| 2bg9 |
| ID: | 1499474408 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (91) | ||
| Sequences: | 1380 (840.9) | ||
| Seq/Len: | 15.165 | ||
| Nf(neff/√len): | 88.2 |
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: 15.165).
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 |
| 22_V | 36_S | 2.346 | 1.00 |
| 28_D | 89_H | 1.987 | 1.00 |
| 38_S | 41_L | 1.748 | 1.00 |
| 77_S | 80_I | 1.720 | 1.00 |
| 45_V | 49_V | 1.705 | 1.00 |
| 25_L | 35_L | 1.623 | 1.00 |
| 31_E | 34_T | 1.549 | 1.00 |
| 77_S | 81_V | 1.506 | 1.00 |
| 32_K | 83_V | 1.503 | 1.00 |
| 43_L | 75_V | 1.444 | 1.00 |
| 25_L | 33_M | 1.433 | 1.00 |
| 30_G | 34_T | 1.427 | 1.00 |
| 5_V | 9_I | 1.396 | 0.99 |
| 8_V | 13_L | 1.309 | 0.99 |
| 15_F | 43_L | 1.302 | 0.99 |
| 16_S | 71_T | 1.300 | 0.99 |
| 19_T | 75_V | 1.293 | 0.99 |
| 31_E | 38_S | 1.253 | 0.99 |
| 74_F | 78_S | 1.238 | 0.98 |
| 24_Y | 34_T | 1.233 | 0.98 |
| 39_V | 42_S | 1.221 | 0.98 |
| 18_L | 48_L | 1.206 | 0.98 |
| 13_L | 18_L | 1.201 | 0.98 |
| 12_C | 72_M | 1.161 | 0.97 |
| 8_V | 53_L | 1.146 | 0.97 |
| 3_Y | 50_I | 1.141 | 0.97 |
| 34_T | 38_S | 1.138 | 0.97 |
| 15_F | 19_T | 1.134 | 0.97 |
| 17_F | 53_L | 1.124 | 0.97 |
| 67_Y | 71_T | 1.117 | 0.96 |
| 53_L | 56_S | 1.115 | 0.96 |
| 81_V | 85_V | 1.111 | 0.96 |
| 32_K | 74_F | 1.101 | 0.96 |
| 16_S | 22_V | 1.095 | 0.96 |
| 68_M | 71_T | 1.086 | 0.96 |
| 17_F | 21_L | 1.086 | 0.96 |
| 25_L | 28_D | 1.083 | 0.96 |
| 30_G | 86_I | 1.081 | 0.95 |
| 22_V | 38_S | 1.074 | 0.95 |
| 84_V | 88_T | 1.051 | 0.94 |
| 51_V | 54_I | 1.050 | 0.94 |
| 39_V | 48_L | 1.048 | 0.94 |
| 3_Y | 58_S | 1.042 | 0.94 |
| 75_V | 85_V | 1.041 | 0.94 |
| 59_S | 64_I | 1.039 | 0.94 |
| 21_L | 33_M | 1.029 | 0.94 |
| 66_K | 69_L | 1.028 | 0.94 |
| 61_V | 70_F | 1.022 | 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 | |
| 1oedC | 1 | 1 | 99.9 | 0.093 | Contact Map |
| 4aq5C | 1 | 1 | 99.9 | 0.1 | Contact Map |
| 1oedB | 1 | 1 | 99.9 | 0.102 | Contact Map |
| 1oedA | 2 | 1 | 99.9 | 0.106 | Contact Map |
| 4aq5B | 1 | 1 | 99.9 | 0.108 | Contact Map |
| 1oedE | 1 | 1 | 99.9 | 0.11 | Contact Map |
| 4aq5E | 1 | 1 | 99.9 | 0.112 | Contact Map |
| 4aq5A | 2 | 1 | 99.9 | 0.113 | Contact Map |
| 4pirA | 5 | 0.956 | 99.9 | 0.142 | Contact Map |
| 2bg9C | 1 | 1 | 99.9 | 0.158 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)