| arpc1b |
| ID: | 1501024353 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 372 (354) | ||
| Sequences: | 2624 (2187.3) | ||
| Seq/Len: | 7.412 | ||
| Nf(neff/√len): | 116.3 |
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: 7.412).
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 |
| 141_I | 159_A | 3.621 | 1.00 |
| 95_I | 113_V | 3.546 | 1.00 |
| 51_H | 69_T | 3.407 | 1.00 |
| 32_V | 69_T | 3.268 | 1.00 |
| 101_C | 114_G | 3.103 | 1.00 |
| 159_A | 169_F | 3.099 | 1.00 |
| 24_A | 67_I | 3.055 | 1.00 |
| 113_V | 123_C | 2.935 | 1.00 |
| 147_S | 160_G | 2.910 | 1.00 |
| 25_I | 35_Y | 2.878 | 1.00 |
| 112_A | 157_L | 2.791 | 1.00 |
| 120_I | 159_A | 2.778 | 1.00 |
| 201_S | 219_W | 2.777 | 1.00 |
| 68_V | 111_F | 2.738 | 1.00 |
| 51_H | 73_D | 2.614 | 1.00 |
| 219_W | 229_A | 2.563 | 1.00 |
| 24_A | 60_W | 2.527 | 1.00 |
| 58_I | 69_T | 2.376 | 1.00 |
| 112_A | 150_W | 2.371 | 1.00 |
| 158_A | 217_V | 2.365 | 1.00 |
| 57_G | 70_C | 2.344 | 1.00 |
| 71_G | 75_N | 2.329 | 1.00 |
| 201_S | 223_D | 2.083 | 1.00 |
| 26_C | 30_H | 1.997 | 1.00 |
| 220_V | 224_S | 1.944 | 1.00 |
| 163_D | 167_R | 1.831 | 1.00 |
| 68_V | 78_V | 1.769 | 1.00 |
| 141_I | 161_S | 1.767 | 1.00 |
| 68_V | 104_W | 1.758 | 1.00 |
| 25_I | 29_N | 1.756 | 1.00 |
| 69_T | 79_W | 1.744 | 1.00 |
| 95_I | 123_C | 1.738 | 1.00 |
| 160_G | 164_F | 1.708 | 1.00 |
| 218_A | 252_F | 1.706 | 1.00 |
| 68_V | 102_V | 1.706 | 1.00 |
| 166_C | 219_W | 1.701 | 1.00 |
| 59_D | 103_R | 1.681 | 1.00 |
| 207_G | 220_V | 1.669 | 1.00 |
| 141_I | 163_D | 1.660 | 1.00 |
| 17_N | 21_T | 1.631 | 1.00 |
| 50_E | 79_W | 1.594 | 1.00 |
| 298_A | 301_R | 1.575 | 1.00 |
| 297_T | 301_R | 1.570 | 1.00 |
| 24_A | 34_I | 1.559 | 1.00 |
| 117_S | 121_S | 1.555 | 1.00 |
| 76_A | 113_V | 1.533 | 1.00 |
| 58_I | 67_I | 1.527 | 1.00 |
| 95_I | 115_S | 1.517 | 0.99 |
| 114_G | 145_V | 1.512 | 0.99 |
| 211_S | 214_G | 1.492 | 0.99 |
| 51_H | 71_G | 1.468 | 0.99 |
| 13_C | 26_C | 1.464 | 0.99 |
| 141_I | 169_F | 1.462 | 0.99 |
| 7_L | 25_I | 1.452 | 0.99 |
| 95_I | 99_A | 1.442 | 0.99 |
| 50_E | 77_Y | 1.427 | 0.99 |
| 99_A | 113_V | 1.417 | 0.99 |
| 159_A | 163_D | 1.383 | 0.99 |
| 253_I | 256_N | 1.377 | 0.99 |
| 112_A | 122_I | 1.376 | 0.99 |
| 160_G | 205_V | 1.368 | 0.99 |
| 301_R | 304_N | 1.364 | 0.99 |
| 158_A | 168_I | 1.331 | 0.98 |
| 152_P | 210_F | 1.327 | 0.98 |
| 289_K | 293_Q | 1.319 | 0.98 |
| 62_P | 108_E | 1.319 | 0.98 |
| 309_A | 313_G | 1.318 | 0.98 |
| 25_I | 33_H | 1.315 | 0.98 |
| 56_T | 72_T | 1.309 | 0.98 |
| 27_P | 33_H | 1.307 | 0.98 |
| 220_V | 247_L | 1.307 | 0.98 |
| 95_I | 117_S | 1.307 | 0.98 |
| 106_P | 150_W | 1.305 | 0.98 |
| 69_T | 73_D | 1.301 | 0.98 |
| 219_W | 223_D | 1.294 | 0.98 |
| 105_A | 150_W | 1.292 | 0.98 |
| 208_V | 219_W | 1.288 | 0.98 |
| 70_C | 99_A | 1.273 | 0.98 |
| 208_V | 217_V | 1.266 | 0.97 |
| 348_T | 354_M | 1.265 | 0.97 |
| 346_C | 356_I | 1.265 | 0.97 |
| 114_G | 118_R | 1.260 | 0.97 |
| 61_A | 104_W | 1.257 | 0.97 |
| 296_L | 299_R | 1.257 | 0.97 |
| 115_S | 119_V | 1.250 | 0.97 |
| 303_Q | 308_K | 1.243 | 0.97 |
| 306_D | 310_S | 1.242 | 0.97 |
| 161_S | 165_K | 1.242 | 0.97 |
| 288_P | 292_S | 1.241 | 0.97 |
| 243_E | 264_D | 1.237 | 0.97 |
| 303_Q | 307_K | 1.231 | 0.97 |
| 298_A | 302_F | 1.231 | 0.97 |
| 158_A | 210_F | 1.228 | 0.97 |
| 36_E | 39_G | 1.202 | 0.96 |
| 305_L | 308_K | 1.200 | 0.96 |
| 27_P | 31_E | 1.198 | 0.96 |
| 300_E | 303_Q | 1.186 | 0.96 |
| 51_H | 79_W | 1.186 | 0.96 |
| 160_G | 208_V | 1.182 | 0.96 |
| 282_G | 285_L | 1.181 | 0.96 |
| 311_S | 314_G | 1.179 | 0.96 |
| 295_G | 300_E | 1.178 | 0.96 |
| 27_P | 30_H | 1.175 | 0.96 |
| 303_Q | 306_D | 1.164 | 0.95 |
| 288_P | 291_S | 1.159 | 0.95 |
| 261_A | 265_C | 1.147 | 0.95 |
| 35_Y | 44_K | 1.147 | 0.95 |
| 301_R | 307_K | 1.144 | 0.95 |
| 16_W | 23_I | 1.142 | 0.95 |
| 300_E | 304_N | 1.140 | 0.95 |
| 115_S | 118_R | 1.135 | 0.94 |
| 332_I | 347_T | 1.127 | 0.94 |
| 299_R | 310_S | 1.122 | 0.94 |
| 103_R | 149_D | 1.116 | 0.94 |
| 79_W | 86_W | 1.115 | 0.94 |
| 318_G | 321_L | 1.114 | 0.94 |
| 299_R | 302_F | 1.114 | 0.94 |
| 29_N | 33_H | 1.104 | 0.93 |
| 60_W | 67_I | 1.103 | 0.93 |
| 290_Q | 293_Q | 1.088 | 0.93 |
| 124_Y | 127_Q | 1.087 | 0.93 |
| 291_S | 294_R | 1.087 | 0.93 |
| 205_V | 208_V | 1.083 | 0.92 |
| 289_K | 292_S | 1.083 | 0.92 |
| 57_G | 101_C | 1.081 | 0.92 |
| 17_N | 60_W | 1.080 | 0.92 |
| 301_R | 308_K | 1.078 | 0.92 |
| 260_A | 264_D | 1.078 | 0.92 |
| 285_L | 288_P | 1.076 | 0.92 |
| 223_D | 227_C | 1.072 | 0.92 |
| 113_V | 121_S | 1.071 | 0.92 |
| 201_S | 221_S | 1.069 | 0.92 |
| 298_A | 303_Q | 1.067 | 0.92 |
| 299_R | 304_N | 1.067 | 0.92 |
| 289_K | 295_G | 1.065 | 0.92 |
| 218_A | 250_L | 1.064 | 0.91 |
| 32_V | 55_V | 1.059 | 0.91 |
| 102_V | 113_V | 1.058 | 0.91 |
| 243_E | 247_L | 1.058 | 0.91 |
| 158_A | 169_F | 1.055 | 0.91 |
| 299_R | 303_Q | 1.053 | 0.91 |
| 51_H | 55_V | 1.052 | 0.91 |
| 149_D | 208_V | 1.051 | 0.91 |
| 259_V | 269_L | 1.050 | 0.91 |
| 324_L | 328_S | 1.048 | 0.91 |
| 307_K | 310_S | 1.046 | 0.91 |
| 115_S | 121_S | 1.043 | 0.90 |
| 296_L | 301_R | 1.037 | 0.90 |
| 118_R | 144_T | 1.035 | 0.90 |
| 170_S | 173_I | 1.035 | 0.90 |
| 138_K | 141_I | 1.028 | 0.89 |
| 71_G | 77_Y | 1.024 | 0.89 |
| 285_L | 291_S | 1.023 | 0.89 |
| 325_H | 329_V | 1.020 | 0.89 |
| 287_V | 290_Q | 1.019 | 0.89 |
| 290_Q | 294_R | 1.018 | 0.89 |
| 325_H | 347_T | 1.016 | 0.89 |
| 295_G | 299_R | 1.015 | 0.89 |
| 303_Q | 309_A | 1.011 | 0.88 |
| 284_R | 287_V | 1.010 | 0.88 |
| 56_T | 100_R | 1.009 | 0.88 |
| 301_R | 310_S | 1.003 | 0.88 |
| 98_A | 116_G | 1.000 | 0.88 |
| 287_V | 294_R | 1.000 | 0.88 |
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 | |
| 1k8kC | 1 | 0.9516 | 100 | 0.249 | Contact Map |
| 3dwlC | 2 | 0.8575 | 100 | 0.287 | Contact Map |
| 1vyhC | 10 | 0.7715 | 100 | 0.306 | Contact Map |
| 3dm0A | 1 | 0.793 | 100 | 0.338 | Contact Map |
| 3fm0A | 1 | 0.828 | 100 | 0.343 | Contact Map |
| 4wjuA | 2 | 0.8199 | 100 | 0.344 | Contact Map |
| 3sfzA | 1 | 0.9543 | 100 | 0.345 | Contact Map |
| 4bpeR | 1 | 0.8306 | 100 | 0.346 | Contact Map |
| 3j60g | 1 | 0.8226 | 100 | 0.346 | Contact Map |
| 3ow8A | 4 | 0.7823 | 100 | 0.35 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)