| Pdenitr_cIII_ISP |
| ID: | 1441215292 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (186) | ||
| Sequences: | 2679 (1640.3) | ||
| Seq/Len: | 14.403 | ||
| Nf(neff/√len): | 120.3 |
Jackhmmer Results: (2015_08)
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: 14.403).
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 |
| 83_E | 87_Q | 3.244 | 1.00 |
| 183_D | 186_T | 3.002 | 1.00 |
| 80_R | 124_E | 2.996 | 1.00 |
| 157_S | 170_A | 2.942 | 1.00 |
| 127_V | 187_I | 2.806 | 1.00 |
| 137_C | 154_C | 2.734 | 1.00 |
| 133_T | 170_A | 2.228 | 1.00 |
| 128_M | 176_I | 2.012 | 1.00 |
| 20_Y | 24_A | 1.933 | 1.00 |
| 172_Q | 175_H | 1.926 | 1.00 |
| 159_Y | 172_Q | 1.881 | 1.00 |
| 87_Q | 90_R | 1.875 | 1.00 |
| 28_T | 32_G | 1.810 | 1.00 |
| 113_T | 116_N | 1.795 | 1.00 |
| 40_N | 43_N | 1.783 | 1.00 |
| 76_V | 189_L | 1.762 | 1.00 |
| 114_D | 117_R | 1.755 | 1.00 |
| 62_E | 65_T | 1.718 | 1.00 |
| 134_H | 155_H | 1.692 | 1.00 |
| 63_T | 83_E | 1.648 | 1.00 |
| 182_L | 188_K | 1.635 | 1.00 |
| 112_A | 116_N | 1.582 | 1.00 |
| 93_D | 96_Q | 1.558 | 1.00 |
| 87_Q | 91_E | 1.555 | 1.00 |
| 182_L | 186_T | 1.535 | 1.00 |
| 107_K | 110_A | 1.511 | 1.00 |
| 133_T | 159_Y | 1.505 | 1.00 |
| 143_G | 147_F | 1.496 | 1.00 |
| 38_L | 41_Q | 1.484 | 1.00 |
| 45_S | 48_V | 1.483 | 1.00 |
| 182_L | 185_T | 1.466 | 1.00 |
| 25_G | 29_V | 1.454 | 1.00 |
| 92_V | 97_L | 1.442 | 1.00 |
| 128_M | 174_L | 1.440 | 1.00 |
| 152_C | 155_H | 1.439 | 1.00 |
| 180_E | 188_K | 1.423 | 1.00 |
| 120_D | 123_G | 1.404 | 0.99 |
| 111_P | 114_D | 1.399 | 0.99 |
| 143_G | 146_D | 1.389 | 0.99 |
| 92_V | 95_G | 1.362 | 0.99 |
| 129_I | 175_H | 1.359 | 0.99 |
| 46_A | 49_Q | 1.347 | 0.99 |
| 132_C | 152_C | 1.327 | 0.99 |
| 55_Q | 188_K | 1.312 | 0.99 |
| 132_C | 155_H | 1.303 | 0.99 |
| 134_H | 152_C | 1.292 | 0.99 |
| 88_A | 91_E | 1.285 | 0.99 |
| 26_A | 30_A | 1.272 | 0.99 |
| 144_A | 147_F | 1.272 | 0.99 |
| 29_V | 32_G | 1.265 | 0.99 |
| 109_D | 113_T | 1.257 | 0.99 |
| 158_H | 167_R | 1.252 | 0.99 |
| 90_R | 93_D | 1.252 | 0.99 |
| 56_V | 61_V | 1.246 | 0.98 |
| 57_D | 60_G | 1.237 | 0.98 |
| 63_T | 82_T | 1.236 | 0.98 |
| 21_Y | 25_G | 1.234 | 0.98 |
| 115_E | 118_T | 1.223 | 0.98 |
| 110_A | 113_T | 1.217 | 0.98 |
| 125_W | 181_F | 1.217 | 0.98 |
| 109_D | 114_D | 1.184 | 0.98 |
| 32_G | 37_T | 1.173 | 0.98 |
| 110_A | 114_D | 1.169 | 0.97 |
| 36_W | 40_N | 1.168 | 0.97 |
| 82_T | 85_E | 1.164 | 0.97 |
| 34_A | 37_T | 1.162 | 0.97 |
| 133_T | 175_H | 1.158 | 0.97 |
| 111_P | 116_N | 1.156 | 0.97 |
| 68_T | 71_W | 1.135 | 0.97 |
| 160_D | 164_R | 1.126 | 0.97 |
| 12_G | 15_R | 1.118 | 0.96 |
| 79_R | 85_E | 1.116 | 0.96 |
| 146_D | 158_H | 1.087 | 0.96 |
| 11_H | 14_T | 1.085 | 0.96 |
| 88_A | 92_V | 1.082 | 0.96 |
| 112_A | 115_E | 1.081 | 0.95 |
| 130_G | 138_V | 1.080 | 0.95 |
| 92_V | 96_Q | 1.079 | 0.95 |
| 84_D | 87_Q | 1.078 | 0.95 |
| 111_P | 117_R | 1.075 | 0.95 |
| 61_V | 125_W | 1.059 | 0.95 |
| 38_L | 42_M | 1.047 | 0.94 |
| 80_R | 125_W | 1.045 | 0.94 |
| 108_P | 111_P | 1.039 | 0.94 |
| 53_S | 188_K | 1.038 | 0.94 |
| 112_A | 117_R | 1.036 | 0.94 |
| 131_V | 138_V | 1.021 | 0.93 |
| 182_L | 187_I | 1.020 | 0.93 |
| 185_T | 188_K | 1.017 | 0.93 |
| 31_A | 35_A | 1.016 | 0.93 |
| 7_H | 10_D | 1.015 | 0.93 |
| 19_L | 23_T | 1.014 | 0.93 |
| 102_A | 106_N | 1.007 | 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 | |
| 2qjyC | 6 | 0.9316 | 100 | 0.259 | Contact Map |
| 1pp9E | 2 | 0.9263 | 100 | 0.269 | Contact Map |
| 4d6tE | 3 | 0.9263 | 100 | 0.272 | Contact Map |
| 3cx5E | 2 | 0.9211 | 100 | 0.287 | Contact Map |
| 4ogqD | 1 | 0.7842 | 100 | 0.337 | Contact Map |
| 4aayB | 4 | 0.5947 | 100 | 0.364 | Contact Map |
| 2nwfA | 1 | 0.7316 | 99.9 | 0.446 | Contact Map |
| 1rieA | 1 | 0.6684 | 99.9 | 0.473 | Contact Map |
| 1jm1A | 1 | 0.7211 | 99.8 | 0.519 | Contact Map |
| 1nykA | 2 | 0.7474 | 99.8 | 0.533 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)