| pglC_aln |
| ID: | 1420659129 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (185) | ||
| Sequences: | 3902 (3015) | ||
| Seq/Len: | 21.092 | ||
| Nf(neff/√len): | 221.7 |
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: 21.092).
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 |
| 8_R | 12_F | 3.634 | 1.00 |
| 45_N | 53_I | 3.223 | 1.00 |
| 29_T | 91_L | 3.158 | 1.00 |
| 43_T | 55_K | 3.012 | 1.00 |
| 158_Y | 162_N | 3.004 | 1.00 |
| 32_L | 82_F | 2.961 | 1.00 |
| 45_N | 55_K | 2.890 | 1.00 |
| 100_V | 135_I | 2.780 | 1.00 |
| 61_T | 86_V | 2.675 | 1.00 |
| 85_I | 89_L | 2.595 | 1.00 |
| 36_T | 81_A | 2.311 | 1.00 |
| 19_L | 98_F | 2.293 | 1.00 |
| 127_L | 161_K | 2.272 | 1.00 |
| 138_W | 142_N | 2.227 | 1.00 |
| 30_A | 40_V | 2.029 | 1.00 |
| 170_K | 174_L | 2.012 | 1.00 |
| 108_V | 136_T | 1.965 | 1.00 |
| 151_K | 154_E | 1.954 | 1.00 |
| 10_F | 14_L | 1.902 | 1.00 |
| 138_W | 158_Y | 1.893 | 1.00 |
| 16_L | 101_L | 1.858 | 1.00 |
| 48_G | 133_P | 1.840 | 1.00 |
| 57_Y | 99_N | 1.821 | 1.00 |
| 34_K | 40_V | 1.762 | 1.00 |
| 29_T | 86_V | 1.762 | 1.00 |
| 43_T | 57_Y | 1.742 | 1.00 |
| 15_A | 19_L | 1.725 | 1.00 |
| 11_D | 106_S | 1.711 | 1.00 |
| 41_I | 57_Y | 1.706 | 1.00 |
| 114_L | 117_Y | 1.700 | 1.00 |
| 29_T | 59_F | 1.610 | 1.00 |
| 174_L | 178_K | 1.600 | 1.00 |
| 34_K | 38_G | 1.583 | 1.00 |
| 53_I | 115_V | 1.542 | 1.00 |
| 113_L | 117_Y | 1.518 | 1.00 |
| 177_L | 181_K | 1.509 | 1.00 |
| 26_I | 59_F | 1.492 | 1.00 |
| 7_K | 168_D | 1.487 | 1.00 |
| 131_V | 160_V | 1.481 | 1.00 |
| 108_V | 172_M | 1.479 | 1.00 |
| 127_L | 130_K | 1.474 | 1.00 |
| 28_I | 32_L | 1.467 | 1.00 |
| 98_F | 102_K | 1.462 | 1.00 |
| 22_F | 26_I | 1.454 | 1.00 |
| 14_L | 107_F | 1.447 | 1.00 |
| 158_Y | 167_L | 1.432 | 1.00 |
| 47_P | 53_I | 1.415 | 1.00 |
| 31_L | 35_I | 1.411 | 1.00 |
| 82_F | 86_V | 1.407 | 0.99 |
| 39_S | 64_D | 1.386 | 0.99 |
| 143_G | 147_I | 1.381 | 0.99 |
| 90_S | 144_R | 1.363 | 0.99 |
| 18_L | 22_F | 1.336 | 0.99 |
| 49_L | 132_R | 1.328 | 0.99 |
| 39_S | 60_K | 1.302 | 0.99 |
| 137_G | 140_Q | 1.288 | 0.99 |
| 7_K | 11_D | 1.287 | 0.99 |
| 18_L | 107_F | 1.285 | 0.99 |
| 20_V | 23_S | 1.274 | 0.99 |
| 15_A | 101_L | 1.255 | 0.99 |
| 88_S | 182_R | 1.251 | 0.99 |
| 33_L | 36_T | 1.251 | 0.99 |
| 12_F | 16_L | 1.240 | 0.98 |
| 138_W | 171_I | 1.224 | 0.98 |
| 107_F | 172_M | 1.212 | 0.98 |
| 18_L | 97_L | 1.211 | 0.98 |
| 12_F | 101_L | 1.174 | 0.98 |
| 19_L | 23_S | 1.159 | 0.97 |
| 159_Y | 168_D | 1.157 | 0.97 |
| 97_L | 107_F | 1.157 | 0.97 |
| 138_W | 167_L | 1.152 | 0.97 |
| 142_N | 174_L | 1.140 | 0.97 |
| 137_G | 152_K | 1.136 | 0.97 |
| 44_Q | 56_I | 1.111 | 0.96 |
| 12_F | 15_A | 1.109 | 0.96 |
| 172_M | 176_A | 1.096 | 0.96 |
| 117_Y | 121_Y | 1.088 | 0.96 |
| 63_S | 66_R | 1.086 | 0.96 |
| 128_R | 156_D | 1.080 | 0.95 |
| 113_L | 118_L | 1.075 | 0.95 |
| 115_V | 119_S | 1.072 | 0.95 |
| 99_N | 104_D | 1.066 | 0.95 |
| 165_F | 169_L | 1.059 | 0.95 |
| 16_L | 20_V | 1.040 | 0.94 |
| 94_L | 97_L | 1.038 | 0.94 |
| 179_V | 184_G | 1.038 | 0.94 |
| 7_K | 106_S | 1.032 | 0.94 |
| 3_E | 163_I | 1.032 | 0.94 |
| 138_W | 155_L | 1.012 | 0.93 |
| 24_P | 27_L | 1.004 | 0.93 |
| 113_L | 149_W | 1.002 | 0.92 |
| 51_E | 129_H | 1.001 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3hinA | 2 | 0.39 | 3.3 | 0.972 | Contact Map |
| 3wguG | 2 | 0.175 | 3 | 0.972 | Contact Map |
| 4c48C | 1 | 0.23 | 2.6 | 0.973 | Contact Map |
| 2clyA | 2 | 0.095 | 2 | 0.975 | Contact Map |
| 1ul1X | 3 | 0.325 | 1.9 | 0.975 | Contact Map |
| 4k0jA | 6 | 0.165 | 1.8 | 0.975 | Contact Map |
| 4q0wA | 2 | 0.29 | 1.6 | 0.976 | Contact Map |
| 1hywA | 1 | 0.24 | 1.6 | 0.976 | Contact Map |
| 3j7aN | 1 | 0.2 | 1.5 | 0.977 | Contact Map |
| 2bzwB | 1 | 0.135 | 1.5 | 0.977 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)