| C52JH |
| ID: | 1465847941 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (188) | ||
| Sequences: | 4393 (2487.2) | ||
| Seq/Len: | 23.367 | ||
| Nf(neff/√len): | 181.4 |
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: 23.367).
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 |
| 27_L | 163_A | 3.918 | 1.00 |
| 24_A | 167_G | 2.545 | 1.00 |
| 22_I | 26_G | 2.417 | 1.00 |
| 54_C | 64_C | 2.404 | 1.00 |
| 29_M | 47_W | 2.287 | 1.00 |
| 19_G | 23_L | 2.251 | 1.00 |
| 137_C | 141_N | 2.035 | 1.00 |
| 82_A | 86_S | 2.030 | 1.00 |
| 28_P | 52_M | 1.908 | 1.00 |
| 48_K | 53_S | 1.788 | 1.00 |
| 14_C | 125_Y | 1.778 | 1.00 |
| 136_L | 167_G | 1.777 | 1.00 |
| 25_C | 84_T | 1.768 | 1.00 |
| 75_T | 79_A | 1.767 | 1.00 |
| 76_E | 80_A | 1.726 | 1.00 |
| 24_A | 170_A | 1.722 | 1.00 |
| 82_A | 85_V | 1.694 | 1.00 |
| 65_K | 68_D | 1.664 | 1.00 |
| 149_D | 152_V | 1.654 | 1.00 |
| 160_L | 168_W | 1.648 | 1.00 |
| 122_G | 178_G | 1.609 | 1.00 |
| 31_Q | 48_K | 1.608 | 1.00 |
| 135_P | 139_F | 1.593 | 1.00 |
| 17_G | 177_G | 1.587 | 1.00 |
| 20_G | 166_I | 1.559 | 1.00 |
| 126_L | 130_L | 1.523 | 1.00 |
| 132_A | 170_A | 1.519 | 1.00 |
| 165_Y | 169_A | 1.491 | 1.00 |
| 78_Q | 81_R | 1.479 | 1.00 |
| 23_L | 27_L | 1.452 | 1.00 |
| 148_Y | 151_S | 1.431 | 1.00 |
| 84_T | 87_A | 1.403 | 0.99 |
| 129_G | 175_M | 1.382 | 0.99 |
| 126_L | 178_G | 1.367 | 0.99 |
| 140_A | 168_W | 1.363 | 0.99 |
| 69_S | 72_A | 1.346 | 0.99 |
| 32_V | 161_G | 1.346 | 0.99 |
| 20_G | 170_A | 1.340 | 0.99 |
| 122_G | 129_G | 1.329 | 0.99 |
| 133_L | 171_T | 1.323 | 0.99 |
| 27_L | 162_A | 1.299 | 0.99 |
| 21_L | 170_A | 1.292 | 0.99 |
| 50_L | 54_C | 1.289 | 0.99 |
| 84_T | 88_V | 1.287 | 0.99 |
| 132_A | 171_T | 1.278 | 0.99 |
| 129_G | 178_G | 1.275 | 0.99 |
| 148_Y | 152_V | 1.259 | 0.99 |
| 77_V | 81_R | 1.247 | 0.99 |
| 132_A | 136_L | 1.231 | 0.98 |
| 137_C | 140_A | 1.225 | 0.98 |
| 179_C | 183_C | 1.221 | 0.98 |
| 134_V | 138_W | 1.212 | 0.98 |
| 137_C | 168_W | 1.194 | 0.98 |
| 178_G | 182_C | 1.190 | 0.98 |
| 78_Q | 82_A | 1.189 | 0.98 |
| 79_A | 83_L | 1.188 | 0.98 |
| 80_A | 83_L | 1.179 | 0.98 |
| 18_W | 91_A | 1.168 | 0.97 |
| 162_A | 166_I | 1.165 | 0.97 |
| 10_G | 177_G | 1.161 | 0.97 |
| 49_G | 54_C | 1.161 | 0.97 |
| 78_Q | 85_V | 1.158 | 0.97 |
| 86_S | 93_V | 1.156 | 0.97 |
| 85_V | 89_L | 1.142 | 0.97 |
| 27_L | 49_G | 1.134 | 0.97 |
| 112_P | 116_R | 1.133 | 0.97 |
| 135_P | 138_W | 1.130 | 0.97 |
| 2_G | 6_L | 1.128 | 0.97 |
| 149_D | 153_P | 1.127 | 0.97 |
| 147_F | 150_P | 1.127 | 0.97 |
| 17_G | 174_L | 1.125 | 0.97 |
| 45_T | 56_V | 1.119 | 0.96 |
| 23_L | 26_G | 1.111 | 0.96 |
| 40_I | 43_A | 1.108 | 0.96 |
| 130_L | 134_V | 1.105 | 0.96 |
| 83_L | 86_S | 1.103 | 0.96 |
| 10_G | 181_L | 1.092 | 0.96 |
| 33_T | 46_T | 1.068 | 0.95 |
| 98_T | 121_G | 1.055 | 0.95 |
| 18_W | 92_F | 1.055 | 0.95 |
| 133_L | 137_C | 1.055 | 0.95 |
| 21_L | 24_A | 1.052 | 0.95 |
| 122_G | 125_Y | 1.044 | 0.94 |
| 86_S | 89_L | 1.040 | 0.94 |
| 78_Q | 83_L | 1.038 | 0.94 |
| 29_M | 32_V | 1.033 | 0.94 |
| 64_C | 67_Y | 1.031 | 0.94 |
| 171_T | 175_M | 1.028 | 0.94 |
| 146_E | 150_P | 1.027 | 0.94 |
| 7_E | 11_L | 1.021 | 0.93 |
| 10_G | 14_C | 1.001 | 0.92 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3x29A | 2 | 0.8789 | 100 | 0.173 | Contact Map |
| 4p79A | 1 | 0.9316 | 100 | 0.201 | Contact Map |
| 1nkzA | 3 | 0.2263 | 11.7 | 0.924 | Contact Map |
| 1fftB | 2 | 0.2474 | 10 | 0.926 | Contact Map |
| 1xrdA | 1 | 0.2211 | 9.6 | 0.926 | Contact Map |
| 2kluA | 1 | 0.2 | 8.5 | 0.928 | Contact Map |
| 4jc95 | 14 | 0.1895 | 8.4 | 0.929 | Contact Map |
| 1iijA | 1 | 0.1842 | 5 | 0.936 | Contact Map |
| 3wmmA | 16 | 0.2368 | 4.9 | 0.936 | Contact Map |
| 4yayA | 1 | 0 | 4.3 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)