| TM_SLC26A4 wt 321-420 |
| ID: | 1476762389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (100) | ||
| Sequences: | 9232 (4503.8) | ||
| Seq/Len: | 92.320 | ||
| Nf(neff/√len): | 450.4 |
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: 92.320).
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 |
| 81_V | 93_A | 3.449 | 1.00 |
| 6_Q | 16_A | 3.416 | 1.00 |
| 26_I | 30_A | 2.489 | 1.00 |
| 62_P | 66_R | 2.421 | 1.00 |
| 77_F | 97_F | 2.372 | 1.00 |
| 6_Q | 11_G | 2.301 | 1.00 |
| 19_I | 23_I | 2.301 | 1.00 |
| 86_G | 89_L | 2.262 | 1.00 |
| 80_I | 84_I | 2.250 | 1.00 |
| 81_V | 85_L | 2.172 | 1.00 |
| 11_G | 16_A | 2.157 | 1.00 |
| 78_T | 94_G | 2.100 | 1.00 |
| 82_S | 90_G | 2.069 | 1.00 |
| 57_Q | 60_D | 1.799 | 1.00 |
| 65_W | 72_A | 1.745 | 1.00 |
| 68_N | 71_D | 1.645 | 1.00 |
| 59_C | 62_P | 1.610 | 1.00 |
| 5_V | 9_T | 1.580 | 1.00 |
| 15_V | 19_I | 1.557 | 1.00 |
| 22_A | 26_I | 1.523 | 1.00 |
| 2_R | 54_M | 1.500 | 1.00 |
| 85_L | 89_L | 1.499 | 1.00 |
| 27_A | 35_L | 1.490 | 1.00 |
| 63_R | 67_Q | 1.472 | 1.00 |
| 65_W | 69_K | 1.426 | 1.00 |
| 60_D | 63_R | 1.410 | 1.00 |
| 63_R | 66_R | 1.401 | 0.99 |
| 27_A | 31_L | 1.394 | 0.99 |
| 56_M | 61_I | 1.369 | 0.99 |
| 61_I | 75_W | 1.341 | 0.99 |
| 2_R | 47_V | 1.285 | 0.99 |
| 69_K | 73_V | 1.249 | 0.99 |
| 69_K | 72_A | 1.202 | 0.98 |
| 18_I | 22_A | 1.161 | 0.97 |
| 76_V | 80_I | 1.147 | 0.97 |
| 34_L | 37_P | 1.133 | 0.97 |
| 78_T | 87_L | 1.132 | 0.97 |
| 92_L | 96_I | 1.104 | 0.96 |
| 75_W | 79_C | 1.089 | 0.96 |
| 4_A | 8_S | 1.077 | 0.95 |
| 86_G | 90_G | 1.067 | 0.95 |
| 58_L | 62_P | 1.066 | 0.95 |
| 72_A | 76_V | 1.063 | 0.95 |
| 41_S | 45_A | 1.058 | 0.95 |
| 67_Q | 71_D | 1.051 | 0.94 |
| 73_V | 77_F | 1.045 | 0.94 |
| 30_A | 33_K | 1.041 | 0.94 |
| 21_A | 25_M | 1.032 | 0.94 |
| 15_V | 18_I | 1.030 | 0.94 |
| 49_A | 52_K | 1.025 | 0.93 |
| 77_F | 80_I | 1.022 | 0.93 |
| 8_S | 53_G | 1.006 | 0.93 |
| 62_P | 65_W | 1.001 | 0.92 |
| 74_I | 97_F | 1.001 | 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 | |
| 3qe7A | 1 | 0.98 | 98.7 | 0.547 | Contact Map |
| 3agdA | 2 | 0.94 | 16.1 | 0.88 | Contact Map |
| 4eneA | 2 | 0.37 | 3 | 0.915 | Contact Map |
| 3d31C | 2 | 0.72 | 2.7 | 0.917 | Contact Map |
| 2onkC | 4 | 0.7 | 2.6 | 0.918 | Contact Map |
| 3p12A | 4 | 0.26 | 2.5 | 0.919 | Contact Map |
| 3nd0A | 2 | 0.24 | 2.4 | 0.919 | Contact Map |
| 3zdqA | 1 | 0.44 | 2.3 | 0.92 | Contact Map |
| 3b60A | 4 | 0.43 | 2.3 | 0.92 | Contact Map |
| 3aqpA | 2 | 0.61 | 1.9 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)