| Q53VV3_sub |
| ID: | 1379708582 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (170) | ||
| Sequences: | 2167 (1874.5) | ||
| Seq/Len: | 12.747 | ||
| Nf(neff/√len): | 143.8 |
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: 12.747).
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 | 4.483 | 1.00 |
| 31_F | 45_L | 3.575 | 1.00 |
| 160_T | 168_R | 3.175 | 1.00 |
| 17_V | 31_F | 3.033 | 1.00 |
| 108_R | 160_T | 2.916 | 1.00 |
| 14_T | 32_D | 2.899 | 1.00 |
| 32_D | 50_H | 2.807 | 1.00 |
| 17_V | 68_I | 2.633 | 1.00 |
| 106_R | 163_E | 2.534 | 1.00 |
| 137_V | 162_L | 2.506 | 1.00 |
| 106_R | 137_V | 2.455 | 1.00 |
| 16_Q | 72_R | 2.294 | 1.00 |
| 14_T | 50_H | 2.178 | 1.00 |
| 14_T | 30_R | 2.093 | 1.00 |
| 107_V | 159_A | 2.078 | 1.00 |
| 104_R | 141_E | 2.074 | 1.00 |
| 16_Q | 30_R | 2.050 | 1.00 |
| 161_V | 171_V | 1.988 | 1.00 |
| 165_E | 169_R | 1.960 | 1.00 |
| 16_Q | 28_T | 1.923 | 1.00 |
| 29_Y | 49_N | 1.899 | 1.00 |
| 110_S | 158_H | 1.896 | 1.00 |
| 18_T | 70_D | 1.882 | 1.00 |
| 18_T | 28_T | 1.882 | 1.00 |
| 108_R | 137_V | 1.828 | 1.00 |
| 7_R | 11_E | 1.780 | 1.00 |
| 108_R | 135_S | 1.745 | 1.00 |
| 169_R | 173_A | 1.744 | 1.00 |
| 108_R | 162_L | 1.721 | 1.00 |
| 107_V | 138_W | 1.707 | 1.00 |
| 106_R | 139_Q | 1.672 | 1.00 |
| 29_Y | 63_L | 1.654 | 1.00 |
| 13_R | 73_L | 1.612 | 1.00 |
| 129_E | 137_V | 1.576 | 1.00 |
| 14_T | 76_E | 1.570 | 1.00 |
| 31_F | 47_G | 1.565 | 1.00 |
| 106_R | 162_L | 1.563 | 1.00 |
| 35_A | 85_V | 1.563 | 1.00 |
| 16_Q | 74_T | 1.557 | 1.00 |
| 145_S | 166_E | 1.515 | 1.00 |
| 131_L | 135_S | 1.483 | 1.00 |
| 131_L | 137_V | 1.480 | 1.00 |
| 157_P | 174_W | 1.437 | 1.00 |
| 49_N | 63_L | 1.415 | 1.00 |
| 104_R | 139_Q | 1.400 | 0.99 |
| 108_R | 131_L | 1.370 | 0.99 |
| 152_I | 159_A | 1.352 | 0.99 |
| 109_F | 117_I | 1.343 | 0.99 |
| 34_Y | 78_F | 1.343 | 0.99 |
| 49_N | 61_K | 1.337 | 0.99 |
| 153_V | 174_W | 1.305 | 0.99 |
| 152_I | 171_V | 1.293 | 0.99 |
| 17_V | 63_L | 1.283 | 0.99 |
| 129_E | 139_Q | 1.271 | 0.99 |
| 52_S | 63_L | 1.270 | 0.99 |
| 145_S | 170_R | 1.267 | 0.99 |
| 48_A | 58_D | 1.244 | 0.98 |
| 149_V | 174_W | 1.241 | 0.98 |
| 36_L | 65_L | 1.233 | 0.98 |
| 4_R | 73_L | 1.218 | 0.98 |
| 49_N | 52_S | 1.204 | 0.98 |
| 42_H | 64_R | 1.198 | 0.98 |
| 109_F | 159_A | 1.192 | 0.98 |
| 13_R | 75_R | 1.190 | 0.98 |
| 104_R | 163_E | 1.177 | 0.98 |
| 105_V | 142_V | 1.172 | 0.98 |
| 47_G | 63_L | 1.154 | 0.97 |
| 12_R | 78_F | 1.113 | 0.96 |
| 30_R | 74_T | 1.104 | 0.96 |
| 12_R | 80_K | 1.098 | 0.96 |
| 109_F | 155_Y | 1.074 | 0.95 |
| 32_D | 78_F | 1.070 | 0.95 |
| 68_I | 71_L | 1.068 | 0.95 |
| 4_R | 71_L | 1.066 | 0.95 |
| 35_A | 46_V | 1.065 | 0.95 |
| 33_P | 45_L | 1.060 | 0.95 |
| 7_R | 73_L | 1.057 | 0.95 |
| 20_K | 24_G | 1.052 | 0.95 |
| 17_V | 47_G | 1.042 | 0.94 |
| 168_R | 172_V | 1.040 | 0.94 |
| 20_K | 69_L | 1.035 | 0.94 |
| 112_E | 158_H | 1.029 | 0.94 |
| 103_V | 166_E | 1.010 | 0.93 |
| 17_V | 71_L | 1.005 | 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 | 25.1 | 0.922 | Contact Map |
| 2e9xC | 2 | 0.4716 | 9.4 | 0.935 | Contact Map |
| 4akzA | 5 | 0.2614 | 5.2 | 0.943 | Contact Map |
| 1v0dA | 1 | 0.3295 | 4.7 | 0.944 | Contact Map |
| 3zxwB | 4 | 0.3864 | 3.5 | 0.948 | Contact Map |
| 1rblM | 8 | 0.4659 | 3.2 | 0.948 | Contact Map |
| 1svdM | 1 | 0.4602 | 3 | 0.949 | Contact Map |
| 1el6A | 3 | 0.3864 | 2.5 | 0.951 | Contact Map |
| 2gksA | 2 | 0.6364 | 2.5 | 0.951 | Contact Map |
| 4g1iA | 2 | 0.3466 | 2.5 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)