| atp6 |
| ID: | 1499246287 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 184 (184) | ||
| Sequences: | 1322 (506.5) | ||
| Seq/Len: | 7.185 | ||
| Nf(neff/√len): | 37.3 |
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: 7.185).
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 |
| 155_T | 158_F | 3.149 | 1.00 |
| 71_V | 131_L | 2.940 | 1.00 |
| 65_L | 70_V | 2.736 | 1.00 |
| 152_S | 155_T | 2.385 | 1.00 |
| 124_V | 127_T | 2.369 | 1.00 |
| 103_K | 108_F | 2.152 | 1.00 |
| 33_M | 36_E | 2.044 | 1.00 |
| 62_F | 67_S | 2.039 | 1.00 |
| 4_F | 146_K | 1.944 | 1.00 |
| 56_G | 63_P | 1.913 | 1.00 |
| 82_V | 181_F | 1.769 | 1.00 |
| 58_L | 61_G | 1.705 | 1.00 |
| 54_L | 163_L | 1.703 | 1.00 |
| 157_W | 160_V | 1.691 | 1.00 |
| 83_N | 119_V | 1.630 | 1.00 |
| 155_T | 160_V | 1.586 | 1.00 |
| 26_P | 31_S | 1.570 | 1.00 |
| 156_L | 159_G | 1.534 | 0.99 |
| 14_L | 18_F | 1.517 | 0.99 |
| 84_I | 88_D | 1.508 | 0.99 |
| 68_W | 128_V | 1.498 | 0.99 |
| 122_R | 183_P | 1.454 | 0.99 |
| 98_K | 101_V | 1.452 | 0.99 |
| 50_I | 167_L | 1.428 | 0.99 |
| 33_M | 37_R | 1.420 | 0.99 |
| 63_P | 66_S | 1.418 | 0.99 |
| 108_F | 111_L | 1.373 | 0.99 |
| 65_L | 82_V | 1.285 | 0.98 |
| 83_N | 94_S | 1.262 | 0.97 |
| 96_K | 157_W | 1.258 | 0.97 |
| 50_I | 120_I | 1.236 | 0.97 |
| 34_H | 37_R | 1.235 | 0.97 |
| 69_E | 101_V | 1.226 | 0.97 |
| 20_I | 51_T | 1.225 | 0.97 |
| 96_K | 184_K | 1.218 | 0.96 |
| 48_F | 70_V | 1.211 | 0.96 |
| 87_T | 95_L | 1.201 | 0.96 |
| 82_V | 99_Q | 1.193 | 0.96 |
| 10_S | 15_I | 1.187 | 0.96 |
| 99_Q | 173_F | 1.187 | 0.96 |
| 26_P | 30_F | 1.185 | 0.96 |
| 152_S | 160_V | 1.181 | 0.95 |
| 141_C | 145_A | 1.176 | 0.95 |
| 15_I | 153_P | 1.154 | 0.95 |
| 28_G | 31_S | 1.134 | 0.94 |
| 21_F | 44_S | 1.132 | 0.94 |
| 14_L | 22_F | 1.128 | 0.94 |
| 60_W | 127_T | 1.128 | 0.94 |
| 29_L | 35_S | 1.127 | 0.94 |
| 138_A | 162_E | 1.124 | 0.94 |
| 133_N | 137_G | 1.121 | 0.94 |
| 170_S | 174_L | 1.120 | 0.93 |
| 30_F | 150_F | 1.118 | 0.93 |
| 56_G | 134_A | 1.117 | 0.93 |
| 54_L | 167_L | 1.103 | 0.93 |
| 92_F | 96_K | 1.093 | 0.92 |
| 2_T | 157_W | 1.083 | 0.92 |
| 63_P | 134_A | 1.078 | 0.92 |
| 148_V | 156_L | 1.074 | 0.92 |
| 152_S | 158_F | 1.072 | 0.91 |
| 24_Y | 33_M | 1.067 | 0.91 |
| 7_Q | 125_T | 1.062 | 0.91 |
| 17_F | 153_P | 1.061 | 0.91 |
| 45_L | 50_I | 1.057 | 0.91 |
| 162_E | 180_Y | 1.052 | 0.90 |
| 178_K | 182_R | 1.052 | 0.90 |
| 44_S | 68_W | 1.050 | 0.90 |
| 10_S | 22_F | 1.048 | 0.90 |
| 79_F | 171_S | 1.046 | 0.90 |
| 38_W | 58_L | 1.045 | 0.90 |
| 103_K | 111_L | 1.038 | 0.90 |
| 137_G | 162_E | 1.038 | 0.90 |
| 6_D | 9_M | 1.038 | 0.90 |
| 136_V | 143_S | 1.037 | 0.90 |
| 62_F | 160_V | 1.033 | 0.89 |
| 97_F | 165_V | 1.024 | 0.89 |
| 66_S | 134_A | 1.024 | 0.89 |
| 42_L | 85_L | 1.017 | 0.88 |
| 68_W | 73_G | 1.014 | 0.88 |
| 125_T | 141_C | 1.013 | 0.88 |
| 162_E | 169_Q | 1.012 | 0.88 |
| 51_T | 78_L | 1.010 | 0.88 |
| 14_L | 20_I | 1.005 | 0.87 |
| 17_F | 33_M | 1.004 | 0.87 |
| 86_Q | 116_T | 1.003 | 0.87 |
| 22_F | 45_L | 1.003 | 0.87 |
| 161_W | 172_L | 1.002 | 0.87 |
| 150_F | 155_T | 1.001 | 0.87 |
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 | |
| 1c17M | 1 | 0.6739 | 100 | 0.425 | Contact Map |
| 2lzpA | 1 | 0.1685 | 1.2 | 0.975 | Contact Map |
| 2vpbB | 1 | 0.1141 | 0.9 | 0.977 | Contact Map |
| 2yp5A | 1 | 0.2935 | 0.8 | 0.978 | Contact Map |
| 2a65A | 1 | 0.5272 | 0.8 | 0.978 | Contact Map |
| 4khaA | 1 | 0.3207 | 0.5 | 0.98 | Contact Map |
| 2bp3S | 2 | 0.0924 | 0.5 | 0.98 | Contact Map |
| 3zpvB | 18 | 0.1141 | 0.5 | 0.981 | Contact Map |
| 4k1cA | 2 | 0.2554 | 0.4 | 0.982 | Contact Map |
| 4q4hA | 1 | 0.4946 | 0.4 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)