| Q53VV3_sub |
| ID: | 1379705018 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (171) | ||
| Sequences: | 2771 (2369.3) | ||
| Seq/Len: | 16.205 | ||
| Nf(neff/√len): | 181.2 |
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: 16.205).
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 |
| 5_A | 15_C | 4.018 | 1.00 |
| 17_V | 31_F | 3.200 | 1.00 |
| 31_F | 45_L | 3.179 | 1.00 |
| 160_T | 168_R | 3.072 | 1.00 |
| 32_D | 50_H | 3.066 | 1.00 |
| 108_R | 160_T | 2.780 | 1.00 |
| 14_T | 32_D | 2.713 | 1.00 |
| 106_R | 163_E | 2.632 | 1.00 |
| 106_R | 137_V | 2.614 | 1.00 |
| 17_V | 68_I | 2.502 | 1.00 |
| 16_Q | 72_R | 2.501 | 1.00 |
| 137_V | 162_L | 2.239 | 1.00 |
| 14_T | 50_H | 2.192 | 1.00 |
| 104_R | 141_E | 2.131 | 1.00 |
| 110_S | 158_H | 2.118 | 1.00 |
| 16_Q | 28_T | 2.114 | 1.00 |
| 18_T | 70_D | 2.051 | 1.00 |
| 18_T | 28_T | 2.005 | 1.00 |
| 16_Q | 30_R | 1.941 | 1.00 |
| 14_T | 30_R | 1.934 | 1.00 |
| 165_E | 169_R | 1.924 | 1.00 |
| 157_P | 174_W | 1.919 | 1.00 |
| 107_V | 159_A | 1.912 | 1.00 |
| 161_V | 171_V | 1.879 | 1.00 |
| 29_Y | 49_N | 1.877 | 1.00 |
| 108_R | 162_L | 1.866 | 1.00 |
| 106_R | 139_Q | 1.820 | 1.00 |
| 108_R | 135_S | 1.792 | 1.00 |
| 7_R | 11_E | 1.744 | 1.00 |
| 31_F | 47_G | 1.721 | 1.00 |
| 29_Y | 63_L | 1.698 | 1.00 |
| 47_G | 63_L | 1.678 | 1.00 |
| 169_R | 173_A | 1.668 | 1.00 |
| 108_R | 137_V | 1.628 | 1.00 |
| 106_R | 162_L | 1.591 | 1.00 |
| 104_R | 139_Q | 1.589 | 1.00 |
| 104_R | 163_E | 1.514 | 1.00 |
| 14_T | 76_E | 1.500 | 1.00 |
| 145_S | 166_E | 1.498 | 1.00 |
| 13_R | 73_L | 1.472 | 1.00 |
| 49_N | 61_K | 1.466 | 1.00 |
| 20_K | 69_L | 1.463 | 1.00 |
| 131_L | 135_S | 1.450 | 1.00 |
| 16_Q | 74_T | 1.447 | 1.00 |
| 131_L | 137_V | 1.436 | 1.00 |
| 153_V | 174_W | 1.414 | 1.00 |
| 152_I | 171_V | 1.407 | 0.99 |
| 109_F | 117_I | 1.389 | 0.99 |
| 129_E | 137_V | 1.386 | 0.99 |
| 20_K | 24_G | 1.386 | 0.99 |
| 49_N | 63_L | 1.378 | 0.99 |
| 17_V | 63_L | 1.322 | 0.99 |
| 152_I | 159_A | 1.311 | 0.99 |
| 149_V | 170_R | 1.300 | 0.99 |
| 34_Y | 78_F | 1.291 | 0.99 |
| 149_V | 174_W | 1.237 | 0.98 |
| 108_R | 131_L | 1.226 | 0.98 |
| 32_D | 78_F | 1.224 | 0.98 |
| 12_R | 78_F | 1.221 | 0.98 |
| 42_H | 64_R | 1.219 | 0.98 |
| 12_R | 80_K | 1.211 | 0.98 |
| 52_S | 61_K | 1.173 | 0.98 |
| 7_R | 73_L | 1.169 | 0.97 |
| 49_N | 52_S | 1.167 | 0.97 |
| 36_L | 65_L | 1.160 | 0.97 |
| 48_A | 58_D | 1.147 | 0.97 |
| 17_V | 71_L | 1.139 | 0.97 |
| 129_E | 139_Q | 1.135 | 0.97 |
| 13_R | 75_R | 1.134 | 0.97 |
| 4_R | 73_L | 1.125 | 0.97 |
| 145_S | 170_R | 1.120 | 0.96 |
| 103_V | 166_E | 1.113 | 0.96 |
| 52_S | 63_L | 1.098 | 0.96 |
| 107_V | 138_W | 1.095 | 0.96 |
| 109_F | 159_A | 1.090 | 0.96 |
| 112_E | 158_H | 1.090 | 0.96 |
| 168_R | 172_V | 1.078 | 0.95 |
| 18_T | 69_L | 1.053 | 0.95 |
| 84_D | 87_A | 1.046 | 0.94 |
| 109_F | 155_Y | 1.045 | 0.94 |
| 34_Y | 60_V | 1.043 | 0.94 |
| 35_A | 46_V | 1.043 | 0.94 |
| 35_A | 85_V | 1.040 | 0.94 |
| 30_R | 74_T | 1.031 | 0.94 |
| 21_N | 25_E | 1.029 | 0.94 |
| 68_I | 71_L | 1.025 | 0.93 |
| 17_V | 47_G | 1.021 | 0.93 |
| 4_R | 7_R | 1.017 | 0.93 |
| 18_T | 26_V | 1.010 | 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 | |
| 1sg5A | 1 | 0.4148 | 17 | 0.92 | Contact Map |
| 1v0dA | 1 | 0.3295 | 9.8 | 0.928 | Contact Map |
| 2e9xC | 2 | 0.4716 | 3 | 0.944 | Contact Map |
| 2bo9B | 2 | 0.3182 | 2.8 | 0.945 | Contact Map |
| 1el6A | 3 | 0.3864 | 2.7 | 0.945 | Contact Map |
| 4g1iA | 2 | 0.3466 | 2.7 | 0.945 | Contact Map |
| 3dtdA | 12 | 0.2955 | 2.5 | 0.946 | Contact Map |
| 2vb2X | 1 | 0.1932 | 2.5 | 0.946 | Contact Map |
| 2qcpX | 1 | 0.1989 | 2.3 | 0.947 | Contact Map |
| 2m7oA | 1 | 0.3295 | 2.2 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)