| 4B6IA |
| ID: | 1397852365 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 0% gaps before running GREMLIN. |
| Length: | 102 (85) | ||
| Sequences: | 97 (67.4) | ||
| Seq/Len: | 1.141 | ||
| Nf(neff/√len): | 7.3 |
Jackhmmer Results: (2014_03_19)
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: 1.141).
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 |
| 71_S | 86_S | 1.961 | 0.96 |
| 54_D | 92_E | 1.841 | 0.94 |
| 54_D | 68_N | 1.657 | 0.88 |
| 20_L | 45_Y | 1.534 | 0.82 |
| 82_L | 85_L | 1.503 | 0.80 |
| 54_D | 64_E | 1.482 | 0.79 |
| 67_A | 83_D | 1.446 | 0.77 |
| 15_L | 67_A | 1.435 | 0.76 |
| 58_Q | 61_K | 1.402 | 0.73 |
| 76_Q | 81_T | 1.400 | 0.73 |
| 16_Y | 43_S | 1.373 | 0.71 |
| 92_E | 95_T | 1.330 | 0.68 |
| 71_S | 83_D | 1.321 | 0.67 |
| 32_E | 58_Q | 1.312 | 0.66 |
| 17_K | 53_M | 1.274 | 0.63 |
| 19_W | 45_Y | 1.260 | 0.62 |
| 44_A | 82_L | 1.233 | 0.59 |
| 25_I | 60_E | 1.232 | 0.59 |
| 43_S | 79_Y | 1.231 | 0.59 |
| 21_T | 62_L | 1.227 | 0.58 |
| 40_R | 83_D | 1.226 | 0.58 |
| 28_S | 67_A | 1.216 | 0.57 |
| 61_K | 65_Q | 1.216 | 0.57 |
| 13_E | 16_Y | 1.210 | 0.57 |
| 17_K | 94_E | 1.207 | 0.57 |
| 22_S | 76_Q | 1.201 | 0.56 |
| 15_L | 18_N | 1.197 | 0.56 |
| 20_L | 77_G | 1.195 | 0.55 |
| 31_S | 60_E | 1.159 | 0.52 |
| 31_S | 68_N | 1.154 | 0.52 |
| 74_S | 77_G | 1.142 | 0.50 |
| 38_A | 90_A | 1.138 | 0.50 |
| 25_I | 38_A | 1.138 | 0.50 |
| 23_R | 42_A | 1.133 | 0.50 |
| 18_N | 45_Y | 1.123 | 0.49 |
| 20_L | 87_L | 1.119 | 0.48 |
| 65_Q | 94_E | 1.117 | 0.48 |
| 55_A | 90_A | 1.109 | 0.47 |
| 17_K | 63_A | 1.099 | 0.46 |
| 41_S | 77_G | 1.081 | 0.45 |
| 20_L | 26_G | 1.079 | 0.44 |
| 49_S | 56_F | 1.066 | 0.43 |
| 53_M | 58_Q | 1.059 | 0.42 |
| 54_D | 95_T | 1.054 | 0.42 |
| 18_N | 88_Q | 1.052 | 0.42 |
| 27_K | 42_A | 1.049 | 0.42 |
| 83_D | 86_S | 1.032 | 0.40 |
| 23_R | 30_D | 1.031 | 0.40 |
| 22_S | 28_S | 1.023 | 0.39 |
| 25_I | 34_T | 1.021 | 0.39 |
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 | |
| 4b6iA | 4 | 1 | 100 | 0.082 | Contact Map |
| 3zibA | 4 | 0.9216 | 100 | 0.153 | Contact Map |
| 4j32B | 1 | 0.9706 | 100 | 0.165 | Contact Map |
| 4hfkB | 2 | 0.9608 | 100 | 0.169 | Contact Map |
| 4ax2A | 1 | 0.9902 | 100 | 0.218 | Contact Map |
| 2lu1A | 1 | 0.2941 | 20.3 | 0.923 | Contact Map |
| 4kk0A | 10 | 0.5588 | 12.8 | 0.93 | Contact Map |
| 1vt0M | 12 | 0.4412 | 9.9 | 0.934 | Contact Map |
| 2r7rA | 1 | 0.4216 | 3.8 | 0.945 | Contact Map |
| 4dayC | 1 | 0.1176 | 3.5 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)