| T0826 1-220 |
| ID: | 1403945944 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 220 (213) | ||
| Sequences: | 571 (456.1) | ||
| Seq/Len: | 2.681 | ||
| Nf(neff/√len): | 31.3 |
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: 2.681).
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 |
| 131_G | 135_A | 3.093 | 1.00 |
| 79_P | 139_I | 2.833 | 1.00 |
| 62_N | 162_S | 2.632 | 1.00 |
| 82_L | 138_Y | 2.600 | 1.00 |
| 52_T | 177_Y | 2.390 | 1.00 |
| 79_P | 135_A | 2.103 | 1.00 |
| 59_F | 165_C | 2.102 | 1.00 |
| 15_L | 138_Y | 2.057 | 1.00 |
| 103_M | 106_N | 2.042 | 1.00 |
| 91_Q | 118_L | 2.005 | 1.00 |
| 22_Y | 27_L | 1.985 | 0.99 |
| 87_A | 127_I | 1.929 | 0.99 |
| 173_Q | 177_Y | 1.928 | 0.99 |
| 49_F | 177_Y | 1.912 | 0.99 |
| 92_E | 99_F | 1.900 | 0.99 |
| 79_P | 138_Y | 1.883 | 0.99 |
| 91_Q | 99_F | 1.813 | 0.99 |
| 151_E | 155_R | 1.763 | 0.98 |
| 23_S | 65_F | 1.696 | 0.98 |
| 188_T | 198_G | 1.676 | 0.98 |
| 19_L | 78_I | 1.640 | 0.97 |
| 104_L | 203_K | 1.633 | 0.97 |
| 108_L | 203_K | 1.611 | 0.97 |
| 129_C | 136_L | 1.542 | 0.96 |
| 152_L | 160_A | 1.526 | 0.95 |
| 100_N | 103_M | 1.450 | 0.93 |
| 136_L | 140_A | 1.442 | 0.93 |
| 174_Y | 178_A | 1.427 | 0.93 |
| 94_F | 138_Y | 1.359 | 0.90 |
| 20_S | 27_L | 1.345 | 0.89 |
| 62_N | 158_L | 1.345 | 0.89 |
| 31_F | 185_K | 1.338 | 0.89 |
| 31_F | 198_G | 1.323 | 0.88 |
| 63_F | 163_F | 1.314 | 0.88 |
| 170_A | 183_N | 1.314 | 0.88 |
| 76_V | 79_P | 1.305 | 0.87 |
| 11_G | 14_A | 1.303 | 0.87 |
| 24_S | 58_F | 1.301 | 0.87 |
| 71_P | 75_K | 1.299 | 0.87 |
| 104_L | 200_G | 1.289 | 0.86 |
| 128_V | 132_V | 1.282 | 0.86 |
| 63_F | 159_A | 1.275 | 0.86 |
| 95_F | 153_L | 1.269 | 0.85 |
| 75_K | 79_P | 1.257 | 0.85 |
| 31_F | 35_V | 1.249 | 0.84 |
| 103_M | 182_R | 1.243 | 0.84 |
| 145_Y | 151_E | 1.234 | 0.83 |
| 99_F | 214_Y | 1.205 | 0.81 |
| 89_S | 126_W | 1.205 | 0.81 |
| 59_F | 169_I | 1.204 | 0.81 |
| 91_Q | 214_Y | 1.199 | 0.80 |
| 49_F | 173_Q | 1.193 | 0.80 |
| 86_A | 131_G | 1.179 | 0.79 |
| 10_L | 18_F | 1.177 | 0.79 |
| 140_A | 144_K | 1.175 | 0.79 |
| 80_L | 84_I | 1.174 | 0.79 |
| 48_I | 51_Y | 1.174 | 0.79 |
| 204_Y | 208_K | 1.166 | 0.78 |
| 179_S | 183_N | 1.164 | 0.78 |
| 190_L | 195_N | 1.163 | 0.78 |
| 16_I | 163_F | 1.162 | 0.78 |
| 93_I | 192_V | 1.153 | 0.77 |
| 21_L | 58_F | 1.139 | 0.76 |
| 23_S | 172_L | 1.133 | 0.75 |
| 192_V | 198_G | 1.131 | 0.75 |
| 95_F | 110_T | 1.124 | 0.74 |
| 115_S | 119_I | 1.109 | 0.73 |
| 11_G | 84_I | 1.108 | 0.73 |
| 43_G | 46_A | 1.105 | 0.72 |
| 63_F | 216_Q | 1.105 | 0.72 |
| 86_A | 161_V | 1.103 | 0.72 |
| 63_F | 166_A | 1.098 | 0.72 |
| 30_A | 93_I | 1.098 | 0.72 |
| 22_Y | 69_A | 1.094 | 0.71 |
| 68_I | 77_L | 1.080 | 0.70 |
| 31_F | 192_V | 1.079 | 0.70 |
| 174_Y | 181_F | 1.079 | 0.70 |
| 23_S | 184_N | 1.059 | 0.68 |
| 9_K | 144_K | 1.054 | 0.67 |
| 31_F | 53_M | 1.054 | 0.67 |
| 33_A | 120_T | 1.046 | 0.66 |
| 55_V | 77_L | 1.046 | 0.66 |
| 31_F | 57_L | 1.046 | 0.66 |
| 100_N | 106_N | 1.045 | 0.66 |
| 24_S | 27_L | 1.045 | 0.66 |
| 103_M | 114_E | 1.043 | 0.66 |
| 91_Q | 123_Y | 1.036 | 0.65 |
| 179_S | 182_R | 1.031 | 0.65 |
| 92_E | 134_P | 1.030 | 0.65 |
| 90_Y | 203_K | 1.027 | 0.64 |
| 126_W | 130_L | 1.027 | 0.64 |
| 108_L | 175_Q | 1.027 | 0.64 |
| 161_V | 164_L | 1.020 | 0.63 |
| 127_I | 132_V | 1.015 | 0.63 |
| 32_F | 35_V | 1.014 | 0.63 |
| 55_V | 125_L | 1.013 | 0.63 |
| 60_L | 161_V | 1.010 | 0.62 |
| 180_F | 195_N | 1.009 | 0.62 |
| 69_A | 207_W | 1.009 | 0.62 |
| 70_L | 73_V | 1.008 | 0.62 |
| 132_V | 164_L | 1.007 | 0.62 |
| 10_L | 14_A | 1.006 | 0.62 |
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 | |
| 2hi2A | 1 | 0.3045 | 2.6 | 0.969 | Contact Map |
| 4httA | 2 | 0.2545 | 2.4 | 0.97 | Contact Map |
| 4b4aA | 1 | 0.2545 | 2.3 | 0.97 | Contact Map |
| 4a82A | 4 | 0.9091 | 2 | 0.971 | Contact Map |
| 1fmeA | 1 | 0.1045 | 1.8 | 0.972 | Contact Map |
| 2r7rA | 1 | 0.2409 | 1.7 | 0.972 | Contact Map |
| 2m7gA | 1 | 0.2773 | 1.6 | 0.973 | Contact Map |
| 4gycB | 1 | 0.2545 | 1.6 | 0.973 | Contact Map |
| 4humA | 1 | 0.8455 | 1.5 | 0.973 | Contact Map |
| 2a65A | 1 | 0.6 | 1.5 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)