| ccka hhb -4 - 8 25- 50 -75 320-540 |
| ID: | 1433238981 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 221 (205) | ||
| Sequences: | 70729 (54093.8) | ||
| Seq/Len: | 345.020 | ||
| Nf(neff/√len): | 3778.1 |
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: 345.020).
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 |
| 159_S | 216_A | 2.998 | 1.00 |
| 64_L | 100_A | 2.751 | 1.00 |
| 206_H | 218_R | 2.721 | 1.00 |
| 157_E | 216_A | 2.659 | 1.00 |
| 153_T | 220_F | 2.605 | 1.00 |
| 157_E | 218_R | 2.525 | 1.00 |
| 195_Y | 199_K | 2.436 | 1.00 |
| 155_F | 218_R | 2.239 | 1.00 |
| 132_R | 157_E | 2.227 | 1.00 |
| 88_I | 130_R | 2.208 | 1.00 |
| 16_L | 36_I | 2.131 | 1.00 |
| 155_F | 220_F | 2.037 | 1.00 |
| 63_V | 99_R | 2.020 | 1.00 |
| 128_V | 161_D | 1.979 | 1.00 |
| 166_P | 169_V | 1.963 | 1.00 |
| 13_Q | 40_G | 1.915 | 1.00 |
| 100_A | 201_S | 1.907 | 1.00 |
| 210_R | 213_E | 1.890 | 1.00 |
| 13_Q | 41_V | 1.888 | 1.00 |
| 170_M | 209_S | 1.884 | 1.00 |
| 194_V | 205_I | 1.869 | 1.00 |
| 90_D | 132_R | 1.867 | 1.00 |
| 160_D | 164_G | 1.867 | 1.00 |
| 208_H | 218_R | 1.858 | 1.00 |
| 130_R | 159_S | 1.851 | 1.00 |
| 88_I | 128_V | 1.801 | 1.00 |
| 172_K | 178_F | 1.752 | 1.00 |
| 169_V | 172_K | 1.747 | 1.00 |
| 120_V | 161_D | 1.744 | 1.00 |
| 208_H | 216_A | 1.731 | 1.00 |
| 65_D | 68_E | 1.720 | 1.00 |
| 134_A | 155_F | 1.719 | 1.00 |
| 207_V | 217_F | 1.694 | 1.00 |
| 167_P | 170_M | 1.674 | 1.00 |
| 174_F | 205_I | 1.647 | 1.00 |
| 170_M | 207_V | 1.645 | 1.00 |
| 44_A | 48_R | 1.632 | 1.00 |
| 63_V | 97_Q | 1.622 | 1.00 |
| 120_V | 124_K | 1.621 | 1.00 |
| 132_R | 159_S | 1.608 | 1.00 |
| 20_L | 37_R | 1.606 | 1.00 |
| 108_A | 198_V | 1.585 | 1.00 |
| 72_E | 106_E | 1.584 | 1.00 |
| 204_W | 220_F | 1.558 | 1.00 |
| 198_V | 203_G | 1.549 | 1.00 |
| 86_K | 128_V | 1.545 | 1.00 |
| 169_V | 178_F | 1.543 | 1.00 |
| 172_K | 175_D | 1.542 | 1.00 |
| 165_I | 173_I | 1.540 | 1.00 |
| 13_Q | 44_A | 1.529 | 1.00 |
| 134_A | 157_E | 1.526 | 1.00 |
| 77_L | 110_M | 1.515 | 1.00 |
| 114_V | 118_D | 1.507 | 1.00 |
| 108_A | 194_V | 1.442 | 1.00 |
| 104_Q | 200_Q | 1.436 | 1.00 |
| 165_I | 215_A | 1.426 | 1.00 |
| 12_I | 40_G | 1.424 | 1.00 |
| 62_E | 102_K | 1.402 | 0.99 |
| 90_D | 130_R | 1.400 | 0.99 |
| 206_H | 220_F | 1.394 | 0.99 |
| 37_R | 41_V | 1.352 | 0.99 |
| 166_P | 211_P | 1.351 | 0.99 |
| 109_V | 156_I | 1.337 | 0.99 |
| 108_A | 197_I | 1.330 | 0.99 |
| 127_G | 161_D | 1.329 | 0.99 |
| 209_S | 215_A | 1.325 | 0.99 |
| 198_V | 219_I | 1.307 | 0.99 |
| 175_D | 178_F | 1.262 | 0.99 |
| 165_I | 169_V | 1.259 | 0.99 |
| 61_R | 99_R | 1.253 | 0.99 |
| 20_L | 34_N | 1.241 | 0.98 |
| 17_D | 37_R | 1.240 | 0.98 |
| 13_Q | 37_R | 1.239 | 0.98 |
| 101_D | 104_Q | 1.230 | 0.98 |
| 6_N | 48_R | 1.229 | 0.98 |
| 100_A | 105_L | 1.226 | 0.98 |
| 4_D | 107_T | 1.192 | 0.98 |
| 197_I | 201_S | 1.184 | 0.98 |
| 67_G | 71_S | 1.182 | 0.98 |
| 16_L | 37_R | 1.175 | 0.98 |
| 11_A | 15_R | 1.168 | 0.97 |
| 15_R | 32_G | 1.167 | 0.97 |
| 150_D | 155_F | 1.164 | 0.97 |
| 112_L | 194_V | 1.161 | 0.97 |
| 169_V | 180_T | 1.154 | 0.97 |
| 174_F | 207_V | 1.140 | 0.97 |
| 26_G | 29_S | 1.122 | 0.97 |
| 15_R | 35_E | 1.121 | 0.97 |
| 11_A | 39_T | 1.120 | 0.96 |
| 39_T | 42_R | 1.116 | 0.96 |
| 111_N | 194_V | 1.109 | 0.96 |
| 102_K | 106_E | 1.108 | 0.96 |
| 112_L | 217_F | 1.102 | 0.96 |
| 130_R | 161_D | 1.099 | 0.96 |
| 76_L | 106_E | 1.089 | 0.96 |
| 111_N | 114_V | 1.076 | 0.95 |
| 45_D | 103_S | 1.074 | 0.95 |
| 116_A | 129_V | 1.063 | 0.95 |
| 199_K | 204_W | 1.061 | 0.95 |
| 198_V | 205_I | 1.059 | 0.95 |
| 71_S | 89_T | 1.049 | 0.94 |
| 104_Q | 107_T | 1.046 | 0.94 |
| 156_I | 219_I | 1.043 | 0.94 |
| 65_D | 97_Q | 1.038 | 0.94 |
| 106_E | 110_M | 1.033 | 0.94 |
| 196_G | 200_Q | 1.027 | 0.94 |
| 74_E | 78_R | 1.015 | 0.93 |
| 209_S | 213_E | 1.014 | 0.93 |
| 209_S | 212_N | 1.010 | 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 | |
| 3a0rA | 1 | 0.8778 | 100 | -0.084 | Contact Map |
| 4i5sA | 2 | 0.8914 | 100 | 0.098 | Contact Map |
| 3jz3A | 2 | 0.6968 | 100 | 0.12 | Contact Map |
| 4gczA | 2 | 0.9276 | 100 | 0.123 | Contact Map |
| 4mpcA | 1 | 0.8643 | 100 | 0.127 | Contact Map |
| 4q20A | 2 | 0.905 | 100 | 0.128 | Contact Map |
| 3d36A | 2 | 0.9095 | 100 | 0.13 | Contact Map |
| 2e0aA | 2 | 0.9231 | 100 | 0.142 | Contact Map |
| 4e01A | 1 | 0.9005 | 100 | 0.145 | Contact Map |
| 1y8oA | 1 | 0.8914 | 100 | 0.167 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)