| AligNitrilase |
| ID: | 1508347698 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 366 (314) | ||
| Sequences: | 3236 (1910.9) | ||
| Seq/Len: | 10.306 | ||
| Nf(neff/√len): | 107.8 |
Jackhmmer Results: (2016_04)
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: 10.306).
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 |
| 9_K | 279_D | 5.264 | 1.00 |
| 154_D | 159_R | 3.741 | 1.00 |
| 268_L | 274_G | 3.694 | 1.00 |
| 12_A | 223_V | 3.608 | 1.00 |
| 34_A | 96_H | 3.165 | 1.00 |
| 39_N | 277_Y | 3.093 | 1.00 |
| 34_A | 95_D | 2.985 | 1.00 |
| 45_A | 186_V | 2.880 | 1.00 |
| 309_N | 313_T | 2.852 | 1.00 |
| 111_S | 143_G | 2.457 | 1.00 |
| 35_E | 39_N | 2.456 | 1.00 |
| 127_A | 153_Y | 2.395 | 1.00 |
| 82_D | 86_V | 2.385 | 1.00 |
| 11_A | 41_C | 2.350 | 1.00 |
| 30_V | 88_R | 2.346 | 1.00 |
| 118_I | 162_A | 2.305 | 1.00 |
| 120_D | 126_V | 2.290 | 1.00 |
| 27_D | 88_R | 2.253 | 1.00 |
| 44_V | 98_I | 2.223 | 1.00 |
| 89_L | 102_V | 2.211 | 1.00 |
| 10_V | 223_V | 2.192 | 1.00 |
| 99_A | 121_A | 2.129 | 1.00 |
| 258_G | 262_R | 2.128 | 1.00 |
| 28_K | 273_E | 2.107 | 1.00 |
| 115_T | 128_R | 2.079 | 1.00 |
| 256_I | 278_A | 2.047 | 1.00 |
| 10_V | 280_I | 2.032 | 1.00 |
| 90_L | 119_I | 2.027 | 1.00 |
| 52_P | 77_N | 2.003 | 1.00 |
| 163_L | 173_T | 1.952 | 1.00 |
| 43_L | 157_F | 1.934 | 1.00 |
| 92_A | 96_H | 1.924 | 1.00 |
| 155_M | 158_A | 1.918 | 1.00 |
| 41_C | 44_V | 1.899 | 1.00 |
| 30_V | 92_A | 1.882 | 1.00 |
| 13_V | 275_I | 1.881 | 1.00 |
| 268_L | 272_E | 1.879 | 1.00 |
| 91_D | 95_D | 1.840 | 1.00 |
| 16_Q | 28_K | 1.794 | 1.00 |
| 8_F | 280_I | 1.790 | 1.00 |
| 8_F | 184_V | 1.789 | 1.00 |
| 21_D | 24_K | 1.773 | 1.00 |
| 41_C | 275_I | 1.752 | 1.00 |
| 210_A | 213_M | 1.740 | 1.00 |
| 41_C | 277_Y | 1.736 | 1.00 |
| 78_S | 105_S | 1.726 | 1.00 |
| 33_I | 100_V | 1.707 | 1.00 |
| 7_T | 279_D | 1.706 | 1.00 |
| 215_A | 222_V | 1.701 | 1.00 |
| 132_L | 303_V | 1.701 | 1.00 |
| 133_K | 144_E | 1.665 | 1.00 |
| 76_E | 283_S | 1.658 | 1.00 |
| 116_Q | 162_A | 1.645 | 1.00 |
| 23_A | 85_H | 1.632 | 1.00 |
| 42_E | 121_A | 1.620 | 1.00 |
| 101_V | 118_I | 1.618 | 1.00 |
| 43_L | 186_V | 1.610 | 1.00 |
| 11_A | 36_A | 1.589 | 1.00 |
| 93_A | 100_V | 1.589 | 1.00 |
| 121_A | 156_P | 1.587 | 1.00 |
| 180_M | 310_Q | 1.582 | 1.00 |
| 87_Q | 91_D | 1.582 | 1.00 |
| 89_L | 100_V | 1.581 | 1.00 |
| 34_A | 92_A | 1.563 | 1.00 |
| 204_V | 253_F | 1.545 | 1.00 |
| 265_A | 276_L | 1.543 | 1.00 |
| 29_T | 102_V | 1.533 | 1.00 |
| 104_I | 117_L | 1.496 | 1.00 |
| 37_A | 96_H | 1.480 | 1.00 |
| 161_G | 182_E | 1.454 | 1.00 |
| 82_D | 87_Q | 1.444 | 1.00 |
| 15_A | 32_N | 1.441 | 1.00 |
| 120_D | 124_Q | 1.415 | 1.00 |
| 36_A | 275_I | 1.412 | 1.00 |
| 29_T | 50_F | 1.412 | 1.00 |
| 72_V | 76_E | 1.410 | 1.00 |
| 9_K | 39_N | 1.410 | 1.00 |
| 267_P | 274_G | 1.395 | 0.99 |
| 87_Q | 90_L | 1.385 | 0.99 |
| 161_G | 177_M | 1.384 | 0.99 |
| 29_T | 89_L | 1.376 | 0.99 |
| 18_V | 25_T | 1.370 | 0.99 |
| 99_A | 156_P | 1.369 | 0.99 |
| 231_P | 235_E | 1.364 | 0.99 |
| 11_A | 277_Y | 1.344 | 0.99 |
| 152_V | 159_R | 1.335 | 0.99 |
| 99_A | 118_I | 1.331 | 0.99 |
| 101_V | 116_Q | 1.325 | 0.99 |
| 12_A | 225_T | 1.322 | 0.99 |
| 86_V | 117_L | 1.317 | 0.99 |
| 221_F | 264_L | 1.308 | 0.99 |
| 13_V | 44_V | 1.308 | 0.99 |
| 12_A | 276_L | 1.306 | 0.99 |
| 26_V | 30_V | 1.299 | 0.99 |
| 34_A | 38_R | 1.293 | 0.99 |
| 101_V | 186_V | 1.293 | 0.99 |
| 29_T | 33_I | 1.292 | 0.99 |
| 159_R | 181_H | 1.272 | 0.99 |
| 45_A | 223_V | 1.261 | 0.99 |
| 41_C | 98_I | 1.255 | 0.99 |
| 97_N | 121_A | 1.252 | 0.99 |
| 183_Q | 289_K | 1.249 | 0.99 |
| 178_Y | 218_G | 1.247 | 0.99 |
| 265_A | 278_A | 1.242 | 0.98 |
| 120_D | 156_P | 1.241 | 0.98 |
| 172_L | 175_Y | 1.240 | 0.98 |
| 182_E | 185_H | 1.225 | 0.98 |
| 284_A | 287_L | 1.213 | 0.98 |
| 33_I | 92_A | 1.212 | 0.98 |
| 35_E | 277_Y | 1.209 | 0.98 |
| 267_P | 276_L | 1.207 | 0.98 |
| 15_A | 273_E | 1.206 | 0.98 |
| 86_V | 90_L | 1.202 | 0.98 |
| 26_V | 88_R | 1.193 | 0.98 |
| 23_A | 27_D | 1.190 | 0.98 |
| 24_K | 27_D | 1.190 | 0.98 |
| 106_E | 130_R | 1.177 | 0.98 |
| 92_A | 100_V | 1.171 | 0.98 |
| 23_A | 88_R | 1.171 | 0.98 |
| 49_V | 105_S | 1.166 | 0.97 |
| 79_L | 85_H | 1.164 | 0.97 |
| 74_Y | 105_S | 1.160 | 0.97 |
| 22_A | 51_I | 1.158 | 0.97 |
| 205_D | 212_R | 1.157 | 0.97 |
| 31_S | 35_E | 1.153 | 0.97 |
| 81_M | 117_L | 1.150 | 0.97 |
| 139_R | 298_Y | 1.148 | 0.97 |
| 42_E | 157_F | 1.146 | 0.97 |
| 99_A | 157_F | 1.140 | 0.97 |
| 90_L | 124_Q | 1.139 | 0.97 |
| 28_K | 32_N | 1.134 | 0.97 |
| 25_T | 51_I | 1.134 | 0.97 |
| 183_Q | 282_L | 1.133 | 0.97 |
| 27_D | 31_S | 1.131 | 0.97 |
| 99_A | 120_D | 1.123 | 0.97 |
| 6_N | 183_Q | 1.117 | 0.96 |
| 45_A | 225_T | 1.103 | 0.96 |
| 305_S | 309_N | 1.097 | 0.96 |
| 211_T | 224_C | 1.095 | 0.96 |
| 206_A | 216_L | 1.093 | 0.96 |
| 30_V | 34_A | 1.092 | 0.96 |
| 22_A | 85_H | 1.087 | 0.96 |
| 208_L | 263_D | 1.079 | 0.95 |
| 99_A | 155_M | 1.077 | 0.95 |
| 25_T | 29_T | 1.077 | 0.95 |
| 155_M | 160_L | 1.068 | 0.95 |
| 32_N | 275_I | 1.066 | 0.95 |
| 75_H | 112_L | 1.061 | 0.95 |
| 101_V | 162_A | 1.059 | 0.95 |
| 114_M | 164_N | 1.047 | 0.94 |
| 30_V | 96_H | 1.042 | 0.94 |
| 9_K | 277_Y | 1.035 | 0.94 |
| 29_T | 51_I | 1.033 | 0.94 |
| 15_A | 50_F | 1.031 | 0.94 |
| 258_G | 264_L | 1.024 | 0.93 |
| 120_D | 123_G | 1.018 | 0.93 |
| 91_D | 94_R | 1.017 | 0.93 |
| 22_A | 26_V | 1.017 | 0.93 |
| 26_V | 89_L | 1.014 | 0.93 |
| 117_L | 125_L | 1.011 | 0.93 |
| 113_Y | 130_R | 1.005 | 0.93 |
| 84_P | 87_Q | 1.002 | 0.92 |
| 12_A | 254_A | 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
- 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 | |
| 3wuyA | 2 | 0.7842 | 100 | 0.332 | Contact Map |
| 2vhhA | 4 | 0.8333 | 100 | 0.467 | Contact Map |
| 1uf5A | 2 | 0.7705 | 100 | 0.478 | Contact Map |
| 3ivzA | 2 | 0.7077 | 100 | 0.483 | Contact Map |
| 1emsA | 2 | 0.8825 | 100 | 0.487 | Contact Map |
| 4izuA | 1 | 0.6885 | 100 | 0.488 | Contact Map |
| 3p8kA | 2 | 0.7186 | 100 | 0.49 | Contact Map |
| 2w1vA | 2 | 0.7213 | 100 | 0.493 | Contact Map |
| 2dyuA | 2 | 0.7842 | 100 | 0.498 | Contact Map |
| 4hg5A | 4 | 0.7432 | 100 | 0.501 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)