| SrtA_sp |
| ID: | 1402323253 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (193) | ||
| Sequences: | 1782 (1580.6) | ||
| Seq/Len: | 9.233 | ||
| Nf(neff/√len): | 113.8 |
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: 9.233).
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 |
| 157_L | 179_E | 3.510 | 1.00 |
| 114_P | 117_R | 3.381 | 1.00 |
| 160_V | 178_G | 3.095 | 1.00 |
| 95_S | 160_V | 2.898 | 1.00 |
| 79_A | 97_A | 2.778 | 1.00 |
| 124_I | 178_G | 2.716 | 1.00 |
| 124_I | 160_V | 2.596 | 1.00 |
| 54_G | 63_N | 2.497 | 1.00 |
| 138_K | 179_E | 2.490 | 1.00 |
| 159_E | 177_K | 2.487 | 1.00 |
| 136_I | 181_K | 2.461 | 1.00 |
| 58_P | 125_Y | 2.407 | 1.00 |
| 126_L | 160_V | 2.400 | 1.00 |
| 53_G | 66_I | 2.381 | 1.00 |
| 136_I | 179_E | 2.343 | 1.00 |
| 59_E | 118_A | 2.284 | 1.00 |
| 59_E | 122_M | 2.175 | 1.00 |
| 123_S | 134_E | 2.162 | 1.00 |
| 79_A | 99_H | 2.157 | 1.00 |
| 141_F | 150_V | 2.155 | 1.00 |
| 134_E | 183_E | 2.014 | 1.00 |
| 139_D | 177_K | 1.881 | 1.00 |
| 56_A | 127_T | 1.850 | 1.00 |
| 93_N | 161_T | 1.828 | 1.00 |
| 110_M | 114_P | 1.732 | 1.00 |
| 112_F | 162_L | 1.728 | 1.00 |
| 86_Q | 153_D | 1.724 | 1.00 |
| 158_K | 180_L | 1.699 | 1.00 |
| 57_I | 60_L | 1.672 | 1.00 |
| 115_L | 118_A | 1.598 | 1.00 |
| 141_F | 177_K | 1.596 | 1.00 |
| 123_S | 136_I | 1.587 | 1.00 |
| 101_I | 116_E | 1.558 | 1.00 |
| 56_A | 63_N | 1.553 | 1.00 |
| 125_Y | 134_E | 1.523 | 1.00 |
| 78_G | 81_T | 1.504 | 1.00 |
| 166_T | 172_E | 1.495 | 1.00 |
| 138_K | 177_K | 1.487 | 1.00 |
| 71_G | 74_E | 1.459 | 1.00 |
| 18_K | 21_E | 1.441 | 1.00 |
| 56_A | 125_Y | 1.439 | 1.00 |
| 74_E | 80_G | 1.411 | 0.99 |
| 154_T | 159_E | 1.396 | 0.99 |
| 118_A | 137_I | 1.381 | 0.99 |
| 57_I | 118_A | 1.366 | 0.99 |
| 133_Y | 180_L | 1.363 | 0.99 |
| 138_K | 159_E | 1.360 | 0.99 |
| 161_T | 177_K | 1.353 | 0.99 |
| 68_K | 81_T | 1.336 | 0.99 |
| 53_G | 126_L | 1.320 | 0.99 |
| 72_N | 76_I | 1.317 | 0.99 |
| 40_L | 44_M | 1.317 | 0.99 |
| 52_I | 68_K | 1.314 | 0.99 |
| 66_I | 126_L | 1.301 | 0.99 |
| 101_I | 168_I | 1.284 | 0.99 |
| 123_S | 181_K | 1.273 | 0.98 |
| 143_V | 163_V | 1.263 | 0.98 |
| 92_N | 153_D | 1.259 | 0.98 |
| 64_L | 111_L | 1.256 | 0.98 |
| 92_N | 156_G | 1.251 | 0.98 |
| 154_T | 157_L | 1.250 | 0.98 |
| 115_L | 174_I | 1.221 | 0.98 |
| 27_D | 30_A | 1.218 | 0.98 |
| 15_Q | 18_K | 1.215 | 0.98 |
| 163_V | 175_I | 1.208 | 0.98 |
| 137_I | 176_V | 1.194 | 0.97 |
| 144_A | 172_E | 1.189 | 0.97 |
| 55_I | 124_I | 1.181 | 0.97 |
| 191_A | 195_K | 1.158 | 0.97 |
| 42_A | 46_A | 1.141 | 0.96 |
| 60_L | 118_A | 1.138 | 0.96 |
| 143_V | 175_I | 1.120 | 0.96 |
| 131_K | 183_E | 1.115 | 0.96 |
| 140_V | 174_I | 1.114 | 0.96 |
| 112_F | 164_T | 1.114 | 0.96 |
| 125_Y | 132_I | 1.106 | 0.96 |
| 139_D | 150_V | 1.101 | 0.95 |
| 69_G | 80_G | 1.100 | 0.95 |
| 166_T | 169_E | 1.065 | 0.94 |
| 142_T | 166_T | 1.058 | 0.94 |
| 67_F | 74_E | 1.056 | 0.94 |
| 100_H | 116_E | 1.054 | 0.94 |
| 100_H | 113_S | 1.053 | 0.94 |
| 145_P | 170_A | 1.044 | 0.93 |
| 166_T | 170_A | 1.038 | 0.93 |
| 186_F | 190_P | 1.035 | 0.93 |
| 23_K | 26_F | 1.031 | 0.93 |
| 118_A | 122_M | 1.030 | 0.93 |
| 12_S | 15_Q | 1.018 | 0.92 |
| 86_Q | 94_Y | 1.013 | 0.92 |
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 | |
| 3fn5A | 2 | 0.7913 | 100 | 0.245 | Contact Map |
| 3rccA | 18 | 0.665 | 100 | 0.257 | Contact Map |
| 2w1jA | 2 | 0.8738 | 100 | 0.258 | Contact Map |
| 3g66A | 2 | 0.8786 | 100 | 0.26 | Contact Map |
| 3o0pA | 1 | 0.8835 | 100 | 0.26 | Contact Map |
| 4g1hA | 1 | 0.8107 | 100 | 0.263 | Contact Map |
| 4g1jA | 2 | 0.9272 | 100 | 0.264 | Contact Map |
| 2w1kA | 2 | 0.9369 | 100 | 0.267 | Contact Map |
| 2xwgA | 5 | 0.835 | 100 | 0.271 | Contact Map |
| 2kw8A | 1 | 0.7621 | 100 | 0.294 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)