| test_gml |
| ID: | 1483981575 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 193 (185) | ||
| Sequences: | 7845 (6978.3) | ||
| Seq/Len: | 42.405 | ||
| Nf(neff/√len): | 513.1 |
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: 42.405).
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 |
| 128_F | 131_A | 1.865 | 1.00 |
| 40_Q | 43_K | 1.811 | 1.00 |
| 73_Q | 76_K | 1.804 | 1.00 |
| 53_K | 57_E | 1.707 | 1.00 |
| 156_E | 160_Q | 1.647 | 1.00 |
| 95_F | 98_A | 1.642 | 1.00 |
| 172_Q | 175_E | 1.618 | 1.00 |
| 84_F | 87_E | 1.590 | 1.00 |
| 75_E | 79_Q | 1.583 | 1.00 |
| 62_F | 65_E | 1.555 | 1.00 |
| 106_Q | 109_K | 1.525 | 1.00 |
| 161_F | 164_A | 1.509 | 1.00 |
| 141_E | 145_Q | 1.496 | 1.00 |
| 150_F | 153_E | 1.489 | 1.00 |
| 29_F | 32_V | 1.479 | 1.00 |
| 163_S | 167_D | 1.413 | 1.00 |
| 86_K | 90_E | 1.390 | 0.99 |
| 19_V | 22_L | 1.365 | 0.99 |
| 111_A | 115_L | 1.355 | 0.99 |
| 51_F | 54_D | 1.340 | 0.99 |
| 157_T | 160_Q | 1.338 | 0.99 |
| 164_A | 167_D | 1.304 | 0.99 |
| 179_S | 183_F | 1.303 | 0.99 |
| 178_E | 182_K | 1.302 | 0.99 |
| 93_Q | 97_S | 1.297 | 0.99 |
| 142_K | 145_Q | 1.295 | 0.99 |
| 41_A | 85_H | 1.291 | 0.99 |
| 67_A | 71_I | 1.272 | 0.99 |
| 129_L | 133_A | 1.259 | 0.99 |
| 100_A | 104_I | 1.258 | 0.99 |
| 31_S | 35_A | 1.251 | 0.99 |
| 54_D | 58_T | 1.251 | 0.99 |
| 174_K | 178_E | 1.246 | 0.98 |
| 97_S | 101_Q | 1.229 | 0.98 |
| 162_L | 166_A | 1.221 | 0.98 |
| 61_Q | 65_E | 1.221 | 0.98 |
| 24_L | 28_E | 1.215 | 0.98 |
| 134_Q | 138_A | 1.215 | 0.98 |
| 34_T | 38_Q | 1.209 | 0.98 |
| 17_E | 21_E | 1.209 | 0.98 |
| 18_K | 21_E | 1.208 | 0.98 |
| 41_A | 44_Q | 1.206 | 0.98 |
| 169_R | 172_Q | 1.205 | 0.98 |
| 30_L | 33_T | 1.204 | 0.98 |
| 117_F | 120_E | 1.198 | 0.98 |
| 74_A | 118_Y | 1.192 | 0.98 |
| 83_A | 87_E | 1.184 | 0.98 |
| 159_Q | 163_S | 1.183 | 0.98 |
| 168_A | 172_Q | 1.181 | 0.98 |
| 68_Q | 71_I | 1.177 | 0.98 |
| 118_Y | 121_V | 1.173 | 0.98 |
| 45_A | 49_Q | 1.162 | 0.97 |
| 105_A | 108_E | 1.159 | 0.97 |
| 133_A | 137_I | 1.159 | 0.97 |
| 124_T | 128_F | 1.159 | 0.97 |
| 53_K | 56_Q | 1.154 | 0.97 |
| 11_E | 14_S | 1.153 | 0.97 |
| 163_S | 166_A | 1.142 | 0.97 |
| 74_A | 77_Q | 1.131 | 0.97 |
| 115_L | 119_Q | 1.130 | 0.97 |
| 31_S | 34_T | 1.129 | 0.97 |
| 78_A | 100_A | 1.127 | 0.97 |
| 49_Q | 53_K | 1.122 | 0.97 |
| 23_S | 27_R | 1.121 | 0.97 |
| 130_S | 134_Q | 1.120 | 0.96 |
| 64_S | 68_Q | 1.117 | 0.96 |
| 131_A | 134_Q | 1.116 | 0.96 |
| 157_T | 161_F | 1.116 | 0.96 |
| 46_Q | 50_A | 1.114 | 0.96 |
| 107_A | 151_H | 1.114 | 0.96 |
| 63_L | 107_A | 1.114 | 0.96 |
| 22_L | 25_E | 1.111 | 0.96 |
| 152_K | 156_E | 1.110 | 0.96 |
| 146_E | 149_A | 1.103 | 0.96 |
| 118_Y | 140_A | 1.099 | 0.96 |
| 173_A | 177_K | 1.098 | 0.96 |
| 109_K | 112_Q | 1.093 | 0.96 |
| 96_L | 140_A | 1.092 | 0.96 |
| 74_A | 96_L | 1.092 | 0.96 |
| 18_K | 22_L | 1.090 | 0.96 |
| 42_E | 45_A | 1.088 | 0.96 |
| 137_I | 141_E | 1.088 | 0.96 |
| 139_Q | 142_K | 1.083 | 0.96 |
| 84_F | 106_Q | 1.079 | 0.95 |
| 75_E | 78_A | 1.077 | 0.95 |
| 170_T | 174_K | 1.075 | 0.95 |
| 144_A | 148_L | 1.069 | 0.95 |
| 101_Q | 104_I | 1.068 | 0.95 |
| 149_A | 153_E | 1.064 | 0.95 |
| 64_S | 67_A | 1.059 | 0.95 |
| 57_E | 61_Q | 1.057 | 0.95 |
| 183_F | 186_D | 1.054 | 0.95 |
| 151_H | 155_Q | 1.052 | 0.95 |
| 32_V | 35_A | 1.051 | 0.94 |
| 145_Q | 149_A | 1.051 | 0.94 |
| 135_A | 139_Q | 1.051 | 0.94 |
| 152_K | 155_Q | 1.051 | 0.94 |
| 181_L | 185_Q | 1.047 | 0.94 |
| 113_E | 117_F | 1.042 | 0.94 |
| 20_A | 24_L | 1.038 | 0.94 |
| 13_Q | 17_E | 1.036 | 0.94 |
| 80_E | 84_F | 1.034 | 0.94 |
| 148_L | 152_K | 1.031 | 0.94 |
| 61_Q | 64_S | 1.026 | 0.94 |
| 24_L | 27_R | 1.025 | 0.93 |
| 135_A | 138_A | 1.025 | 0.93 |
| 72_A | 76_K | 1.024 | 0.93 |
| 174_K | 177_K | 1.020 | 0.93 |
| 180_L | 183_F | 1.014 | 0.93 |
| 63_L | 85_H | 1.014 | 0.93 |
| 40_Q | 62_F | 1.013 | 0.93 |
| 160_Q | 163_S | 1.005 | 0.93 |
| 43_K | 46_Q | 1.004 | 0.93 |
| 179_S | 182_K | 1.003 | 0.93 |
| 108_E | 112_Q | 1.003 | 0.93 |
| 87_E | 90_E | 1.002 | 0.92 |
| 60_Q | 64_S | 1.000 | 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 | |
| 3s84A | 2 | 1 | 99.1 | 0.302 | Contact Map |
| 2a01A | 3 | 1 | 99.1 | 0.311 | Contact Map |
| 2lemA | 1 | 0.9845 | 98.6 | 0.421 | Contact Map |
| 2l7bA | 1 | 1 | 98.5 | 0.438 | Contact Map |
| 3r2pA | 1 | 0.9016 | 98.4 | 0.454 | Contact Map |
| 1nfnA | 1 | 0.658 | 97.9 | 0.515 | Contact Map |
| 1gs9A | 1 | 0.7202 | 97 | 0.595 | Contact Map |
| 1eq1A | 1 | 0.8238 | 91.6 | 0.701 | Contact Map |
| 2nrjA | 1 | 0.9326 | 42.9 | 0.804 | Contact Map |
| 4lwsA | 1 | 0.4767 | 40.8 | 0.807 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)