| ncor 1-96 -force run -force run |
| ID: | 1477670142 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 100 (95) | ||
| Sequences: | 58 (24.4) | ||
| Seq/Len: | 0.611 | ||
| Nf(neff/√len): | 2.5 |
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: 0.611).
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 |
| 69_D | 78_D | 2.258 | 0.95 |
| 43_Q | 46_T | 1.989 | 0.89 |
| 19_K | 22_K | 1.791 | 0.81 |
| 43_Q | 48_I | 1.696 | 0.76 |
| 43_Q | 49_F | 1.696 | 0.76 |
| 44_P | 48_I | 1.696 | 0.76 |
| 44_P | 49_F | 1.696 | 0.76 |
| 46_T | 49_F | 1.696 | 0.76 |
| 61_S | 89_D | 1.461 | 0.59 |
| 62_S | 65_H | 1.449 | 0.58 |
| 64_S | 78_D | 1.418 | 0.56 |
| 47_E | 52_P | 1.403 | 0.55 |
| 17_M | 29_L | 1.397 | 0.54 |
| 4_L | 9_T | 1.349 | 0.50 |
| 7_F | 10_K | 1.331 | 0.49 |
| 58_G | 61_S | 1.287 | 0.45 |
| 60_V | 65_H | 1.278 | 0.45 |
| 88_F | 95_H | 1.253 | 0.43 |
| 58_G | 64_S | 1.246 | 0.42 |
| 64_S | 68_A | 1.232 | 0.41 |
| 43_Q | 47_E | 1.229 | 0.41 |
| 43_Q | 52_P | 1.229 | 0.41 |
| 44_P | 47_E | 1.229 | 0.41 |
| 44_P | 52_P | 1.229 | 0.41 |
| 46_T | 52_P | 1.229 | 0.41 |
| 67_F | 74_L | 1.223 | 0.40 |
| 61_S | 66_S | 1.222 | 0.40 |
| 34_G | 39_M | 1.213 | 0.39 |
| 43_Q | 50_N | 1.192 | 0.38 |
| 44_P | 50_N | 1.192 | 0.38 |
| 46_T | 50_N | 1.192 | 0.38 |
| 3_Y | 78_D | 1.192 | 0.38 |
| 58_G | 87_S | 1.149 | 0.35 |
| 70_P | 74_L | 1.144 | 0.34 |
| 3_Y | 69_D | 1.142 | 0.34 |
| 22_K | 55_T | 1.135 | 0.34 |
| 48_I | 52_P | 1.129 | 0.33 |
| 49_F | 52_P | 1.129 | 0.33 |
| 11_L | 21_K | 1.107 | 0.32 |
| 16_P | 51_L | 1.102 | 0.31 |
| 4_L | 27_R | 1.095 | 0.31 |
| 91_K | 96_G | 1.095 | 0.31 |
| 62_S | 68_A | 1.083 | 0.30 |
| 12_E | 15_S | 1.076 | 0.29 |
| 68_A | 74_L | 1.070 | 0.29 |
| 7_F | 20_S | 1.067 | 0.29 |
| 19_K | 55_T | 1.063 | 0.29 |
| 47_E | 53_A | 1.053 | 0.28 |
| 45_G | 48_I | 1.036 | 0.27 |
| 45_G | 49_F | 1.036 | 0.27 |
| 69_D | 88_F | 1.035 | 0.27 |
| 60_V | 66_S | 1.034 | 0.27 |
| 64_S | 69_D | 1.026 | 0.26 |
| 59_A | 62_S | 1.025 | 0.26 |
| 42_A | 51_L | 1.025 | 0.26 |
| 10_K | 20_S | 1.025 | 0.26 |
| 26_F | 89_D | 1.018 | 0.26 |
| 26_F | 32_S | 1.011 | 0.25 |
| 9_T | 27_R | 1.011 | 0.25 |
| 66_S | 90_D | 1.000 | 0.25 |
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 | |
| 2ovmB | 1 | 0.11 | 99.1 | 0.767 | Contact Map |
| 2gpvG | 3 | 0.12 | 98.6 | 0.8 | Contact Map |
| 2wh0Q | 2 | 0.11 | 7.4 | 0.954 | Contact Map |
| 1a32A | 1 | 0.78 | 5.5 | 0.957 | Contact Map |
| 1b4uA | 2 | 0.69 | 4.7 | 0.958 | Contact Map |
| 2mnjA | 1 | 0 | 4.1 | 0.959 | Contact Map |
| 1hn0A | 1 | 0.28 | 3.9 | 0.96 | Contact Map |
| 4a5uB | 1 | 0.69 | 3.8 | 0.96 | Contact Map |
| 3j21k | 1 | 0.74 | 3.8 | 0.96 | Contact Map |
| 3a6pA | 2 | 0.14 | 3.4 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)