| GCase_as_3 |
| ID: | 1387752557 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 277 (135) | ||
| Sequences: | 835 (622.1) | ||
| Seq/Len: | 6.185 | ||
| Nf(neff/√len): | 53.5 |
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: 6.185).
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 |
| 71_S | 91_R | 4.216 | 1.00 |
| 100_V | 132_Y | 3.209 | 1.00 |
| 122_T | 132_Y | 2.589 | 1.00 |
| 91_R | 95_S | 2.092 | 1.00 |
| 71_S | 95_S | 2.064 | 1.00 |
| 10_N | 18_W | 2.057 | 1.00 |
| 22_N | 25_L | 2.012 | 1.00 |
| 88_A | 98_V | 2.003 | 1.00 |
| 11_L | 67_I | 1.813 | 1.00 |
| 45_D | 50_A | 1.723 | 1.00 |
| 124_S | 130_H | 1.695 | 1.00 |
| 61_G | 65_K | 1.659 | 1.00 |
| 44_V | 51_F | 1.551 | 0.99 |
| 12_L | 87_V | 1.547 | 0.99 |
| 68_P | 71_S | 1.542 | 0.99 |
| 3_Y | 6_S | 1.525 | 0.99 |
| 74_V | 96_A | 1.451 | 0.99 |
| 107_D | 123_V | 1.414 | 0.98 |
| 73_R | 89_L | 1.414 | 0.98 |
| 54_Q | 58_Y | 1.412 | 0.98 |
| 71_S | 93_D | 1.402 | 0.98 |
| 20_D | 41_P | 1.401 | 0.98 |
| 105_S | 127_Y | 1.372 | 0.98 |
| 84_L | 100_V | 1.370 | 0.98 |
| 66_F | 131_T | 1.343 | 0.98 |
| 20_D | 60_L | 1.335 | 0.98 |
| 76_L | 86_T | 1.323 | 0.97 |
| 40_S | 43_I | 1.311 | 0.97 |
| 67_I | 89_L | 1.308 | 0.97 |
| 25_L | 29_G | 1.303 | 0.97 |
| 109_P | 123_V | 1.291 | 0.97 |
| 4_S | 59_H | 1.241 | 0.96 |
| 43_I | 54_Q | 1.241 | 0.96 |
| 100_V | 124_S | 1.212 | 0.95 |
| 85_E | 103_R | 1.211 | 0.95 |
| 17_G | 23_L | 1.203 | 0.95 |
| 68_P | 91_R | 1.186 | 0.94 |
| 33_W | 38_V | 1.169 | 0.94 |
| 100_V | 110_L | 1.166 | 0.94 |
| 98_V | 112_I | 1.161 | 0.93 |
| 41_P | 56_M | 1.160 | 0.93 |
| 72_Q | 75_A | 1.157 | 0.93 |
| 20_D | 39_D | 1.150 | 0.93 |
| 8_I | 87_V | 1.150 | 0.93 |
| 45_D | 48_K | 1.148 | 0.93 |
| 22_N | 62_H | 1.145 | 0.93 |
| 71_S | 92_P | 1.142 | 0.93 |
| 24_A | 51_F | 1.128 | 0.92 |
| 109_P | 124_S | 1.121 | 0.92 |
| 32_N | 38_V | 1.118 | 0.92 |
| 35_R | 38_V | 1.112 | 0.91 |
| 17_G | 55_P | 1.112 | 0.91 |
| 58_Y | 62_H | 1.111 | 0.91 |
| 39_D | 43_I | 1.092 | 0.90 |
| 59_H | 129_I | 1.073 | 0.89 |
| 114_D | 134_W | 1.055 | 0.88 |
| 110_L | 124_S | 1.052 | 0.88 |
| 107_D | 126_G | 1.047 | 0.88 |
| 125_P | 132_Y | 1.037 | 0.87 |
| 90_L | 121_E | 1.035 | 0.87 |
| 9_T | 13_Y | 1.024 | 0.86 |
| 4_S | 101_L | 1.012 | 0.85 |
| 23_L | 31_P | 1.009 | 0.85 |
| 75_A | 94_G | 1.006 | 0.85 |
| 51_F | 62_H | 1.005 | 0.84 |
| 120_L | 132_Y | 1.003 | 0.84 |
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 | |
| 1xq8A | 1 | 0.5054 | 100 | 0.505 | Contact Map |
| 2nt0A | 4 | 0.4946 | 100 | 0.642 | Contact Map |
| 2wnwA | 2 | 0.4874 | 100 | 0.669 | Contact Map |
| 3clwA | 6 | 0.4549 | 100 | 0.714 | Contact Map |
| 4ccdA | 1 | 0.8448 | 99.9 | 0.74 | Contact Map |
| 3kl0A | 4 | 0.4513 | 99.9 | 0.741 | Contact Map |
| 4fmvA | 1 | 0.426 | 99.9 | 0.742 | Contact Map |
| 2y24A | 1 | 0.426 | 99.9 | 0.746 | Contact Map |
| 2c7fA | 6 | 0.5415 | 99.1 | 0.874 | Contact Map |
| 4m29A | 1 | 0.509 | 99 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)