| double_motif -force run |
| ID: | 1419354744 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 88 (88) | ||
| Sequences: | 56 (31.8) | ||
| Seq/Len: | 0.636 | ||
| Nf(neff/√len): | 3.4 |
Jackhmmer Results: (2014_04_16)
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: 0.636).
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 |
| 47_A | 84_T | 2.313 | 0.96 |
| 28_T | 47_A | 2.276 | 0.96 |
| 13_D | 32_W | 1.872 | 0.86 |
| 49_P | 85_A | 1.557 | 0.68 |
| 2_Q | 25_S | 1.545 | 0.67 |
| 53_G | 61_R | 1.522 | 0.65 |
| 17_D | 35_P | 1.486 | 0.63 |
| 2_Q | 35_P | 1.404 | 0.56 |
| 6_N | 82_E | 1.338 | 0.51 |
| 19_A | 39_R | 1.324 | 0.50 |
| 54_R | 80_Y | 1.312 | 0.49 |
| 13_D | 86_R | 1.271 | 0.45 |
| 49_P | 54_R | 1.249 | 0.43 |
| 31_P | 45_L | 1.240 | 0.43 |
| 8_R | 65_A | 1.231 | 0.42 |
| 48_G | 54_R | 1.229 | 0.42 |
| 76_S | 84_T | 1.229 | 0.42 |
| 6_N | 9_I | 1.225 | 0.41 |
| 50_W | 81_V | 1.221 | 0.41 |
| 43_N | 81_V | 1.221 | 0.41 |
| 43_N | 50_W | 1.221 | 0.41 |
| 36_P | 81_V | 1.221 | 0.41 |
| 36_P | 50_W | 1.221 | 0.41 |
| 36_P | 43_N | 1.221 | 0.41 |
| 20_S | 87_Q | 1.204 | 0.40 |
| 52_T | 69_A | 1.199 | 0.39 |
| 6_N | 33_I | 1.192 | 0.39 |
| 33_I | 86_R | 1.170 | 0.37 |
| 47_A | 53_G | 1.169 | 0.37 |
| 74_L | 80_Y | 1.169 | 0.37 |
| 18_E | 84_T | 1.143 | 0.35 |
| 13_D | 34_A | 1.142 | 0.35 |
| 48_G | 60_P | 1.141 | 0.35 |
| 31_P | 46_Q | 1.106 | 0.32 |
| 49_P | 80_Y | 1.073 | 0.30 |
| 10_T | 25_S | 1.070 | 0.30 |
| 34_A | 81_V | 1.068 | 0.30 |
| 34_A | 50_W | 1.068 | 0.30 |
| 34_A | 43_N | 1.068 | 0.30 |
| 8_R | 33_I | 1.052 | 0.29 |
| 45_L | 63_N | 1.051 | 0.29 |
| 18_E | 35_P | 1.049 | 0.28 |
| 30_Q | 60_P | 1.046 | 0.28 |
| 31_P | 75_P | 1.043 | 0.28 |
| 16_A | 46_Q | 1.036 | 0.28 |
| 4_Q | 7_S | 1.035 | 0.27 |
| 4_Q | 25_S | 1.035 | 0.27 |
| 67_L | 72_A | 1.031 | 0.27 |
| 48_G | 80_Y | 1.020 | 0.27 |
| 9_I | 25_S | 1.006 | 0.26 |
| 27_P | 30_Q | 1.006 | 0.26 |
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 | |
| 4emtA | 2 | 0.3977 | 5.2 | 0.944 | Contact Map |
| 2mekA | 1 | 0.3523 | 3.4 | 0.949 | Contact Map |
| 2jjzA | 1 | 0.125 | 2.2 | 0.954 | Contact Map |
| 3i2wA | 2 | 0.3523 | 2.1 | 0.954 | Contact Map |
| 4kc5A | 4 | 0.5114 | 2.1 | 0.954 | Contact Map |
| 1lqvA | 2 | 0.5568 | 2 | 0.955 | Contact Map |
| 1y0nA | 1 | 0.3864 | 2 | 0.955 | Contact Map |
| 3q9kA | 1 | 0.4091 | 1.9 | 0.956 | Contact Map |
| 3abhA | 2 | 0.3295 | 1.9 | 0.956 | Contact Map |
| 1go9A | 1 | 0.1477 | 1.7 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)