| NMB0181 |
| ID: | 1415624410 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (162) | ||
| Sequences: | 1161 (906.5) | ||
| Seq/Len: | 7.167 | ||
| Nf(neff/√len): | 71.2 |
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: 7.167).
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 |
| 137_E | 158_S | 3.362 | 1.00 |
| 134_A | 142_I | 2.795 | 1.00 |
| 42_K | 164_N | 2.669 | 1.00 |
| 136_Q | 162_E | 2.651 | 1.00 |
| 70_L | 74_R | 2.320 | 1.00 |
| 133_I | 159_V | 2.226 | 1.00 |
| 33_N | 145_N | 2.206 | 1.00 |
| 72_L | 96_L | 2.126 | 1.00 |
| 56_S | 60_D | 2.120 | 1.00 |
| 89_A | 92_K | 2.082 | 1.00 |
| 49_K | 52_D | 2.047 | 1.00 |
| 36_R | 40_E | 2.040 | 1.00 |
| 85_K | 88_Q | 2.009 | 1.00 |
| 69_G | 93_W | 1.999 | 1.00 |
| 43_Q | 125_N | 1.999 | 1.00 |
| 132_K | 162_E | 1.940 | 1.00 |
| 54_E | 114_R | 1.940 | 1.00 |
| 140_D | 150_N | 1.861 | 1.00 |
| 114_R | 117_E | 1.822 | 1.00 |
| 87_A | 91_E | 1.811 | 1.00 |
| 98_A | 102_K | 1.772 | 1.00 |
| 67_R | 71_D | 1.748 | 1.00 |
| 63_Q | 67_R | 1.705 | 1.00 |
| 83_N | 87_A | 1.675 | 1.00 |
| 47_I | 122_L | 1.674 | 1.00 |
| 52_D | 56_S | 1.657 | 1.00 |
| 71_D | 75_Q | 1.645 | 1.00 |
| 75_Q | 79_G | 1.616 | 1.00 |
| 74_R | 78_E | 1.612 | 1.00 |
| 131_V | 135_K | 1.611 | 1.00 |
| 59_Q | 63_Q | 1.552 | 1.00 |
| 68_E | 72_L | 1.537 | 0.99 |
| 124_Q | 128_R | 1.507 | 0.99 |
| 37_I | 160_I | 1.450 | 0.99 |
| 69_G | 100_F | 1.440 | 0.99 |
| 31_F | 141_V | 1.437 | 0.99 |
| 91_E | 95_G | 1.421 | 0.99 |
| 65_L | 99_A | 1.399 | 0.99 |
| 157_D | 161_K | 1.399 | 0.99 |
| 58_R | 110_D | 1.366 | 0.99 |
| 161_K | 165_A | 1.355 | 0.98 |
| 129_V | 133_I | 1.348 | 0.98 |
| 45_R | 49_K | 1.343 | 0.98 |
| 88_Q | 92_K | 1.343 | 0.98 |
| 68_E | 96_L | 1.341 | 0.98 |
| 74_R | 77_A | 1.336 | 0.98 |
| 134_A | 148_Y | 1.328 | 0.98 |
| 33_N | 36_R | 1.310 | 0.98 |
| 79_G | 89_A | 1.276 | 0.97 |
| 118_E | 121_S | 1.266 | 0.97 |
| 30_G | 139_Y | 1.259 | 0.97 |
| 69_G | 73_E | 1.228 | 0.97 |
| 158_S | 161_K | 1.209 | 0.96 |
| 139_Y | 142_I | 1.187 | 0.96 |
| 114_R | 118_E | 1.171 | 0.95 |
| 73_E | 77_A | 1.165 | 0.95 |
| 75_Q | 89_A | 1.165 | 0.95 |
| 113_L | 117_E | 1.161 | 0.95 |
| 93_W | 97_V | 1.156 | 0.95 |
| 49_K | 53_S | 1.144 | 0.94 |
| 62_L | 107_F | 1.141 | 0.94 |
| 162_E | 165_A | 1.136 | 0.94 |
| 66_Q | 70_L | 1.135 | 0.94 |
| 72_L | 92_K | 1.127 | 0.94 |
| 120_A | 124_Q | 1.116 | 0.93 |
| 37_I | 126_A | 1.101 | 0.93 |
| 81_L | 89_A | 1.099 | 0.93 |
| 36_R | 160_I | 1.098 | 0.93 |
| 66_Q | 100_F | 1.086 | 0.92 |
| 83_N | 86_K | 1.065 | 0.91 |
| 31_F | 149_V | 1.056 | 0.91 |
| 140_D | 152_Q | 1.047 | 0.90 |
| 112_N | 115_R | 1.034 | 0.89 |
| 67_R | 70_L | 1.031 | 0.89 |
| 61_E | 64_K | 1.029 | 0.89 |
| 129_V | 162_E | 1.024 | 0.89 |
| 29_I | 143_L | 1.023 | 0.89 |
| 36_R | 157_D | 1.009 | 0.88 |
| 115_R | 119_F | 1.007 | 0.88 |
| 46_K | 50_T | 1.006 | 0.87 |
| 41_S | 126_A | 1.005 | 0.87 |
| 53_S | 56_S | 1.004 | 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 | |
| 1u2mA | 3 | 0.8434 | 100 | 0.276 | Contact Map |
| 4kqtA | 1 | 0.9096 | 100 | 0.281 | Contact Map |
| 4cgkA | 2 | 0.6687 | 94.2 | 0.84 | Contact Map |
| 3layA | 10 | 0.4639 | 72.5 | 0.885 | Contact Map |
| 1dj7A | 1 | 0.241 | 43.3 | 0.904 | Contact Map |
| 1gaxA | 2 | 0.6265 | 20.8 | 0.918 | Contact Map |
| 3zg1A | 4 | 0.5904 | 20.3 | 0.919 | Contact Map |
| 4kzkA | 1 | 0.4759 | 20 | 0.919 | Contact Map |
| 2ld3A | 1 | 0.5301 | 18 | 0.921 | Contact Map |
| 4fczB | 2 | 0.8072 | 15.6 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)