| Ulp1 Cterm |
| ID: | 1491701865 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 219 (214) | ||
| Sequences: | 1539 (1118.8) | ||
| Seq/Len: | 7.192 | ||
| Nf(neff/√len): | 76.5 |
HHblits Results: (2016_02)
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: 7.192).
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 |
| 174_N | 177_D | 5.127 | 1.00 |
| 95_Q | 98_K | 2.878 | 1.00 |
| 116_G | 146_L | 2.762 | 1.00 |
| 56_M | 186_T | 2.662 | 1.00 |
| 169_C | 185_N | 2.597 | 1.00 |
| 114_A | 127_Y | 2.155 | 1.00 |
| 55_F | 183_C | 2.044 | 1.00 |
| 115_L | 182_V | 2.022 | 1.00 |
| 117_I | 189_G | 1.978 | 1.00 |
| 119_D | 126_G | 1.956 | 1.00 |
| 95_Q | 158_I | 1.913 | 1.00 |
| 187_L | 191_A | 1.813 | 1.00 |
| 37_D | 48_N | 1.718 | 1.00 |
| 102_I | 118_I | 1.713 | 1.00 |
| 41_L | 51_I | 1.701 | 1.00 |
| 65_N | 100_D | 1.666 | 1.00 |
| 73_F | 77_L | 1.626 | 1.00 |
| 184_M | 188_Y | 1.597 | 1.00 |
| 119_D | 122_K | 1.589 | 1.00 |
| 50_T | 53_E | 1.585 | 1.00 |
| 67_V | 99_L | 1.580 | 1.00 |
| 184_M | 205_M | 1.567 | 1.00 |
| 184_M | 187_L | 1.535 | 0.99 |
| 104_T | 146_L | 1.530 | 0.99 |
| 103_F | 115_L | 1.485 | 0.99 |
| 47_L | 180_I | 1.481 | 0.99 |
| 211_H | 215_T | 1.478 | 0.99 |
| 76_N | 80_R | 1.474 | 0.99 |
| 55_F | 59_I | 1.467 | 0.99 |
| 74_Y | 145_D | 1.449 | 0.99 |
| 10_D | 14_Q | 1.432 | 0.99 |
| 12_Q | 15_K | 1.432 | 0.99 |
| 174_N | 178_C | 1.397 | 0.99 |
| 31_I | 40_T | 1.380 | 0.99 |
| 53_E | 71_S | 1.377 | 0.99 |
| 100_D | 121_K | 1.368 | 0.99 |
| 154_S | 158_I | 1.365 | 0.99 |
| 6_N | 12_Q | 1.364 | 0.99 |
| 5_L | 13_V | 1.354 | 0.98 |
| 11_D | 18_A | 1.350 | 0.98 |
| 58_Y | 212_L | 1.339 | 0.98 |
| 7_E | 11_D | 1.300 | 0.98 |
| 23_T | 26_M | 1.278 | 0.97 |
| 107_N | 110_Q | 1.260 | 0.97 |
| 82_Y | 85_V | 1.254 | 0.97 |
| 101_K | 117_I | 1.229 | 0.97 |
| 9_D | 12_Q | 1.222 | 0.96 |
| 40_T | 51_I | 1.222 | 0.96 |
| 54_F | 213_I | 1.221 | 0.96 |
| 183_C | 209_I | 1.210 | 0.96 |
| 11_D | 14_Q | 1.197 | 0.96 |
| 14_Q | 20_R | 1.190 | 0.96 |
| 8_K | 18_A | 1.187 | 0.96 |
| 18_A | 21_E | 1.183 | 0.96 |
| 11_D | 15_K | 1.180 | 0.95 |
| 60_E | 68_A | 1.178 | 0.95 |
| 10_D | 18_A | 1.173 | 0.95 |
| 101_K | 119_D | 1.173 | 0.95 |
| 44_R | 176_Y | 1.169 | 0.95 |
| 52_I | 182_V | 1.166 | 0.95 |
| 7_E | 15_K | 1.163 | 0.95 |
| 132_S | 171_Q | 1.162 | 0.95 |
| 7_E | 14_Q | 1.157 | 0.95 |
| 46_W | 49_D | 1.154 | 0.95 |
| 8_K | 14_Q | 1.152 | 0.95 |
| 13_V | 16_A | 1.151 | 0.95 |
| 149_Y | 153_E | 1.150 | 0.95 |
| 12_Q | 18_A | 1.150 | 0.95 |
| 55_F | 58_Y | 1.148 | 0.95 |
| 4_E | 12_Q | 1.141 | 0.94 |
| 6_N | 9_D | 1.140 | 0.94 |
| 15_K | 18_A | 1.139 | 0.94 |
| 115_L | 186_T | 1.130 | 0.94 |
| 14_Q | 22_N | 1.108 | 0.93 |
| 10_D | 207_R | 1.097 | 0.93 |
| 148_K | 152_E | 1.094 | 0.92 |
| 74_Y | 78_S | 1.086 | 0.92 |
| 136_N | 164_L | 1.086 | 0.92 |
| 11_D | 22_N | 1.086 | 0.92 |
| 59_I | 68_A | 1.082 | 0.92 |
| 11_D | 16_A | 1.066 | 0.91 |
| 172_Q | 179_G | 1.066 | 0.91 |
| 20_R | 24_Q | 1.066 | 0.91 |
| 7_E | 12_Q | 1.061 | 0.91 |
| 46_W | 176_Y | 1.060 | 0.91 |
| 55_F | 209_I | 1.054 | 0.90 |
| 22_N | 25_L | 1.054 | 0.90 |
| 37_D | 40_T | 1.051 | 0.90 |
| 13_V | 19_S | 1.050 | 0.90 |
| 118_I | 125_I | 1.049 | 0.90 |
| 89_M | 157_T | 1.048 | 0.90 |
| 8_K | 11_D | 1.046 | 0.90 |
| 208_F | 212_L | 1.040 | 0.90 |
| 23_T | 35_V | 1.035 | 0.89 |
| 202_A | 205_M | 1.032 | 0.89 |
| 181_Y | 185_N | 1.031 | 0.89 |
| 188_Y | 196_D | 1.030 | 0.89 |
| 173_P | 199_Y | 1.022 | 0.89 |
| 76_N | 88_W | 1.019 | 0.88 |
| 187_L | 205_M | 1.019 | 0.88 |
| 66_T | 103_F | 1.017 | 0.88 |
| 76_N | 84_G | 1.013 | 0.88 |
| 4_E | 7_E | 1.008 | 0.88 |
| 13_V | 17_L | 1.007 | 0.88 |
| 53_E | 72_F | 1.005 | 0.87 |
| 112_H | 178_C | 1.002 | 0.87 |
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 | |
| 1euvA | 1 | 1 | 100 | 0.07 | Contact Map |
| 2xphA | 2 | 0.968 | 100 | 0.138 | Contact Map |
| 3zo5A | 1 | 0.9589 | 100 | 0.152 | Contact Map |
| 3eayA | 1 | 0.8858 | 100 | 0.233 | Contact Map |
| 2bkrA | 1 | 0.8721 | 100 | 0.285 | Contact Map |
| 2oixA | 1 | 0.7397 | 100 | 0.351 | Contact Map |
| 4ekfA | 1 | 0.6484 | 94.6 | 0.883 | Contact Map |
| 4q2jA | 4 | 0.4201 | 10 | 0.949 | Contact Map |
| 3zuaA | 1 | 0.2237 | 8.1 | 0.951 | Contact Map |
| 2h2mA | 1 | 0.2968 | 7.1 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)