| 1K0S |
| ID: | 1429456003 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (142) | ||
| Sequences: | 4234 (3172.1) | ||
| Seq/Len: | 29.817 | ||
| Nf(neff/√len): | 266.2 |
HHblits Results: (2013_03)
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: 29.817).
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 |
| 32_M | 56_R | 3.887 | 1.00 |
| 81_I | 92_G | 3.154 | 1.00 |
| 17_E | 97_R | 3.111 | 1.00 |
| 22_A | 131_R | 2.896 | 1.00 |
| 110_D | 127_K | 2.697 | 1.00 |
| 54_N | 57_G | 2.648 | 1.00 |
| 13_V | 24_A | 2.621 | 1.00 |
| 58_R | 90_E | 2.539 | 1.00 |
| 31_E | 85_R | 2.498 | 1.00 |
| 62_V | 81_I | 2.450 | 1.00 |
| 12_E | 103_R | 2.383 | 1.00 |
| 51_G | 64_N | 2.230 | 1.00 |
| 29_N | 139_D | 2.145 | 1.00 |
| 66_A | 96_D | 2.138 | 1.00 |
| 60_I | 83_V | 2.100 | 1.00 |
| 105_T | 108_Q | 2.049 | 1.00 |
| 104_I | 126_V | 2.007 | 1.00 |
| 17_E | 99_L | 1.878 | 1.00 |
| 36_K | 39_I | 1.779 | 1.00 |
| 31_E | 90_E | 1.720 | 1.00 |
| 109_L | 124_G | 1.714 | 1.00 |
| 50_E | 64_N | 1.694 | 1.00 |
| 50_E | 94_L | 1.660 | 1.00 |
| 50_E | 67_K | 1.611 | 1.00 |
| 137_D | 140_K | 1.607 | 1.00 |
| 17_E | 20_E | 1.584 | 1.00 |
| 54_N | 59_I | 1.552 | 1.00 |
| 123_K | 137_D | 1.460 | 1.00 |
| 60_I | 90_E | 1.435 | 1.00 |
| 53_I | 81_I | 1.426 | 1.00 |
| 13_V | 104_I | 1.413 | 1.00 |
| 79_K | 94_L | 1.404 | 0.99 |
| 19_D | 66_A | 1.375 | 0.99 |
| 73_F | 76_Q | 1.374 | 0.99 |
| 64_N | 67_K | 1.370 | 0.99 |
| 85_R | 90_E | 1.341 | 0.99 |
| 16_F | 82_I | 1.294 | 0.99 |
| 22_A | 99_L | 1.285 | 0.99 |
| 84_A | 93_F | 1.272 | 0.99 |
| 24_A | 133_I | 1.256 | 0.99 |
| 122_S | 134_I | 1.246 | 0.98 |
| 143_E | 146_T | 1.241 | 0.98 |
| 55_L | 83_V | 1.237 | 0.98 |
| 26_D | 29_N | 1.225 | 0.98 |
| 9_K | 106_E | 1.217 | 0.98 |
| 14_L | 33_V | 1.196 | 0.98 |
| 33_V | 98_V | 1.159 | 0.97 |
| 39_I | 62_V | 1.158 | 0.97 |
| 109_L | 135_Y | 1.153 | 0.97 |
| 91_V | 142_I | 1.147 | 0.97 |
| 82_I | 95_V | 1.124 | 0.97 |
| 47_H | 67_K | 1.114 | 0.96 |
| 9_K | 105_T | 1.113 | 0.96 |
| 25_F | 138_I | 1.099 | 0.96 |
| 11_F | 26_D | 1.092 | 0.96 |
| 62_V | 92_G | 1.090 | 0.96 |
| 15_S | 100_G | 1.079 | 0.95 |
| 13_V | 135_Y | 1.077 | 0.95 |
| 128_T | 131_R | 1.077 | 0.95 |
| 24_A | 126_V | 1.063 | 0.95 |
| 65_L | 141_I | 1.061 | 0.95 |
| 15_S | 102_L | 1.061 | 0.95 |
| 128_T | 133_I | 1.061 | 0.95 |
| 15_S | 24_A | 1.057 | 0.95 |
| 36_K | 94_L | 1.045 | 0.94 |
| 43_P | 51_G | 1.010 | 0.93 |
| 32_M | 55_L | 1.009 | 0.93 |
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 | |
| 4jpbW | 1 | 0.9205 | 100 | 0.157 | Contact Map |
| 2ho9A | 1 | 1 | 100 | 0.162 | Contact Map |
| 2qdlA | 2 | 0.9934 | 100 | 0.173 | Contact Map |
| 1b3qA | 2 | 0.8874 | 99.7 | 0.459 | Contact Map |
| 1oewA | 1 | 0.4834 | 5.7 | 0.927 | Contact Map |
| 1qdmA | 3 | 0.4901 | 2.8 | 0.937 | Contact Map |
| 3j8eG | 4 | 0.2185 | 2.3 | 0.94 | Contact Map |
| 2eelA | 1 | 0.543 | 2.2 | 0.94 | Contact Map |
| 1izdA | 1 | 0.4967 | 2.1 | 0.942 | Contact Map |
| 1bxoA | 1 | 0.4967 | 2 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)