| T0826 11-211 |
| ID: | 1406428352 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 201 (193) | ||
| Sequences: | 556 (455.9) | ||
| Seq/Len: | 2.881 | ||
| Nf(neff/√len): | 32.8 |
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: 2.881).
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 |
| 121_G | 125_A | 3.023 | 1.00 |
| 52_N | 152_S | 2.824 | 1.00 |
| 72_L | 128_Y | 2.683 | 1.00 |
| 42_T | 167_Y | 2.300 | 1.00 |
| 69_P | 129_I | 2.210 | 1.00 |
| 81_Q | 108_L | 2.185 | 1.00 |
| 163_Q | 167_Y | 2.179 | 1.00 |
| 69_P | 125_A | 2.138 | 1.00 |
| 39_F | 167_Y | 2.054 | 1.00 |
| 49_F | 155_C | 2.004 | 1.00 |
| 81_Q | 89_F | 1.983 | 1.00 |
| 82_E | 89_F | 1.923 | 0.99 |
| 5_L | 128_Y | 1.921 | 0.99 |
| 12_Y | 17_L | 1.917 | 0.99 |
| 77_A | 117_I | 1.912 | 0.99 |
| 69_P | 128_Y | 1.905 | 0.99 |
| 94_L | 193_K | 1.845 | 0.99 |
| 93_M | 96_N | 1.816 | 0.99 |
| 13_S | 55_F | 1.780 | 0.99 |
| 98_L | 193_K | 1.770 | 0.99 |
| 141_E | 145_R | 1.696 | 0.98 |
| 178_T | 188_G | 1.683 | 0.98 |
| 84_F | 128_Y | 1.557 | 0.96 |
| 53_F | 153_F | 1.555 | 0.96 |
| 14_S | 48_F | 1.544 | 0.96 |
| 61_P | 65_K | 1.471 | 0.95 |
| 52_N | 148_L | 1.458 | 0.94 |
| 9_L | 68_I | 1.423 | 0.93 |
| 21_F | 188_G | 1.404 | 0.93 |
| 142_L | 150_A | 1.403 | 0.93 |
| 151_V | 154_L | 1.391 | 0.92 |
| 126_L | 130_A | 1.356 | 0.91 |
| 53_F | 156_A | 1.350 | 0.91 |
| 164_Y | 168_A | 1.332 | 0.90 |
| 39_F | 163_Q | 1.327 | 0.90 |
| 21_F | 175_K | 1.320 | 0.89 |
| 66_V | 69_P | 1.320 | 0.89 |
| 90_N | 93_M | 1.307 | 0.89 |
| 10_S | 17_L | 1.297 | 0.88 |
| 21_F | 182_V | 1.296 | 0.88 |
| 65_K | 69_P | 1.286 | 0.88 |
| 85_F | 143_L | 1.285 | 0.88 |
| 21_F | 47_L | 1.266 | 0.87 |
| 12_Y | 16_V | 1.257 | 0.86 |
| 76_A | 151_V | 1.252 | 0.86 |
| 6_I | 153_F | 1.243 | 0.85 |
| 160_A | 173_N | 1.241 | 0.85 |
| 70_L | 74_I | 1.213 | 0.83 |
| 118_V | 122_V | 1.210 | 0.83 |
| 146_L | 150_A | 1.197 | 0.82 |
| 83_I | 182_V | 1.184 | 0.81 |
| 13_S | 71_I | 1.182 | 0.81 |
| 58_I | 67_L | 1.179 | 0.81 |
| 49_F | 159_I | 1.164 | 0.80 |
| 117_I | 122_V | 1.156 | 0.79 |
| 21_F | 25_V | 1.156 | 0.79 |
| 20_A | 83_I | 1.156 | 0.79 |
| 11_L | 48_F | 1.139 | 0.77 |
| 53_F | 149_A | 1.135 | 0.77 |
| 119_C | 126_L | 1.130 | 0.77 |
| 153_F | 157_L | 1.130 | 0.77 |
| 93_M | 172_R | 1.126 | 0.76 |
| 95_N | 99_Q | 1.121 | 0.76 |
| 50_L | 87_I | 1.114 | 0.75 |
| 135_Y | 141_E | 1.110 | 0.75 |
| 180_L | 185_N | 1.096 | 0.74 |
| 154_L | 157_L | 1.075 | 0.71 |
| 116_W | 120_L | 1.075 | 0.71 |
| 76_A | 121_G | 1.075 | 0.71 |
| 89_F | 108_L | 1.063 | 0.70 |
| 5_L | 68_I | 1.051 | 0.69 |
| 130_A | 134_K | 1.046 | 0.68 |
| 170_F | 185_N | 1.044 | 0.68 |
| 22_F | 182_V | 1.041 | 0.68 |
| 169_S | 173_N | 1.035 | 0.67 |
| 84_F | 112_G | 1.035 | 0.67 |
| 38_I | 41_Y | 1.032 | 0.67 |
| 134_K | 140_K | 1.020 | 0.66 |
| 109_I | 114_V | 1.015 | 0.65 |
| 62_F | 66_V | 1.014 | 0.65 |
| 169_S | 172_R | 1.009 | 0.64 |
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 | |
| 4o6yA | 2 | 0.6368 | 4.5 | 0.963 | Contact Map |
| 3j1zP | 2 | 0.9453 | 3.2 | 0.965 | Contact Map |
| 1fmeA | 1 | 0.1144 | 2.3 | 0.967 | Contact Map |
| 2m3eA | 1 | 0.2438 | 2.2 | 0.968 | Contact Map |
| 1oqwA | 2 | 0.2886 | 2 | 0.969 | Contact Map |
| 3qrxB | 1 | 0.0995 | 1.7 | 0.97 | Contact Map |
| 4httA | 2 | 0.2786 | 1.6 | 0.97 | Contact Map |
| 2m7gA | 1 | 0.2886 | 1.6 | 0.97 | Contact Map |
| 2k1aA | 1 | 0.209 | 1.6 | 0.971 | Contact Map |
| 1q90M | 1 | 0.1642 | 1.4 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)