| krjob |
| ID: | 1488227446 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 188 (166) | ||
| Sequences: | 37586 (20076.7) | ||
| Seq/Len: | 226.422 | ||
| Nf(neff/√len): | 1558.3 |
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: 226.422).
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 |
| 22_Q | 149_R | 3.293 | 1.00 |
| 142_I | 158_T | 3.030 | 1.00 |
| 11_A | 92_D | 2.755 | 1.00 |
| 84_I | 115_G | 2.470 | 1.00 |
| 158_T | 161_R | 2.400 | 1.00 |
| 81_V | 116_N | 2.382 | 1.00 |
| 114_V | 155_A | 2.378 | 1.00 |
| 79_L | 114_V | 2.154 | 1.00 |
| 19_L | 81_V | 2.146 | 1.00 |
| 158_T | 162_E | 2.080 | 1.00 |
| 140_P | 158_T | 2.068 | 1.00 |
| 115_G | 143_E | 2.033 | 1.00 |
| 4_Y | 163_I | 1.968 | 1.00 |
| 97_R | 111_M | 1.960 | 1.00 |
| 118_C | 143_E | 1.935 | 1.00 |
| 116_N | 146_A | 1.878 | 1.00 |
| 7_V | 75_G | 1.876 | 1.00 |
| 114_V | 144_T | 1.842 | 1.00 |
| 8_V | 20_T | 1.812 | 1.00 |
| 77_G | 159_L | 1.802 | 1.00 |
| 151_G | 154_D | 1.795 | 1.00 |
| 118_C | 150_Q | 1.788 | 1.00 |
| 18_A | 146_A | 1.784 | 1.00 |
| 53_L | 160_V | 1.754 | 1.00 |
| 79_L | 159_L | 1.662 | 1.00 |
| 80_C | 97_R | 1.643 | 1.00 |
| 5_K | 54_D | 1.636 | 1.00 |
| 144_T | 155_A | 1.632 | 1.00 |
| 19_L | 152_V | 1.630 | 1.00 |
| 82_F | 141_F | 1.620 | 1.00 |
| 131_Q | 135_R | 1.617 | 1.00 |
| 112_V | 158_T | 1.567 | 1.00 |
| 112_V | 142_I | 1.563 | 1.00 |
| 19_L | 155_A | 1.562 | 1.00 |
| 84_I | 118_C | 1.512 | 1.00 |
| 43_Q | 52_L | 1.453 | 1.00 |
| 162_E | 165_K | 1.422 | 1.00 |
| 130_A | 134_A | 1.418 | 1.00 |
| 82_F | 113_L | 1.407 | 0.99 |
| 85_N | 120_L | 1.396 | 0.99 |
| 83_A | 86_N | 1.386 | 0.99 |
| 97_R | 101_K | 1.360 | 0.99 |
| 87_T | 129_Q | 1.353 | 0.99 |
| 98_E | 102_R | 1.339 | 0.99 |
| 21_I | 29_V | 1.321 | 0.99 |
| 132_D | 136_S | 1.311 | 0.99 |
| 22_Q | 152_V | 1.287 | 0.99 |
| 153_D | 157_Y | 1.262 | 0.99 |
| 127_T | 131_Q | 1.233 | 0.98 |
| 79_L | 112_V | 1.224 | 0.98 |
| 23_L | 156_F | 1.223 | 0.98 |
| 83_A | 117_K | 1.214 | 0.98 |
| 3_E | 54_D | 1.212 | 0.98 |
| 86_N | 89_S | 1.209 | 0.98 |
| 129_Q | 132_D | 1.200 | 0.98 |
| 154_D | 157_Y | 1.200 | 0.98 |
| 77_G | 163_I | 1.190 | 0.98 |
| 51_C | 160_V | 1.187 | 0.98 |
| 131_Q | 134_A | 1.174 | 0.98 |
| 88_K | 91_E | 1.173 | 0.98 |
| 110_P | 162_E | 1.171 | 0.98 |
| 80_C | 93_I | 1.164 | 0.97 |
| 82_F | 115_G | 1.160 | 0.97 |
| 115_G | 141_F | 1.156 | 0.97 |
| 8_V | 79_L | 1.154 | 0.97 |
| 19_L | 23_L | 1.148 | 0.97 |
| 157_Y | 161_R | 1.136 | 0.97 |
| 117_K | 120_L | 1.131 | 0.97 |
| 130_A | 143_E | 1.125 | 0.97 |
| 19_L | 146_A | 1.114 | 0.96 |
| 45_V | 50_T | 1.107 | 0.96 |
| 119_D | 145_S | 1.103 | 0.96 |
| 130_A | 141_F | 1.103 | 0.96 |
| 10_G | 15_G | 1.102 | 0.96 |
| 114_V | 142_I | 1.094 | 0.96 |
| 126_D | 129_Q | 1.087 | 0.96 |
| 132_D | 135_R | 1.072 | 0.95 |
| 133_L | 137_Y | 1.069 | 0.95 |
| 79_L | 155_A | 1.064 | 0.95 |
| 140_P | 162_E | 1.053 | 0.95 |
| 152_V | 156_F | 1.052 | 0.95 |
| 99_Q | 102_R | 1.047 | 0.94 |
| 156_F | 159_L | 1.045 | 0.94 |
| 5_K | 56_L | 1.035 | 0.94 |
| 128_K | 132_D | 1.014 | 0.93 |
| 98_E | 101_K | 1.011 | 0.93 |
| 11_A | 14_V | 1.009 | 0.93 |
| 81_V | 144_T | 1.005 | 0.93 |
| 3_E | 52_L | 1.002 | 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
- 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 | |
| 4dsuA | 1 | 0.9415 | 100 | 0.205 | Contact Map |
| 2j0vA | 4 | 0.8883 | 100 | 0.235 | Contact Map |
| 2gf0A | 4 | 0.9096 | 100 | 0.239 | Contact Map |
| 2bovA | 1 | 0.9096 | 100 | 0.241 | Contact Map |
| 3conA | 1 | 0.8298 | 100 | 0.282 | Contact Map |
| 2ce2X | 1 | 0.883 | 100 | 0.282 | Contact Map |
| 1m7bA | 1 | 0.867 | 100 | 0.285 | Contact Map |
| 3regA | 2 | 0.883 | 100 | 0.286 | Contact Map |
| 4klzA | 1 | 0.8245 | 100 | 0.287 | Contact Map |
| 3kkqA | 1 | 0.883 | 100 | 0.29 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)