| NCS1 Katie |
| ID: | 1509961428 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 190 (148) | ||
| Sequences: | 23711 (14023.6) | ||
| Seq/Len: | 160.209 | ||
| Nf(neff/√len): | 1152.7 |
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: 160.209).
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 |
| 115_Y | 163_K | 3.724 | 1.00 |
| 45_A | 66_T | 2.817 | 1.00 |
| 109_D | 114_G | 2.410 | 1.00 |
| 42_Q | 79_R | 2.393 | 1.00 |
| 102_R | 166_L | 2.382 | 1.00 |
| 113_D | 120_E | 2.287 | 1.00 |
| 118_R | 150_D | 2.175 | 1.00 |
| 31_Y | 35_I | 2.149 | 1.00 |
| 73_D | 76_K | 2.066 | 1.00 |
| 37_D | 40_S | 2.027 | 1.00 |
| 166_L | 170_Q | 2.026 | 1.00 |
| 73_D | 78_G | 2.025 | 1.00 |
| 157_D | 162_G | 1.939 | 1.00 |
| 109_D | 112_N | 1.923 | 1.00 |
| 40_S | 47_G | 1.918 | 1.00 |
| 81_E | 84_E | 1.885 | 1.00 |
| 77_D | 84_E | 1.839 | 1.00 |
| 44_D | 47_G | 1.825 | 1.00 |
| 72_F | 88_A | 1.753 | 1.00 |
| 122_L | 146_E | 1.740 | 1.00 |
| 102_R | 106_K | 1.733 | 1.00 |
| 157_D | 160_A | 1.721 | 1.00 |
| 161_D | 168_E | 1.694 | 1.00 |
| 108_Y | 124_I | 1.691 | 1.00 |
| 82_F | 102_R | 1.663 | 1.00 |
| 109_D | 113_D | 1.617 | 1.00 |
| 73_D | 77_D | 1.596 | 1.00 |
| 79_R | 115_Y | 1.591 | 1.00 |
| 118_R | 122_L | 1.587 | 1.00 |
| 110_L | 123_D | 1.525 | 1.00 |
| 113_D | 117_T | 1.513 | 1.00 |
| 110_L | 120_E | 1.502 | 1.00 |
| 165_T | 168_E | 1.486 | 1.00 |
| 157_D | 168_E | 1.468 | 1.00 |
| 145_P | 148_R | 1.468 | 1.00 |
| 150_D | 154_A | 1.454 | 1.00 |
| 82_F | 86_I | 1.427 | 1.00 |
| 45_A | 69_F | 1.424 | 1.00 |
| 75_N | 84_E | 1.417 | 1.00 |
| 66_T | 70_N | 1.378 | 0.99 |
| 82_F | 85_F | 1.372 | 0.99 |
| 109_D | 120_E | 1.346 | 0.99 |
| 157_D | 161_D | 1.331 | 0.99 |
| 111_D | 120_E | 1.331 | 0.99 |
| 158_K | 171_E | 1.319 | 0.99 |
| 156_M | 172_G | 1.313 | 0.99 |
| 61_P | 64_F | 1.308 | 0.99 |
| 74_E | 87_Q | 1.286 | 0.99 |
| 106_K | 112_N | 1.274 | 0.99 |
| 31_Y | 34_F | 1.264 | 0.99 |
| 97_L | 100_K | 1.234 | 0.98 |
| 117_T | 120_E | 1.229 | 0.98 |
| 23_T | 26_E | 1.187 | 0.98 |
| 70_N | 76_K | 1.163 | 0.97 |
| 161_D | 165_T | 1.161 | 0.97 |
| 77_D | 81_E | 1.160 | 0.97 |
| 49_Q | 53_K | 1.157 | 0.97 |
| 49_Q | 62_T | 1.153 | 0.97 |
| 146_E | 150_D | 1.145 | 0.97 |
| 116_I | 121_M | 1.143 | 0.97 |
| 118_R | 153_F | 1.116 | 0.96 |
| 35_I | 39_P | 1.098 | 0.96 |
| 166_L | 169_F | 1.096 | 0.96 |
| 71_V | 91_V | 1.082 | 0.96 |
| 45_A | 49_Q | 1.075 | 0.95 |
| 75_N | 81_E | 1.073 | 0.95 |
| 74_E | 84_E | 1.072 | 0.95 |
| 154_A | 160_A | 1.064 | 0.95 |
| 35_I | 41_G | 1.055 | 0.95 |
| 111_D | 117_T | 1.051 | 0.94 |
| 27_V | 31_Y | 1.035 | 0.94 |
| 106_K | 166_L | 1.010 | 0.93 |
| 73_D | 84_E | 1.009 | 0.93 |
| 167_Q | 170_Q | 1.006 | 0.93 |
| 28_Q | 32_K | 1.003 | 0.93 |
| 45_A | 48_F | 1.002 | 0.92 |
| 47_G | 50_K | 1.002 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4gukA | 4 | 0.9632 | 99.9 | 0.054 | Contact Map |
| 2l2eA | 1 | 0.9947 | 99.9 | 0.056 | Contact Map |
| 1fpwA | 1 | 1 | 99.9 | 0.064 | Contact Map |
| 4m2pA | 1 | 0.9684 | 99.8 | 0.112 | Contact Map |
| 1bjfA | 2 | 0.9526 | 99.8 | 0.113 | Contact Map |
| 3dd4A | 1 | 0.9421 | 99.8 | 0.118 | Contact Map |
| 1s1eA | 1 | 0.9421 | 99.8 | 0.125 | Contact Map |
| 2julA | 1 | 0.9526 | 99.8 | 0.137 | Contact Map |
| 1s6cA | 1 | 0.8684 | 99.8 | 0.141 | Contact Map |
| 1jbaA | 1 | 0.9579 | 99.8 | 0.192 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)