| GC_sapC_2 |
| ID: | 1388084844 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 279 (277) | ||
| Sequences: | 3006 (1282.1) | ||
| Seq/Len: | 10.852 | ||
| Nf(neff/√len): | 77.0 |
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: 10.852).
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 |
| 105_G | 109_A | 2.178 | 1.00 |
| 105_G | 143_Y | 2.061 | 1.00 |
| 21_S | 89_L | 1.943 | 1.00 |
| 118_L | 146_G | 1.897 | 1.00 |
| 107_A | 111_S | 1.847 | 1.00 |
| 92_T | 95_H | 1.724 | 1.00 |
| 47_Q | 51_N | 1.458 | 1.00 |
| 59_A | 62_K | 1.384 | 0.99 |
| 94_E | 133_V | 1.357 | 0.99 |
| 57_L | 111_S | 1.293 | 0.99 |
| 260_I | 273_V | 1.268 | 0.99 |
| 50_A | 54_V | 1.244 | 0.98 |
| 23_T | 31_V | 1.224 | 0.98 |
| 49_W | 53_F | 1.223 | 0.98 |
| 266_N | 269_S | 1.218 | 0.98 |
| 215_S | 265_V | 1.204 | 0.98 |
| 93_P | 133_V | 1.201 | 0.98 |
| 225_E | 228_V | 1.190 | 0.98 |
| 215_S | 259_D | 1.187 | 0.98 |
| 103_D | 106_P | 1.182 | 0.98 |
| 53_F | 70_V | 1.177 | 0.98 |
| 58_D | 111_S | 1.173 | 0.98 |
| 38_K | 44_I | 1.170 | 0.97 |
| 264_E | 276_L | 1.149 | 0.97 |
| 269_S | 272_G | 1.145 | 0.97 |
| 247_Q | 272_G | 1.144 | 0.97 |
| 55_K | 59_A | 1.138 | 0.97 |
| 216_E | 262_I | 1.135 | 0.97 |
| 253_F | 256_S | 1.133 | 0.97 |
| 94_E | 98_D | 1.131 | 0.97 |
| 226_L | 233_N | 1.130 | 0.97 |
| 222_A | 260_I | 1.126 | 0.97 |
| 208_Q | 226_L | 1.119 | 0.96 |
| 224_E | 233_N | 1.118 | 0.96 |
| 70_V | 112_S | 1.110 | 0.96 |
| 248_E | 266_N | 1.109 | 0.96 |
| 71_T | 121_D | 1.108 | 0.96 |
| 54_V | 111_S | 1.108 | 0.96 |
| 228_V | 255_P | 1.108 | 0.96 |
| 272_G | 275_G | 1.107 | 0.96 |
| 248_E | 269_S | 1.107 | 0.96 |
| 118_L | 148_A | 1.106 | 0.96 |
| 248_E | 259_D | 1.104 | 0.96 |
| 164_G | 168_R | 1.103 | 0.96 |
| 252_T | 259_D | 1.097 | 0.96 |
| 232_S | 258_L | 1.097 | 0.96 |
| 236_A | 247_Q | 1.096 | 0.96 |
| 260_I | 264_E | 1.095 | 0.96 |
| 256_S | 262_I | 1.091 | 0.96 |
| 69_A | 116_K | 1.091 | 0.96 |
| 225_E | 273_V | 1.087 | 0.96 |
| 217_L | 228_V | 1.086 | 0.96 |
| 107_A | 110_N | 1.081 | 0.95 |
| 101_S | 143_Y | 1.079 | 0.95 |
| 219_V | 265_V | 1.079 | 0.95 |
| 260_I | 263_H | 1.077 | 0.95 |
| 216_E | 273_V | 1.076 | 0.95 |
| 55_K | 58_D | 1.074 | 0.95 |
| 219_V | 273_V | 1.073 | 0.95 |
| 259_D | 263_H | 1.072 | 0.95 |
| 222_A | 268_S | 1.071 | 0.95 |
| 248_E | 264_E | 1.070 | 0.95 |
| 233_N | 255_P | 1.069 | 0.95 |
| 263_H | 269_S | 1.062 | 0.95 |
| 237_L | 260_I | 1.062 | 0.95 |
| 272_G | 278_A | 1.062 | 0.95 |
| 221_N | 226_L | 1.061 | 0.95 |
| 209_F | 276_L | 1.058 | 0.95 |
| 228_V | 254_G | 1.057 | 0.95 |
| 233_N | 269_S | 1.057 | 0.95 |
| 215_S | 232_S | 1.055 | 0.95 |
| 268_S | 275_G | 1.054 | 0.95 |
| 224_E | 255_P | 1.053 | 0.95 |
| 225_E | 248_E | 1.053 | 0.95 |
| 219_V | 266_N | 1.052 | 0.95 |
| 257_L | 275_G | 1.052 | 0.95 |
| 214_F | 232_S | 1.050 | 0.94 |
| 213_K | 216_E | 1.050 | 0.94 |
| 215_S | 248_E | 1.049 | 0.94 |
| 265_V | 273_V | 1.049 | 0.94 |
| 209_F | 264_E | 1.048 | 0.94 |
| 269_S | 273_V | 1.047 | 0.94 |
| 45_F | 48_T | 1.047 | 0.94 |
| 209_F | 216_E | 1.044 | 0.94 |
| 219_V | 263_H | 1.043 | 0.94 |
| 242_A | 265_V | 1.042 | 0.94 |
| 51_N | 107_A | 1.041 | 0.94 |
| 209_F | 215_S | 1.041 | 0.94 |
| 222_A | 226_L | 1.039 | 0.94 |
| 262_I | 265_V | 1.038 | 0.94 |
| 99_F | 104_L | 1.037 | 0.94 |
| 262_I | 273_V | 1.037 | 0.94 |
| 232_S | 241_P | 1.036 | 0.94 |
| 202_I | 219_V | 1.036 | 0.94 |
| 247_Q | 266_N | 1.035 | 0.94 |
| 248_E | 272_G | 1.034 | 0.94 |
| 248_E | 251_G | 1.034 | 0.94 |
| 236_A | 255_P | 1.033 | 0.94 |
| 215_S | 272_G | 1.033 | 0.94 |
| 242_A | 266_N | 1.032 | 0.94 |
| 232_S | 254_G | 1.028 | 0.94 |
| 213_K | 268_S | 1.026 | 0.94 |
| 106_P | 143_Y | 1.026 | 0.94 |
| 71_T | 148_A | 1.025 | 0.93 |
| 260_I | 265_V | 1.024 | 0.93 |
| 132_E | 136_S | 1.023 | 0.93 |
| 58_D | 61_A | 1.020 | 0.93 |
| 245_K | 264_E | 1.017 | 0.93 |
| 232_S | 252_T | 1.017 | 0.93 |
| 212_N | 215_S | 1.016 | 0.93 |
| 209_F | 212_N | 1.015 | 0.93 |
| 264_E | 275_G | 1.015 | 0.93 |
| 219_V | 233_N | 1.014 | 0.93 |
| 77_T | 120_L | 1.012 | 0.93 |
| 237_L | 240_D | 1.011 | 0.93 |
| 226_L | 247_Q | 1.011 | 0.93 |
| 56_F | 60_Y | 1.010 | 0.93 |
| 225_E | 229_K | 1.010 | 0.93 |
| 242_A | 245_K | 1.010 | 0.93 |
| 229_K | 237_L | 1.009 | 0.93 |
| 212_N | 265_V | 1.008 | 0.93 |
| 209_F | 243_R | 1.008 | 0.93 |
| 213_K | 220_N | 1.007 | 0.93 |
| 226_L | 273_V | 1.007 | 0.93 |
| 219_V | 259_D | 1.007 | 0.93 |
| 237_L | 273_V | 1.007 | 0.93 |
| 248_E | 273_V | 1.006 | 0.93 |
| 263_H | 272_G | 1.005 | 0.93 |
| 264_E | 272_G | 1.004 | 0.93 |
| 203_L | 269_S | 1.003 | 0.93 |
| 234_A | 260_I | 1.002 | 0.92 |
| 206_T | 233_N | 1.002 | 0.92 |
| 216_E | 219_V | 1.002 | 0.92 |
| 264_E | 273_V | 1.002 | 0.92 |
| 208_Q | 254_G | 1.001 | 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 | |
| 2nt0A | 4 | 0.9642 | 100 | 0.455 | Contact Map |
| 2wnwA | 2 | 0.8925 | 100 | 0.512 | Contact Map |
| 3clwA | 6 | 0.8889 | 100 | 0.541 | Contact Map |
| 2y24A | 1 | 0.8387 | 100 | 0.554 | Contact Map |
| 4fmvA | 1 | 0.8566 | 100 | 0.562 | Contact Map |
| 3kl0A | 4 | 0.8495 | 99.9 | 0.59 | Contact Map |
| 4ccdA | 1 | 0.8244 | 99.9 | 0.592 | Contact Map |
| 1uhvA | 4 | 0.9427 | 99.8 | 0.693 | Contact Map |
| 1w91A | 8 | 0.8996 | 99.7 | 0.7 | Contact Map |
| 4aw7A | 1 | 0.8638 | 99.7 | 0.706 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)