| AAA |
| ID: | 1437442018 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (140) | ||
| Sequences: | 3829 (3039.5) | ||
| Seq/Len: | 27.350 | ||
| Nf(neff/√len): | 256.9 |
HHblits Results: (2013_03)
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: 27.350).
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 |
| 96_R | 129_A | 3.461 | 1.00 |
| 6_A | 135_D | 2.689 | 1.00 |
| 23_R | 40_V | 2.474 | 1.00 |
| 17_T | 20_E | 2.327 | 1.00 |
| 25_A | 100_G | 2.311 | 1.00 |
| 133_S | 136_E | 2.244 | 1.00 |
| 27_E | 31_K | 2.198 | 1.00 |
| 12_G | 80_Q | 2.086 | 1.00 |
| 43_M | 100_G | 2.051 | 1.00 |
| 14_K | 82_P | 2.024 | 1.00 |
| 26_G | 40_V | 2.022 | 1.00 |
| 126_E | 130_H | 2.002 | 1.00 |
| 10_F | 28_Q | 1.971 | 1.00 |
| 34_Y | 73_K | 1.963 | 1.00 |
| 36_E | 72_L | 1.960 | 1.00 |
| 84_G | 96_R | 1.960 | 1.00 |
| 15_A | 24_F | 1.908 | 1.00 |
| 30_V | 35_V | 1.877 | 1.00 |
| 15_A | 21_A | 1.831 | 1.00 |
| 81_Y | 98_V | 1.827 | 1.00 |
| 75_G | 102_A | 1.810 | 1.00 |
| 12_G | 82_P | 1.760 | 1.00 |
| 25_A | 79_C | 1.733 | 1.00 |
| 21_A | 98_V | 1.718 | 1.00 |
| 81_Y | 84_G | 1.710 | 1.00 |
| 41_Q | 45_D | 1.697 | 1.00 |
| 39_Y | 102_A | 1.661 | 1.00 |
| 8_N | 32_G | 1.641 | 1.00 |
| 22_I | 43_M | 1.622 | 1.00 |
| 38_E | 70_R | 1.596 | 1.00 |
| 13_R | 79_C | 1.565 | 1.00 |
| 10_F | 24_F | 1.514 | 1.00 |
| 34_Y | 75_G | 1.472 | 1.00 |
| 132_T | 136_E | 1.454 | 1.00 |
| 47_E | 52_T | 1.436 | 1.00 |
| 26_G | 43_M | 1.413 | 1.00 |
| 28_Q | 31_K | 1.401 | 0.99 |
| 6_A | 138_L | 1.395 | 0.99 |
| 81_Y | 96_R | 1.353 | 0.99 |
| 26_G | 100_G | 1.343 | 0.99 |
| 125_I | 129_A | 1.339 | 0.99 |
| 11_L | 80_Q | 1.335 | 0.99 |
| 71_V | 102_A | 1.316 | 0.99 |
| 45_D | 48_K | 1.313 | 0.99 |
| 7_E | 32_G | 1.290 | 0.99 |
| 45_D | 49_L | 1.285 | 0.99 |
| 74_T | 104_R | 1.279 | 0.99 |
| 16_A | 20_E | 1.276 | 0.99 |
| 19_E | 44_L | 1.269 | 0.99 |
| 95_A | 98_V | 1.263 | 0.99 |
| 131_T | 140_L | 1.242 | 0.98 |
| 131_T | 137_V | 1.240 | 0.98 |
| 19_E | 23_R | 1.239 | 0.98 |
| 57_S | 96_R | 1.232 | 0.98 |
| 15_A | 81_Y | 1.201 | 0.98 |
| 135_D | 139_E | 1.201 | 0.98 |
| 46_R | 52_T | 1.192 | 0.98 |
| 22_I | 40_V | 1.186 | 0.98 |
| 9_I | 137_V | 1.174 | 0.98 |
| 78_F | 137_V | 1.160 | 0.97 |
| 131_T | 136_E | 1.152 | 0.97 |
| 23_R | 44_L | 1.143 | 0.97 |
| 79_C | 100_G | 1.133 | 0.97 |
| 56_E | 125_I | 1.124 | 0.97 |
| 42_A | 45_D | 1.091 | 0.96 |
| 42_A | 63_G | 1.090 | 0.96 |
| 30_V | 37_P | 1.080 | 0.95 |
| 76_V | 111_V | 1.070 | 0.95 |
| 13_R | 24_F | 1.067 | 0.95 |
| 134_V | 138_L | 1.059 | 0.95 |
| 80_Q | 97_L | 1.058 | 0.95 |
| 87_F | 98_V | 1.052 | 0.95 |
| 78_F | 97_L | 1.051 | 0.94 |
| 28_Q | 32_G | 1.039 | 0.94 |
| 40_V | 44_L | 1.035 | 0.94 |
| 5_G | 8_N | 1.023 | 0.93 |
| 109_I | 113_T | 1.016 | 0.93 |
| 115_L | 119_L | 1.011 | 0.93 |
| 9_I | 134_V | 1.006 | 0.93 |
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 | |
| 1a3aA | 4 | 1 | 100 | 0.056 | Contact Map |
| 1a6jA | 2 | 0.9793 | 100 | 0.093 | Contact Map |
| 3oxpA | 2 | 0.9793 | 100 | 0.11 | Contact Map |
| 3urrA | 2 | 0.9793 | 100 | 0.117 | Contact Map |
| 2a0jA | 1 | 0.9586 | 100 | 0.118 | Contact Map |
| 2oq3A | 1 | 0.9724 | 100 | 0.127 | Contact Map |
| 4m62S | 2 | 0.9793 | 100 | 0.132 | Contact Map |
| 2oqtA | 4 | 0.9724 | 100 | 0.137 | Contact Map |
| 3t43A | 2 | 0.8759 | 99.9 | 0.17 | Contact Map |
| 3bjvA | 1 | 0.9724 | 99.9 | 0.172 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)