| 62_T | 109_M | 1.008 | 0.55 |
| 107_R | 111_K | 1.007 | 0.55 |
| 64_G | 109_M | 1.007 | 0.55 |
| 179_Q | 182_L | 1.004 | 0.55 |
| 39_E | 42_K | 1.004 | 0.55 |
| 7_K | 55_R | 1.003 | 0.55 |
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 | |
| 3b5xA | 2 | 0.7824 | 25.9 | 0.963 | Contact Map |
| 2l9uA | 2 | 0.2073 | 22.6 | 0.964 | Contact Map |
| 2kncA | 1 | 0.2487 | 18.6 | 0.965 | Contact Map |
| 2m20A | 2 | 0.2487 | 18 | 0.965 | Contact Map |
| 4djkA | 2 | 0.8394 | 17.1 | 0.966 | Contact Map |
| 3wmgA | 1 | 0.772 | 14.5 | 0.967 | Contact Map |
| 2a65A | 1 | 0.9171 | 13.1 | 0.967 | Contact Map |
| 2l2tA | 2 | 0.228 | 12.1 | 0.968 | Contact Map |
| 2kluA | 1 | 0.2642 | 11.8 | 0.968 | Contact Map |
| 2kncB | 1 | 0.2953 | 11.7 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)