| 4x5m |
| ID: | 1489335266 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (86) | ||
| Sequences: | 4980 (3342.6) | ||
| Seq/Len: | 57.907 | ||
| Nf(neff/√len): | 360.4 |
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: 57.907).
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 |
| 77_V | 81_I | 2.726 | 1.00 |
| 23_I | 27_R | 2.667 | 1.00 |
| 14_T | 18_F | 2.266 | 1.00 |
| 25_T | 31_T | 1.922 | 1.00 |
| 30_N | 33_G | 1.920 | 1.00 |
| 15_T | 18_F | 1.837 | 1.00 |
| 31_T | 79_T | 1.736 | 1.00 |
| 78_I | 82_N | 1.716 | 1.00 |
| 14_T | 17_A | 1.681 | 1.00 |
| 7_G | 11_A | 1.619 | 1.00 |
| 53_G | 62_L | 1.571 | 1.00 |
| 24_K | 28_T | 1.544 | 1.00 |
| 59_F | 63_I | 1.504 | 1.00 |
| 23_I | 26_I | 1.474 | 1.00 |
| 43_L | 69_L | 1.460 | 1.00 |
| 29_R | 82_N | 1.446 | 1.00 |
| 42_F | 46_V | 1.430 | 1.00 |
| 26_I | 78_I | 1.427 | 1.00 |
| 47_I | 69_L | 1.394 | 0.99 |
| 62_L | 65_N | 1.378 | 0.99 |
| 21_Q | 33_G | 1.359 | 0.99 |
| 4_L | 8_L | 1.352 | 0.99 |
| 50_I | 66_I | 1.332 | 0.99 |
| 34_I | 39_Y | 1.294 | 0.99 |
| 46_V | 68_T | 1.283 | 0.99 |
| 20_P | 23_I | 1.281 | 0.99 |
| 49_W | 52_Y | 1.268 | 0.99 |
| 65_N | 68_T | 1.226 | 0.98 |
| 50_I | 62_L | 1.191 | 0.98 |
| 75_V | 78_I | 1.175 | 0.98 |
| 72_A | 75_V | 1.141 | 0.97 |
| 49_W | 53_G | 1.133 | 0.97 |
| 74_P | 78_I | 1.124 | 0.97 |
| 15_T | 68_T | 1.111 | 0.96 |
| 4_L | 58_D | 1.090 | 0.96 |
| 79_T | 83_R | 1.087 | 0.96 |
| 68_T | 72_A | 1.082 | 0.96 |
| 69_L | 72_A | 1.076 | 0.95 |
| 22_S | 39_Y | 1.071 | 0.95 |
| 39_Y | 75_V | 1.070 | 0.95 |
| 14_T | 42_F | 1.043 | 0.94 |
| 36_V | 40_I | 1.022 | 0.93 |
| 31_T | 83_R | 1.019 | 0.93 |
| 55_M | 58_D | 1.018 | 0.93 |
| 65_N | 69_L | 1.009 | 0.93 |
| 10_A | 13_F | 1.008 | 0.93 |
| 50_I | 54_I | 1.003 | 0.93 |
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 | |
| 4x5mA | 3 | 1 | 99.7 | 0.123 | Contact Map |
| 4qncA | 2 | 0.9111 | 99.7 | 0.13 | Contact Map |
| 4rngA | 6 | 0.9 | 99.6 | 0.156 | Contact Map |
| 4qndA | 1 | 0.9667 | 99.6 | 0.168 | Contact Map |
| 3l1lA | 1 | 0.9444 | 8.1 | 0.875 | Contact Map |
| 3giaA | 1 | 0.9556 | 6.5 | 0.88 | Contact Map |
| 3kcuA | 5 | 0.8222 | 4.5 | 0.888 | Contact Map |
| 2nq2A | 2 | 0.8667 | 4.4 | 0.89 | Contact Map |
| 3m73A | 1 | 0.9667 | 3.9 | 0.892 | Contact Map |
| 4djkA | 2 | 0.9667 | 3.6 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)