| 2KVC-Rv0543c |
| ID: | 1515087831 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (97) | ||
| Sequences: | 243 (182.8) | ||
| Seq/Len: | 2.505 | ||
| Nf(neff/√len): | 18.6 |
HHblits Results: (2016_02)
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: 2.505).
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 |
| 30_A | 34_L | 2.830 | 1.00 |
| 16_R | 28_S | 2.246 | 1.00 |
| 66_I | 70_T | 2.104 | 1.00 |
| 30_A | 33_A | 1.851 | 0.99 |
| 34_L | 70_T | 1.791 | 0.98 |
| 26_T | 29_F | 1.709 | 0.98 |
| 29_F | 32_L | 1.611 | 0.96 |
| 67_T | 74_P | 1.496 | 0.94 |
| 64_V | 73_L | 1.486 | 0.94 |
| 14_W | 27_D | 1.393 | 0.90 |
| 87_A | 93_L | 1.372 | 0.89 |
| 11_I | 40_S | 1.367 | 0.89 |
| 36_C | 81_R | 1.329 | 0.87 |
| 42_D | 53_R | 1.314 | 0.87 |
| 37_R | 78_D | 1.311 | 0.86 |
| 27_D | 39_L | 1.307 | 0.86 |
| 33_A | 74_P | 1.305 | 0.86 |
| 55_G | 79_V | 1.293 | 0.85 |
| 53_R | 69_F | 1.290 | 0.85 |
| 22_G | 86_L | 1.271 | 0.84 |
| 35_L | 90_G | 1.234 | 0.81 |
| 63_G | 71_D | 1.215 | 0.80 |
| 79_V | 88_A | 1.205 | 0.79 |
| 53_R | 88_A | 1.184 | 0.78 |
| 87_A | 92_P | 1.181 | 0.77 |
| 84_A | 94_D | 1.152 | 0.75 |
| 27_D | 91_W | 1.142 | 0.74 |
| 62_I | 66_I | 1.141 | 0.74 |
| 22_G | 91_W | 1.136 | 0.73 |
| 76_P | 80_E | 1.135 | 0.73 |
| 30_A | 70_T | 1.125 | 0.72 |
| 30_A | 36_C | 1.124 | 0.72 |
| 18_G | 35_L | 1.119 | 0.72 |
| 29_F | 81_R | 1.107 | 0.71 |
| 14_W | 39_L | 1.102 | 0.70 |
| 23_I | 72_E | 1.100 | 0.70 |
| 45_K | 89_Q | 1.093 | 0.69 |
| 23_I | 27_D | 1.093 | 0.69 |
| 63_G | 95_D | 1.090 | 0.69 |
| 25_P | 28_S | 1.085 | 0.68 |
| 56_D | 88_A | 1.070 | 0.67 |
| 60_I | 64_V | 1.060 | 0.66 |
| 86_L | 90_G | 1.057 | 0.65 |
| 22_G | 27_D | 1.051 | 0.65 |
| 46_A | 49_N | 1.044 | 0.64 |
| 38_R | 93_L | 1.037 | 0.63 |
| 40_S | 43_E | 1.028 | 0.62 |
| 71_D | 79_V | 1.026 | 0.62 |
| 62_I | 94_D | 1.023 | 0.62 |
| 90_G | 93_L | 1.023 | 0.62 |
| 33_A | 70_T | 1.018 | 0.61 |
| 77_E | 87_A | 1.018 | 0.61 |
| 5_N | 68_H | 1.004 | 0.60 |
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 | |
| 2kvcA | 1 | 1 | 100 | 0.025 | Contact Map |
| 2lkyA | 1 | 1 | 100 | 0.032 | Contact Map |
| 2m0nA | 1 | 1 | 100 | 0.061 | Contact Map |
| 3ol3A | 2 | 0.9126 | 100 | 0.075 | Contact Map |
| 4giuA | 2 | 0.7379 | 76.6 | 0.881 | Contact Map |
| 3h5qA | 1 | 0.7961 | 72.8 | 0.884 | Contact Map |
| 1uouA | 1 | 0.7087 | 72 | 0.885 | Contact Map |
| 4ga6A | 2 | 0.9903 | 70.8 | 0.886 | Contact Map |
| 1brwA | 2 | 0.767 | 68.4 | 0.888 | Contact Map |
| 4eadA | 1 | 0.7767 | 67.3 | 0.889 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)