| Spcs1a |
| ID: | 1479455053 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (96) | ||
| Sequences: | 374 (266.5) | ||
| Seq/Len: | 3.896 | ||
| Nf(neff/√len): | 27.2 |
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: 3.896).
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 |
| 27_I | 59_S | 3.056 | 1.00 |
| 31_S | 55_G | 2.188 | 1.00 |
| 60_C | 64_L | 2.160 | 1.00 |
| 38_Y | 51_I | 1.779 | 0.99 |
| 15_K | 73_H | 1.777 | 0.99 |
| 96_K | 99_A | 1.552 | 0.98 |
| 45_F | 63_T | 1.488 | 0.97 |
| 93_R | 96_K | 1.451 | 0.97 |
| 94_K | 99_A | 1.423 | 0.96 |
| 23_M | 27_I | 1.406 | 0.96 |
| 91_G | 94_K | 1.395 | 0.96 |
| 38_Y | 47_W | 1.371 | 0.95 |
| 16_G | 74_P | 1.342 | 0.94 |
| 91_G | 95_I | 1.299 | 0.93 |
| 14_Y | 43_E | 1.271 | 0.92 |
| 94_K | 98_H | 1.265 | 0.92 |
| 16_G | 20_A | 1.256 | 0.91 |
| 95_I | 99_A | 1.234 | 0.90 |
| 19_L | 73_H | 1.219 | 0.89 |
| 92_D | 95_I | 1.209 | 0.89 |
| 55_G | 66_P | 1.209 | 0.89 |
| 24_F | 59_S | 1.195 | 0.88 |
| 92_D | 96_K | 1.190 | 0.88 |
| 33_I | 43_E | 1.181 | 0.87 |
| 37_I | 41_V | 1.174 | 0.87 |
| 89_K | 94_K | 1.166 | 0.86 |
| 34_V | 84_G | 1.161 | 0.86 |
| 67_W | 72_R | 1.155 | 0.86 |
| 52_V | 56_F | 1.137 | 0.84 |
| 12_M | 66_P | 1.136 | 0.84 |
| 13_D | 16_G | 1.126 | 0.84 |
| 32_A | 59_S | 1.119 | 0.83 |
| 25_Q | 32_A | 1.115 | 0.83 |
| 25_Q | 52_V | 1.115 | 0.83 |
| 27_I | 62_L | 1.093 | 0.81 |
| 47_W | 50_Y | 1.082 | 0.80 |
| 12_M | 45_F | 1.081 | 0.80 |
| 62_L | 69_I | 1.081 | 0.80 |
| 15_K | 21_E | 1.078 | 0.80 |
| 26_G | 51_I | 1.077 | 0.80 |
| 16_G | 73_H | 1.072 | 0.79 |
| 53_M | 56_F | 1.059 | 0.78 |
| 91_G | 98_H | 1.058 | 0.78 |
| 52_V | 60_C | 1.056 | 0.78 |
| 7_S | 10_T | 1.056 | 0.78 |
| 24_F | 62_L | 1.051 | 0.77 |
| 50_Y | 58_F | 1.050 | 0.77 |
| 95_I | 98_H | 1.048 | 0.77 |
| 9_P | 12_M | 1.043 | 0.77 |
| 28_I | 64_L | 1.043 | 0.77 |
| 23_M | 32_A | 1.042 | 0.77 |
| 67_W | 74_P | 1.039 | 0.76 |
| 90_S | 93_R | 1.038 | 0.76 |
| 54_A | 58_F | 1.028 | 0.75 |
| 91_G | 96_K | 1.025 | 0.75 |
| 42_A | 47_W | 1.024 | 0.75 |
| 48_T | 66_P | 1.023 | 0.75 |
| 15_K | 18_K | 1.020 | 0.74 |
| 13_D | 68_P | 1.010 | 0.73 |
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 | |
| 4ev6A | 5 | 0.7353 | 62.9 | 0.888 | Contact Map |
| 4i0uA | 10 | 0.7255 | 62.5 | 0.888 | Contact Map |
| 4dx5A | 3 | 0.8137 | 32.6 | 0.907 | Contact Map |
| 1pw4A | 1 | 0.8431 | 32.3 | 0.907 | Contact Map |
| 2cfqA | 1 | 0.9412 | 22.2 | 0.914 | Contact Map |
| 4uvmA | 1 | 0.9804 | 20.2 | 0.916 | Contact Map |
| 2zxeA | 1 | 0.8235 | 17.4 | 0.918 | Contact Map |
| 3wdoA | 1 | 0.9706 | 15.8 | 0.92 | Contact Map |
| 3ixzA | 1 | 0.8235 | 14.3 | 0.921 | Contact Map |
| 3aqpA | 2 | 0.7059 | 12.7 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)