| 1gv8 |
| ID: | 1492603429 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (159) | ||
| Sequences: | 772 (456.4) | ||
| Seq/Len: | 4.855 | ||
| Nf(neff/√len): | 36.2 |
HHblits Results: (2016_02)
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: 4.855).
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 |
| 135_E | 143_R | 3.052 | 1.00 |
| 106_Q | 110_D | 2.934 | 1.00 |
| 27_T | 31_R | 2.766 | 1.00 |
| 14_F | 18_D | 2.438 | 1.00 |
| 23_T | 83_Q | 2.410 | 1.00 |
| 2_Y | 119_K | 2.267 | 1.00 |
| 98_Y | 103_G | 2.262 | 1.00 |
| 105_F | 127_A | 2.116 | 1.00 |
| 10_K | 135_E | 2.106 | 1.00 |
| 98_Y | 110_D | 2.049 | 1.00 |
| 138_C | 152_C | 1.867 | 1.00 |
| 68_A | 82_R | 1.833 | 1.00 |
| 100_G | 103_G | 1.810 | 1.00 |
| 81_C | 84_C | 1.765 | 1.00 |
| 148_S | 151_T | 1.734 | 1.00 |
| 130_E | 133_E | 1.635 | 0.99 |
| 28_G | 31_R | 1.629 | 0.99 |
| 27_T | 32_S | 1.598 | 0.99 |
| 119_K | 122_T | 1.531 | 0.99 |
| 31_R | 101_Y | 1.512 | 0.99 |
| 34_G | 38_P | 1.510 | 0.98 |
| 42_L | 48_I | 1.509 | 0.98 |
| 29_L | 71_V | 1.500 | 0.98 |
| 135_E | 145_P | 1.443 | 0.98 |
| 109_K | 134_Y | 1.429 | 0.98 |
| 37_I | 155_A | 1.399 | 0.97 |
| 9_K | 111_G | 1.354 | 0.96 |
| 15_M | 18_D | 1.295 | 0.95 |
| 22_K | 114_D | 1.280 | 0.95 |
| 27_T | 34_G | 1.278 | 0.95 |
| 27_T | 101_Y | 1.277 | 0.95 |
| 128_P | 131_K | 1.260 | 0.94 |
| 23_T | 130_E | 1.258 | 0.94 |
| 88_A | 97_P | 1.256 | 0.94 |
| 63_A | 80_L | 1.238 | 0.93 |
| 120_H | 149_Y | 1.235 | 0.93 |
| 96_A | 99_S | 1.234 | 0.93 |
| 32_S | 36_N | 1.233 | 0.93 |
| 136_L | 149_Y | 1.230 | 0.93 |
| 137_L | 143_R | 1.212 | 0.92 |
| 101_Y | 119_K | 1.209 | 0.92 |
| 102_S | 126_N | 1.206 | 0.92 |
| 27_T | 33_A | 1.202 | 0.92 |
| 1_S | 159_A | 1.202 | 0.92 |
| 27_T | 119_K | 1.199 | 0.92 |
| 136_L | 153_N | 1.166 | 0.90 |
| 105_F | 126_N | 1.159 | 0.90 |
| 19_L | 115_V | 1.154 | 0.90 |
| 140_D | 144_Q | 1.148 | 0.89 |
| 3_Y | 120_H | 1.142 | 0.89 |
| 137_L | 141_G | 1.129 | 0.88 |
| 3_Y | 153_N | 1.110 | 0.87 |
| 144_Q | 148_S | 1.107 | 0.87 |
| 69_S | 80_L | 1.096 | 0.86 |
| 70_C | 84_C | 1.093 | 0.86 |
| 32_S | 101_Y | 1.089 | 0.86 |
| 4_A | 34_G | 1.087 | 0.86 |
| 5_V | 120_H | 1.086 | 0.85 |
| 152_C | 158_A | 1.080 | 0.85 |
| 47_D | 139_L | 1.079 | 0.85 |
| 29_L | 74_A | 1.072 | 0.84 |
| 73_G | 84_C | 1.066 | 0.84 |
| 7_V | 134_Y | 1.065 | 0.84 |
| 71_V | 78_Q | 1.065 | 0.84 |
| 4_A | 37_I | 1.064 | 0.84 |
| 22_K | 48_I | 1.055 | 0.83 |
| 32_S | 40_G | 1.054 | 0.83 |
| 115_V | 125_E | 1.049 | 0.83 |
| 101_Y | 122_T | 1.040 | 0.82 |
| 9_K | 22_K | 1.037 | 0.82 |
| 93_L | 96_A | 1.030 | 0.81 |
| 24_S | 27_T | 1.028 | 0.81 |
| 113_G | 117_F | 1.015 | 0.80 |
| 65_F | 145_P | 1.013 | 0.80 |
| 69_S | 108_L | 1.012 | 0.79 |
| 39_I | 62_V | 1.012 | 0.79 |
| 62_V | 66_F | 1.006 | 0.79 |
| 31_R | 99_S | 1.003 | 0.79 |
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 | |
| 1cb6A | 1 | 0.9811 | 100 | 0.123 | Contact Map |
| 1blfA | 1 | 0.9811 | 100 | 0.128 | Contact Map |
| 2d3iA | 1 | 0.9874 | 100 | 0.128 | Contact Map |
| 3mc2A | 4 | 0.9245 | 100 | 0.132 | Contact Map |
| 3todA | 1 | 0.9308 | 100 | 0.174 | Contact Map |
| 1h45A | 1 | 0.9811 | 100 | 0.179 | Contact Map |
| 3skpA | 1 | 0.9245 | 100 | 0.183 | Contact Map |
| 3v83A | 6 | 0.9245 | 100 | 0.193 | Contact Map |
| 1ryoA | 1 | 0.9497 | 100 | 0.234 | Contact Map |
| 1iejA | 1 | 1 | 100 | 0.236 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)