| csga without signal peptide |
| ID: | 1493190184 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (112) | ||
| Sequences: | 553 (417.4) | ||
| Seq/Len: | 4.938 | ||
| Nf(neff/√len): | 39.4 |
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: 4.938).
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 |
| 27_I | 50_I | 2.507 | 1.00 |
| 83_L | 106_V | 2.223 | 1.00 |
| 72_L | 95_V | 2.093 | 1.00 |
| 65_S | 68_S | 1.932 | 1.00 |
| 52_Q | 74_Q | 1.840 | 1.00 |
| 95_V | 117_V | 1.803 | 1.00 |
| 50_I | 72_L | 1.756 | 1.00 |
| 93_M | 106_V | 1.753 | 1.00 |
| 38_A | 48_L | 1.721 | 1.00 |
| 93_M | 115_V | 1.666 | 0.99 |
| 27_I | 36_A | 1.626 | 0.99 |
| 95_V | 104_A | 1.622 | 0.99 |
| 23_S | 68_S | 1.603 | 0.99 |
| 48_L | 61_V | 1.574 | 0.99 |
| 27_I | 72_L | 1.555 | 0.99 |
| 104_A | 126_A | 1.516 | 0.99 |
| 46_S | 68_S | 1.503 | 0.98 |
| 36_A | 50_I | 1.499 | 0.98 |
| 38_A | 61_V | 1.465 | 0.98 |
| 50_I | 59_A | 1.464 | 0.98 |
| 36_A | 52_Q | 1.442 | 0.98 |
| 40_Q | 130_Q | 1.435 | 0.98 |
| 117_V | 126_A | 1.431 | 0.98 |
| 29_Q | 57_N | 1.413 | 0.97 |
| 76_G | 99_G | 1.405 | 0.97 |
| 63_Q | 85_Q | 1.363 | 0.97 |
| 36_A | 59_A | 1.355 | 0.97 |
| 115_V | 128_A | 1.348 | 0.96 |
| 25_L | 38_A | 1.343 | 0.96 |
| 103_G | 125_N | 1.341 | 0.96 |
| 32_G | 77_F | 1.328 | 0.96 |
| 31_G | 57_N | 1.323 | 0.96 |
| 72_L | 81_A | 1.304 | 0.95 |
| 97_Q | 119_Q | 1.275 | 0.95 |
| 34_N | 79_N | 1.269 | 0.94 |
| 110_A | 113_S | 1.266 | 0.94 |
| 107_D | 129_H | 1.261 | 0.94 |
| 78_G | 127_T | 1.257 | 0.94 |
| 34_N | 57_N | 1.255 | 0.94 |
| 113_S | 126_A | 1.255 | 0.94 |
| 61_V | 83_L | 1.246 | 0.94 |
| 85_Q | 108_Q | 1.241 | 0.94 |
| 100_G | 122_F | 1.240 | 0.94 |
| 104_A | 117_V | 1.216 | 0.93 |
| 32_G | 55_G | 1.182 | 0.91 |
| 40_Q | 63_Q | 1.182 | 0.91 |
| 87_N | 91_S | 1.160 | 0.90 |
| 61_V | 70_I | 1.110 | 0.87 |
| 91_S | 113_S | 1.102 | 0.87 |
| 121_G | 124_N | 1.096 | 0.87 |
| 25_L | 48_L | 1.094 | 0.86 |
| 48_L | 59_A | 1.093 | 0.86 |
| 76_G | 79_N | 1.089 | 0.86 |
| 65_S | 87_N | 1.088 | 0.86 |
| 93_M | 128_A | 1.071 | 0.85 |
| 79_N | 102_N | 1.071 | 0.85 |
| 106_V | 128_A | 1.071 | 0.85 |
| 81_A | 95_V | 1.058 | 0.84 |
| 59_A | 72_L | 1.045 | 0.83 |
| 42_D | 68_S | 1.044 | 0.83 |
| 61_V | 72_L | 1.022 | 0.81 |
| 66_D | 89_K | 1.006 | 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 | |
| 3devA | 2 | 0.3053 | 3 | 0.934 | Contact Map |
| 4py9A | 1 | 0.3282 | 1.9 | 0.941 | Contact Map |
| 2y9wC | 2 | 0.3359 | 1.4 | 0.945 | Contact Map |
| 2p6wA | 1 | 0.3206 | 0.9 | 0.952 | Contact Map |
| 4lnsA | 1 | 0.2901 | 0.7 | 0.954 | Contact Map |
| 2pifA | 2 | 0.2366 | 0.7 | 0.954 | Contact Map |
| 2rt4A | 1 | 0.1908 | 0.7 | 0.955 | Contact Map |
| 1q68B | 1 | 0.0763 | 0.6 | 0.956 | Contact Map |
| 2ysqA | 1 | 0.2061 | 0.6 | 0.957 | Contact Map |
| 1c6vX | 1 | 0.0382 | 0.6 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)