| mota-i1 |
| ID: | 1435308693 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (119) | ||
| Sequences: | 369 (250.3) | ||
| Seq/Len: | 3.101 | ||
| Nf(neff/√len): | 22.9 |
HHblits Results: (2013_03)
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: 3.101).
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 |
| 52_N | 55_E | 3.124 | 1.00 |
| 33_R | 61_S | 2.392 | 1.00 |
| 65_I | 75_I | 2.383 | 1.00 |
| 37_K | 49_D | 1.854 | 0.99 |
| 30_L | 75_I | 1.784 | 0.99 |
| 33_R | 50_I | 1.507 | 0.96 |
| 33_R | 62_Y | 1.493 | 0.96 |
| 70_V | 104_E | 1.438 | 0.95 |
| 69_S | 104_E | 1.418 | 0.94 |
| 30_L | 65_I | 1.411 | 0.94 |
| 78_Y | 99_E | 1.385 | 0.93 |
| 22_A | 26_D | 1.340 | 0.91 |
| 74_F | 99_E | 1.337 | 0.91 |
| 32_Y | 91_E | 1.332 | 0.91 |
| 26_D | 64_R | 1.324 | 0.91 |
| 47_E | 78_Y | 1.323 | 0.91 |
| 31_L | 47_E | 1.309 | 0.90 |
| 3_I | 117_V | 1.304 | 0.90 |
| 20_T | 23_M | 1.292 | 0.89 |
| 10_L | 57_E | 1.291 | 0.89 |
| 19_Y | 88_N | 1.288 | 0.89 |
| 25_M | 28_L | 1.286 | 0.89 |
| 69_S | 103_H | 1.274 | 0.88 |
| 15_R | 67_A | 1.259 | 0.88 |
| 71_M | 75_I | 1.259 | 0.88 |
| 60_A | 66_L | 1.243 | 0.87 |
| 97_D | 102_T | 1.235 | 0.86 |
| 6_T | 9_A | 1.232 | 0.86 |
| 4_K | 8_K | 1.219 | 0.85 |
| 44_F | 78_Y | 1.193 | 0.83 |
| 57_E | 60_A | 1.186 | 0.83 |
| 81_L | 85_G | 1.180 | 0.83 |
| 34_L | 67_A | 1.156 | 0.81 |
| 115_A | 119_D | 1.153 | 0.80 |
| 37_K | 41_M | 1.151 | 0.80 |
| 45_S | 49_D | 1.135 | 0.79 |
| 78_Y | 86_H | 1.128 | 0.78 |
| 88_N | 91_E | 1.120 | 0.78 |
| 22_A | 67_A | 1.120 | 0.78 |
| 85_G | 91_E | 1.118 | 0.78 |
| 74_F | 95_L | 1.113 | 0.77 |
| 115_A | 118_G | 1.109 | 0.77 |
| 51_E | 80_R | 1.103 | 0.76 |
| 91_E | 99_E | 1.100 | 0.76 |
| 58_I | 62_Y | 1.098 | 0.76 |
| 34_L | 46_L | 1.098 | 0.76 |
| 86_H | 99_E | 1.091 | 0.75 |
| 2_A | 113_S | 1.090 | 0.75 |
| 60_A | 100_I | 1.072 | 0.73 |
| 93_E | 99_E | 1.058 | 0.72 |
| 8_K | 22_A | 1.056 | 0.72 |
| 30_L | 62_Y | 1.045 | 0.71 |
| 30_L | 63_P | 1.044 | 0.70 |
| 46_L | 82_I | 1.044 | 0.70 |
| 13_L | 60_A | 1.030 | 0.69 |
| 31_L | 86_H | 1.026 | 0.69 |
| 29_A | 78_Y | 1.025 | 0.68 |
| 47_E | 86_H | 1.024 | 0.68 |
| 91_E | 94_A | 1.022 | 0.68 |
| 85_G | 102_T | 1.016 | 0.67 |
| 4_K | 15_R | 1.013 | 0.67 |
| 78_Y | 96_M | 1.008 | 0.67 |
| 9_A | 13_L | 1.007 | 0.66 |
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 | |
| 3o0yA | 3 | 1 | 33.7 | 0.927 | Contact Map |
| 2e5aA | 1 | 0.3697 | 24.3 | 0.933 | Contact Map |
| 3ip4B | 1 | 0.8824 | 15.4 | 0.938 | Contact Map |
| 1n4kA | 1 | 0.5966 | 15.3 | 0.938 | Contact Map |
| 3qc7A | 1 | 0.3866 | 12.8 | 0.94 | Contact Map |
| 3hdiA | 2 | 1 | 12.6 | 0.941 | Contact Map |
| 2hz7A | 1 | 0 | 10.3 | 0.943 | Contact Map |
| 3uj4A | 2 | 0.3529 | 10.3 | 0.943 | Contact Map |
| 1hr6B | 4 | 1 | 10.3 | 0.943 | Contact Map |
| 3eoqA | 2 | 1 | 9.9 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)