| BAF45D_2 |
| ID: | 1469716784 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 119 (105) | ||
| Sequences: | 747 (503.4) | ||
| Seq/Len: | 7.114 | ||
| Nf(neff/√len): | 49.1 |
HHblits Results: (2016_02)
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: 7.114).
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 |
| 1_C | 4_C | 2.954 | 1.00 |
| 99_C | 102_C | 2.655 | 1.00 |
| 52_C | 55_C | 2.484 | 1.00 |
| 25_D | 51_Q | 2.195 | 1.00 |
| 50_W | 55_C | 2.158 | 1.00 |
| 23_C | 26_C | 1.894 | 1.00 |
| 31_H | 34_C | 1.894 | 1.00 |
| 58_C | 61_C | 1.639 | 1.00 |
| 81_H | 84_C | 1.626 | 1.00 |
| 22_S | 29_S | 1.602 | 1.00 |
| 85_L | 93_P | 1.592 | 1.00 |
| 73_C | 76_C | 1.539 | 0.99 |
| 73_C | 84_C | 1.491 | 0.99 |
| 56_K | 79_G | 1.459 | 0.99 |
| 23_C | 31_H | 1.417 | 0.99 |
| 73_C | 81_H | 1.388 | 0.99 |
| 70_L | 79_G | 1.319 | 0.98 |
| 69_Q | 83_Y | 1.317 | 0.98 |
| 26_C | 31_H | 1.310 | 0.98 |
| 3_F | 7_D | 1.301 | 0.98 |
| 2_D | 7_D | 1.292 | 0.98 |
| 56_K | 72_F | 1.288 | 0.98 |
| 3_F | 6_G | 1.285 | 0.98 |
| 22_S | 27_G | 1.283 | 0.98 |
| 84_C | 99_C | 1.271 | 0.97 |
| 26_C | 34_C | 1.238 | 0.97 |
| 72_F | 77_D | 1.232 | 0.97 |
| 73_C | 99_C | 1.205 | 0.96 |
| 2_D | 5_L | 1.193 | 0.96 |
| 66_N | 101_L | 1.166 | 0.95 |
| 6_G | 11_N | 1.165 | 0.95 |
| 87_P | 97_W | 1.156 | 0.95 |
| 24_S | 37_F | 1.155 | 0.95 |
| 89_M | 93_P | 1.148 | 0.94 |
| 81_H | 99_C | 1.143 | 0.94 |
| 56_K | 62_G | 1.128 | 0.94 |
| 48_Y | 78_R | 1.123 | 0.94 |
| 67_D | 82_M | 1.123 | 0.94 |
| 54_E | 71_L | 1.109 | 0.93 |
| 85_L | 88_S | 1.107 | 0.93 |
| 74_D | 77_D | 1.099 | 0.93 |
| 75_D | 98_S | 1.095 | 0.92 |
| 18_E | 32_P | 1.078 | 0.92 |
| 76_C | 84_C | 1.075 | 0.91 |
| 72_F | 79_G | 1.074 | 0.91 |
| 11_N | 18_E | 1.061 | 0.91 |
| 5_L | 9_K | 1.055 | 0.90 |
| 85_L | 97_W | 1.051 | 0.90 |
| 31_H | 52_C | 1.039 | 0.89 |
| 67_D | 83_Y | 1.034 | 0.89 |
| 26_C | 52_C | 1.032 | 0.89 |
| 32_P | 95_G | 1.028 | 0.89 |
| 5_L | 8_S | 1.022 | 0.88 |
| 31_H | 55_C | 1.008 | 0.87 |
| 27_G | 46_K | 1.007 | 0.87 |
| 55_C | 81_H | 1.007 | 0.87 |
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 | |
| 2kwjA | 1 | 0.9328 | 99.9 | 0.206 | Contact Map |
| 3v43A | 1 | 0.8739 | 99.9 | 0.277 | Contact Map |
| 4lk9A | 1 | 0.8908 | 99.9 | 0.279 | Contact Map |
| 2ysmA | 1 | 0.8571 | 99.8 | 0.326 | Contact Map |
| 2lbmA | 1 | 0.8992 | 99.6 | 0.469 | Contact Map |
| 4gneA | 1 | 0.7311 | 99.5 | 0.475 | Contact Map |
| 3ql9A | 1 | 0.8151 | 99.5 | 0.485 | Contact Map |
| 4tvrA | 1 | 0 | 99.5 | 0.492 | Contact Map |
| 3shbA | 1 | 0.5546 | 99.3 | 0.542 | Contact Map |
| 2e6rA | 1 | 0.6723 | 99.3 | 0.547 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)