| NikRcovariance |
| ID: | 1500905713 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 133 (133) | ||
| Sequences: | 755 (519.9) | ||
| Seq/Len: | 5.677 | ||
| Nf(neff/√len): | 45.1 |
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: 5.677).
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 |
| 91_N | 94_D | 2.960 | 1.00 |
| 87_H | 95_C | 2.886 | 1.00 |
| 56_L | 101_L | 2.805 | 1.00 |
| 30_E | 33_R | 2.294 | 1.00 |
| 62_H | 76_H | 2.266 | 1.00 |
| 76_H | 95_C | 2.184 | 1.00 |
| 8_L | 36_L | 2.129 | 1.00 |
| 116_I | 124_G | 2.127 | 1.00 |
| 89_H | 95_C | 2.105 | 1.00 |
| 94_D | 122_R | 2.094 | 1.00 |
| 30_E | 37_R | 1.965 | 1.00 |
| 25_Y | 34_D | 1.939 | 1.00 |
| 76_H | 89_H | 1.855 | 1.00 |
| 77_H | 114_D | 1.840 | 1.00 |
| 62_H | 89_H | 1.791 | 1.00 |
| 104_D | 107_D | 1.790 | 1.00 |
| 49_G | 106_G | 1.782 | 1.00 |
| 52_G | 108_V | 1.729 | 1.00 |
| 16_L | 31_A | 1.696 | 1.00 |
| 110_H | 114_D | 1.618 | 0.99 |
| 35_I | 39_A | 1.611 | 0.99 |
| 54_A | 101_L | 1.567 | 0.99 |
| 15_T | 44_A | 1.559 | 0.99 |
| 57_S | 127_Q | 1.555 | 0.99 |
| 13_L | 17_D | 1.532 | 0.99 |
| 76_H | 87_H | 1.469 | 0.99 |
| 1_M | 5_T | 1.444 | 0.98 |
| 62_H | 95_C | 1.427 | 0.98 |
| 16_L | 36_L | 1.409 | 0.98 |
| 77_H | 107_D | 1.403 | 0.98 |
| 17_D | 28_R | 1.314 | 0.97 |
| 77_H | 92_H | 1.311 | 0.97 |
| 30_E | 34_D | 1.278 | 0.96 |
| 78_H | 110_H | 1.263 | 0.96 |
| 72_V | 76_H | 1.259 | 0.96 |
| 80_D | 107_D | 1.239 | 0.95 |
| 62_H | 87_H | 1.237 | 0.95 |
| 34_D | 121_V | 1.232 | 0.95 |
| 18_S | 47_Q | 1.207 | 0.94 |
| 4_V | 7_T | 1.206 | 0.94 |
| 83_V | 102_K | 1.198 | 0.94 |
| 25_Y | 30_E | 1.186 | 0.93 |
| 58_Y | 99_A | 1.150 | 0.92 |
| 71_I | 115_V | 1.148 | 0.92 |
| 50_T | 104_D | 1.128 | 0.91 |
| 63_E | 92_H | 1.128 | 0.91 |
| 44_A | 132_E | 1.126 | 0.91 |
| 2_Q | 5_T | 1.110 | 0.90 |
| 1_M | 10_D | 1.100 | 0.89 |
| 18_S | 22_R | 1.093 | 0.89 |
| 58_Y | 115_V | 1.087 | 0.89 |
| 87_H | 97_E | 1.070 | 0.87 |
| 15_T | 24_G | 1.056 | 0.87 |
| 107_D | 110_H | 1.053 | 0.86 |
| 32_I | 98_I | 1.052 | 0.86 |
| 112_A | 124_G | 1.037 | 0.85 |
| 53_F | 90_I | 1.034 | 0.85 |
| 60_Y | 97_E | 1.026 | 0.84 |
| 20_S | 25_Y | 1.020 | 0.84 |
| 79_H | 90_I | 1.012 | 0.83 |
| 16_L | 20_S | 1.011 | 0.83 |
| 86_L | 98_I | 1.004 | 0.83 |
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 | |
| 2wvfA | 2 | 1 | 100 | 0.075 | Contact Map |
| 2hzaA | 2 | 0.985 | 100 | 0.096 | Contact Map |
| 2bj7A | 2 | 1 | 100 | 0.133 | Contact Map |
| 1q5yA | 4 | 0.6316 | 99.9 | 0.464 | Contact Map |
| 2nzcA | 4 | 0.6165 | 99.8 | 0.53 | Contact Map |
| 3kxeC | 2 | 0.5414 | 98.8 | 0.722 | Contact Map |
| 2k5jA | 2 | 0.5414 | 98.7 | 0.727 | Contact Map |
| 4me7E | 2 | 0.594 | 98.7 | 0.732 | Contact Map |
| 2cpgA | 3 | 0.3308 | 98.4 | 0.756 | Contact Map |
| 2k9iA | 2 | 0.3534 | 98 | 0.777 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)