| cc |
| ID: | 1378828938 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (131) | ||
| Sequences: | 558 (432.3) | ||
| Seq/Len: | 4.260 | ||
| Nf(neff/√len): | 37.8 |
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: 4.260).
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 |
| 63_Q | 85_Q | 3.022 | 1.00 |
| 40_Q | 63_Q | 2.929 | 1.00 |
| 93_M | 115_V | 2.704 | 1.00 |
| 40_Q | 85_Q | 2.670 | 1.00 |
| 70_I | 93_M | 2.414 | 1.00 |
| 61_V | 83_L | 2.123 | 1.00 |
| 25_L | 48_L | 2.085 | 1.00 |
| 59_A | 81_A | 1.977 | 1.00 |
| 108_Q | 130_Q | 1.974 | 1.00 |
| 1_G | 5_Q | 1.813 | 1.00 |
| 65_S | 110_A | 1.813 | 1.00 |
| 68_S | 91_S | 1.790 | 1.00 |
| 81_A | 104_A | 1.699 | 0.99 |
| 36_A | 59_A | 1.694 | 0.99 |
| 50_I | 72_L | 1.685 | 0.99 |
| 85_Q | 108_Q | 1.640 | 0.99 |
| 27_I | 50_I | 1.612 | 0.99 |
| 8_G | 11_N | 1.603 | 0.99 |
| 83_L | 106_V | 1.600 | 0.99 |
| 25_L | 38_A | 1.598 | 0.99 |
| 72_L | 95_V | 1.586 | 0.99 |
| 63_Q | 108_Q | 1.541 | 0.98 |
| 42_D | 46_S | 1.528 | 0.98 |
| 20_G | 23_S | 1.479 | 0.98 |
| 55_G | 77_F | 1.478 | 0.98 |
| 115_V | 130_Q | 1.450 | 0.97 |
| 79_N | 102_N | 1.445 | 0.97 |
| 54_G | 76_G | 1.424 | 0.97 |
| 38_A | 61_V | 1.408 | 0.97 |
| 27_I | 36_A | 1.384 | 0.96 |
| 40_Q | 108_Q | 1.367 | 0.96 |
| 57_N | 79_N | 1.344 | 0.95 |
| 7_G | 10_G | 1.329 | 0.95 |
| 65_S | 68_S | 1.326 | 0.95 |
| 13_G | 17_N | 1.323 | 0.95 |
| 110_A | 113_S | 1.295 | 0.94 |
| 33_G | 55_G | 1.265 | 0.93 |
| 65_S | 88_G | 1.252 | 0.92 |
| 93_M | 106_V | 1.196 | 0.90 |
| 97_Q | 119_Q | 1.170 | 0.88 |
| 102_N | 124_N | 1.164 | 0.88 |
| 95_V | 117_V | 1.164 | 0.88 |
| 108_Q | 115_V | 1.156 | 0.87 |
| 88_G | 91_S | 1.133 | 0.86 |
| 36_A | 50_I | 1.132 | 0.86 |
| 81_A | 95_V | 1.124 | 0.85 |
| 48_L | 70_I | 1.088 | 0.83 |
| 42_D | 45_N | 1.088 | 0.83 |
| 106_V | 128_A | 1.080 | 0.82 |
| 46_S | 68_S | 1.077 | 0.82 |
| 11_N | 15_G | 1.077 | 0.82 |
| 24_E | 28_Y | 1.071 | 0.81 |
| 100_G | 122_F | 1.070 | 0.81 |
| 31_G | 54_G | 1.065 | 0.81 |
| 59_A | 104_A | 1.050 | 0.80 |
| 59_A | 72_L | 1.015 | 0.76 |
| 71_D | 94_T | 1.009 | 0.76 |
| 77_F | 100_G | 1.008 | 0.76 |
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 | |
| 1wz4A | 1 | 0.0611 | 0.2 | 0.969 | Contact Map |
| 1rf8B | 1 | 0.2595 | 0.2 | 0.969 | Contact Map |
| 2odkA | 4 | 0.3282 | 0.2 | 0.97 | Contact Map |
| 3gqbB | 2 | 0.3053 | 0.1 | 0.971 | Contact Map |
| 2fiqA | 4 | 0.3359 | 0.1 | 0.971 | Contact Map |
| 1gv3A | 2 | 0.2519 | 0.1 | 0.972 | Contact Map |
| 1jmuA | 3 | 0.1221 | 0.1 | 0.973 | Contact Map |
| 2lpdA | 1 | 0.2443 | 0.1 | 0.974 | Contact Map |
| 1mn8A | 4 | 0.2443 | 0.1 | 0.975 | Contact Map |
| 3mwdB | 1 | 0.3359 | 0.1 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)