| CgHELLPc |
| ID: | 1494421501 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 160 (151) | ||
| Sequences: | 1414 (1176.6) | ||
| Seq/Len: | 9.364 | ||
| Nf(neff/√len): | 95.8 |
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: 9.364).
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 |
| 3_E | 6_G | 6.503 | 1.00 |
| 38_T | 118_Q | 2.873 | 1.00 |
| 16_A | 20_H | 2.858 | 1.00 |
| 4_A | 8_A | 2.782 | 1.00 |
| 5_L | 10_S | 2.620 | 1.00 |
| 45_D | 132_H | 2.448 | 1.00 |
| 28_D | 114_G | 2.242 | 1.00 |
| 13_G | 16_A | 2.180 | 1.00 |
| 83_S | 87_N | 2.172 | 1.00 |
| 57_Q | 61_E | 2.119 | 1.00 |
| 12_V | 17_T | 2.076 | 1.00 |
| 4_A | 7_V | 2.034 | 1.00 |
| 90_G | 94_K | 1.970 | 1.00 |
| 132_H | 137_S | 1.901 | 1.00 |
| 45_D | 125_S | 1.817 | 1.00 |
| 5_L | 9_G | 1.757 | 1.00 |
| 2_A | 6_G | 1.732 | 1.00 |
| 80_A | 83_S | 1.674 | 1.00 |
| 82_C | 131_C | 1.671 | 1.00 |
| 136_T | 140_S | 1.658 | 1.00 |
| 129_Q | 132_H | 1.648 | 1.00 |
| 31_N | 118_Q | 1.614 | 1.00 |
| 89_F | 124_M | 1.481 | 1.00 |
| 111_G | 114_G | 1.468 | 1.00 |
| 1_M | 4_A | 1.435 | 1.00 |
| 129_Q | 133_T | 1.427 | 0.99 |
| 122_K | 126_Q | 1.418 | 0.99 |
| 7_V | 10_S | 1.383 | 0.99 |
| 11_I | 15_V | 1.376 | 0.99 |
| 50_D | 54_E | 1.356 | 0.99 |
| 12_V | 16_A | 1.351 | 0.99 |
| 137_S | 140_S | 1.288 | 0.99 |
| 21_V | 46_L | 1.253 | 0.98 |
| 5_L | 13_G | 1.252 | 0.98 |
| 132_H | 136_T | 1.248 | 0.98 |
| 8_A | 14_I | 1.243 | 0.98 |
| 75_A | 128_L | 1.232 | 0.98 |
| 32_I | 35_A | 1.186 | 0.97 |
| 76_E | 80_A | 1.166 | 0.97 |
| 20_H | 23_R | 1.160 | 0.97 |
| 6_G | 10_S | 1.129 | 0.96 |
| 9_G | 12_V | 1.128 | 0.96 |
| 85_A | 88_T | 1.116 | 0.96 |
| 8_A | 26_V | 1.114 | 0.96 |
| 29_V | 32_I | 1.108 | 0.96 |
| 10_S | 13_G | 1.086 | 0.95 |
| 52_A | 137_S | 1.082 | 0.95 |
| 56_L | 138_M | 1.079 | 0.95 |
| 3_E | 7_V | 1.073 | 0.95 |
| 80_A | 90_G | 1.072 | 0.95 |
| 46_L | 128_L | 1.065 | 0.94 |
| 16_A | 19_L | 1.063 | 0.94 |
| 50_D | 90_G | 1.053 | 0.94 |
| 110_R | 114_G | 1.038 | 0.93 |
| 30_R | 33_H | 1.030 | 0.93 |
| 15_V | 57_Q | 1.018 | 0.92 |
| 9_G | 14_I | 1.016 | 0.92 |
| 8_A | 15_V | 1.003 | 0.92 |
| 49_A | 128_L | 1.003 | 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 | |
| 4btfA | 1 | 0.675 | 96.2 | 0.745 | Contact Map |
| 2wvqA | 2 | 0.9375 | 92.4 | 0.79 | Contact Map |
| 2msvA | 1 | 0.8562 | 91.5 | 0.795 | Contact Map |
| 3qflA | 1 | 0.6875 | 39.5 | 0.868 | Contact Map |
| 2kk1A | 1 | 0.5437 | 33.7 | 0.873 | Contact Map |
| 4j2cA | 2 | 0.5625 | 23.3 | 0.883 | Contact Map |
| 3ghgA | 4 | 0.675 | 23.3 | 0.883 | Contact Map |
| 1zzpA | 1 | 0.5563 | 22.4 | 0.884 | Contact Map |
| 2ljbA | 4 | 0.1875 | 18 | 0.889 | Contact Map |
| 4dndA | 1 | 0.575 | 17.3 | 0.89 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)