| csgafull |
| ID: | 1493258362 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (145) | ||
| Sequences: | 906 (755.3) | ||
| Seq/Len: | 6.248 | ||
| Nf(neff/√len): | 62.7 |
Jackhmmer Results: (2016_04)
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: 6.248).
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 |
| 43_S | 66_S | 2.750 | 1.00 |
| 105_Q | 128_Q | 2.704 | 1.00 |
| 83_Q | 105_Q | 2.667 | 1.00 |
| 115_V | 137_V | 2.567 | 1.00 |
| 47_I | 70_I | 2.367 | 1.00 |
| 92_L | 115_V | 2.334 | 1.00 |
| 60_Q | 83_Q | 2.309 | 1.00 |
| 72_Q | 94_Q | 2.188 | 1.00 |
| 45_L | 68_L | 2.142 | 1.00 |
| 126_V | 148_A | 2.114 | 1.00 |
| 77_N | 99_N | 2.083 | 1.00 |
| 79_A | 101_A | 2.040 | 1.00 |
| 83_Q | 128_Q | 2.012 | 1.00 |
| 70_I | 92_L | 2.005 | 1.00 |
| 111_S | 133_S | 1.995 | 1.00 |
| 90_I | 113_M | 1.983 | 1.00 |
| 113_M | 135_V | 1.980 | 1.00 |
| 94_Q | 117_Q | 1.971 | 1.00 |
| 101_A | 124_A | 1.953 | 1.00 |
| 58_A | 68_L | 1.910 | 1.00 |
| 124_A | 146_A | 1.883 | 1.00 |
| 88_S | 111_S | 1.866 | 1.00 |
| 72_Q | 117_Q | 1.853 | 1.00 |
| 117_Q | 139_Q | 1.852 | 1.00 |
| 60_Q | 105_Q | 1.815 | 1.00 |
| 99_N | 122_N | 1.777 | 1.00 |
| 120_G | 142_F | 1.763 | 1.00 |
| 101_A | 146_A | 1.740 | 1.00 |
| 54_N | 77_N | 1.673 | 1.00 |
| 79_A | 124_A | 1.621 | 1.00 |
| 103_L | 126_V | 1.618 | 1.00 |
| 81_V | 103_L | 1.617 | 1.00 |
| 66_S | 88_S | 1.614 | 1.00 |
| 63_A | 66_S | 1.613 | 1.00 |
| 122_N | 144_N | 1.575 | 0.99 |
| 81_V | 90_I | 1.566 | 0.99 |
| 45_L | 58_A | 1.530 | 0.99 |
| 113_M | 126_V | 1.512 | 0.99 |
| 56_A | 79_A | 1.499 | 0.99 |
| 108_G | 111_S | 1.392 | 0.98 |
| 108_G | 130_A | 1.378 | 0.98 |
| 56_A | 70_I | 1.361 | 0.98 |
| 128_Q | 150_Q | 1.349 | 0.98 |
| 97_F | 120_G | 1.312 | 0.97 |
| 101_A | 115_V | 1.264 | 0.96 |
| 124_A | 137_V | 1.260 | 0.96 |
| 130_A | 133_S | 1.200 | 0.95 |
| 58_A | 81_V | 1.196 | 0.95 |
| 90_I | 135_V | 1.189 | 0.94 |
| 88_S | 133_S | 1.172 | 0.94 |
| 113_M | 128_Q | 1.145 | 0.93 |
| 52_G | 75_G | 1.140 | 0.93 |
| 8_A | 13_V | 1.122 | 0.92 |
| 92_L | 137_V | 1.120 | 0.92 |
| 90_I | 103_L | 1.114 | 0.91 |
| 81_V | 92_L | 1.110 | 0.91 |
| 60_Q | 128_Q | 1.065 | 0.89 |
| 103_L | 113_M | 1.050 | 0.88 |
| 85_S | 88_S | 1.036 | 0.87 |
| 72_Q | 139_Q | 1.032 | 0.87 |
| 82_G | 104_D | 1.028 | 0.86 |
| 101_A | 117_Q | 1.027 | 0.86 |
| 68_L | 113_M | 1.016 | 0.86 |
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 | |
| 3zbiC | 14 | 0.1854 | 11.5 | 0.911 | Contact Map |
| 2jnaA | 2 | 0.5695 | 6.8 | 0.92 | Contact Map |
| 2nocA | 1 | 0.6093 | 4.2 | 0.927 | Contact Map |
| 1tzsX | 1 | 0.0331 | 3.6 | 0.93 | Contact Map |
| 1dbgA | 1 | 0.6954 | 3.1 | 0.932 | Contact Map |
| 2vdaB | 1 | 0.1325 | 2.9 | 0.933 | Contact Map |
| 1qleD | 1 | 0.1391 | 2 | 0.939 | Contact Map |
| 1m56D | 2 | 0.1391 | 2 | 0.939 | Contact Map |
| 3j45G | 1 | 0.1457 | 1.5 | 0.943 | Contact Map |
| 2akhX | 2 | 0.1722 | 1.4 | 0.944 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)