| ctgm |
| ID: | 1443700290 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (135) | ||
| Sequences: | 2254 (1617.6) | ||
| Seq/Len: | 16.696 | ||
| Nf(neff/√len): | 139.2 |
HHblits Results: (2015_06)
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: 16.696).
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 |
| 21_G | 44_A | 3.654 | 1.00 |
| 50_F | 102_G | 3.104 | 1.00 |
| 17_A | 48_A | 3.101 | 1.00 |
| 99_C | 122_I | 2.649 | 1.00 |
| 24_I | 100_S | 2.590 | 1.00 |
| 43_V | 97_L | 2.437 | 1.00 |
| 107_C | 115_A | 2.291 | 1.00 |
| 49_V | 118_A | 2.262 | 1.00 |
| 41_A | 125_A | 2.148 | 1.00 |
| 20_L | 119_T | 2.134 | 1.00 |
| 20_L | 103_I | 1.980 | 1.00 |
| 20_L | 107_C | 1.933 | 1.00 |
| 48_A | 107_C | 1.928 | 1.00 |
| 23_L | 123_L | 1.889 | 1.00 |
| 69_I | 105_V | 1.809 | 1.00 |
| 42_L | 99_C | 1.674 | 1.00 |
| 24_I | 122_I | 1.637 | 1.00 |
| 111_Q | 114_N | 1.606 | 1.00 |
| 13_N | 110_G | 1.557 | 1.00 |
| 40_N | 96_T | 1.538 | 1.00 |
| 40_N | 93_T | 1.511 | 1.00 |
| 9_P | 13_N | 1.479 | 1.00 |
| 18_M | 41_A | 1.475 | 1.00 |
| 51_I | 105_V | 1.468 | 1.00 |
| 46_G | 99_C | 1.446 | 1.00 |
| 17_A | 21_G | 1.407 | 0.99 |
| 103_I | 119_T | 1.392 | 0.99 |
| 11_I | 117_A | 1.378 | 0.99 |
| 22_A | 41_A | 1.363 | 0.99 |
| 7_M | 113_K | 1.359 | 0.99 |
| 22_A | 37_L | 1.352 | 0.99 |
| 20_L | 116_L | 1.347 | 0.99 |
| 78_A | 82_M | 1.332 | 0.99 |
| 20_L | 115_A | 1.332 | 0.99 |
| 96_T | 126_N | 1.314 | 0.99 |
| 68_Q | 71_S | 1.307 | 0.99 |
| 51_I | 66_A | 1.298 | 0.99 |
| 8_F | 11_I | 1.268 | 0.99 |
| 15_L | 19_L | 1.244 | 0.98 |
| 18_M | 45_T | 1.233 | 0.98 |
| 46_G | 101_A | 1.232 | 0.98 |
| 47_A | 101_A | 1.231 | 0.98 |
| 40_N | 100_S | 1.226 | 0.98 |
| 42_L | 122_I | 1.194 | 0.98 |
| 50_F | 74_G | 1.175 | 0.98 |
| 16_A | 107_C | 1.171 | 0.98 |
| 44_A | 100_S | 1.160 | 0.97 |
| 90_G | 94_A | 1.156 | 0.97 |
| 53_S | 106_L | 1.123 | 0.97 |
| 51_I | 109_L | 1.115 | 0.96 |
| 13_N | 52_L | 1.113 | 0.96 |
| 124_C | 128_L | 1.109 | 0.96 |
| 77_G | 94_A | 1.082 | 0.96 |
| 69_I | 72_G | 1.079 | 0.95 |
| 59_P | 65_I | 1.075 | 0.95 |
| 18_M | 125_A | 1.046 | 0.94 |
| 56_T | 111_Q | 1.043 | 0.94 |
| 50_F | 65_I | 1.025 | 0.93 |
| 72_G | 78_A | 1.011 | 0.93 |
| 54_S | 66_A | 1.008 | 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 | |
| 4j05A | 2 | 0.8811 | 7.3 | 0.934 | Contact Map |
| 4ldsA | 2 | 1 | 3.4 | 0.944 | Contact Map |
| 4pypA | 1 | 1 | 2.8 | 0.946 | Contact Map |
| 2nwlA | 3 | 0.8601 | 2.2 | 0.949 | Contact Map |
| 3lb6A | 1 | 0.1469 | 2.2 | 0.949 | Contact Map |
| 3j2wE | 4 | 0.3217 | 2.1 | 0.95 | Contact Map |
| 4huqS | 1 | 0.6643 | 2.1 | 0.95 | Contact Map |
| 2kncB | 1 | 0.3427 | 2 | 0.95 | Contact Map |
| 4gc0A | 1 | 1 | 2 | 0.95 | Contact Map |
| 1kvdA | 2 | 0.2937 | 1.9 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)