| VTE5_NOsignalpeptide |
| ID: | 1488290142 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 245 (233) | ||
| Sequences: | 1164 (827.4) | ||
| Seq/Len: | 4.996 | ||
| Nf(neff/√len): | 54.2 |
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: 4.996).
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 |
| 175_F | 214_T | 3.406 | 1.00 |
| 171_S | 214_T | 3.011 | 1.00 |
| 216_V | 234_A | 2.537 | 1.00 |
| 171_S | 175_F | 2.528 | 1.00 |
| 156_G | 169_A | 2.467 | 1.00 |
| 143_G | 177_F | 2.378 | 1.00 |
| 158_T | 169_A | 2.244 | 1.00 |
| 147_I | 177_F | 2.077 | 1.00 |
| 141_M | 231_V | 2.061 | 1.00 |
| 52_G | 142_C | 1.998 | 1.00 |
| 228_N | 232_P | 1.988 | 1.00 |
| 49_I | 146_G | 1.903 | 1.00 |
| 157_S | 169_A | 1.878 | 1.00 |
| 52_G | 116_Y | 1.873 | 1.00 |
| 151_M | 155_F | 1.866 | 1.00 |
| 151_M | 173_S | 1.834 | 1.00 |
| 133_I | 137_S | 1.829 | 1.00 |
| 213_A | 235_T | 1.802 | 1.00 |
| 174_M | 178_G | 1.662 | 0.99 |
| 144_G | 174_M | 1.656 | 0.99 |
| 79_N | 82_R | 1.609 | 0.99 |
| 175_F | 211_M | 1.583 | 0.99 |
| 119_A | 123_S | 1.576 | 0.99 |
| 147_I | 173_S | 1.535 | 0.99 |
| 45_K | 48_H | 1.506 | 0.99 |
| 227_D | 232_P | 1.493 | 0.98 |
| 170_G | 217_E | 1.453 | 0.98 |
| 212_V | 234_A | 1.421 | 0.98 |
| 101_T | 113_P | 1.377 | 0.97 |
| 41_S | 102_R | 1.362 | 0.97 |
| 177_F | 181_I | 1.356 | 0.97 |
| 73_A | 173_S | 1.356 | 0.97 |
| 113_P | 116_Y | 1.345 | 0.96 |
| 23_Y | 31_S | 1.335 | 0.96 |
| 112_G | 141_M | 1.323 | 0.96 |
| 234_A | 238_A | 1.322 | 0.96 |
| 23_Y | 27_L | 1.322 | 0.96 |
| 151_M | 169_A | 1.321 | 0.96 |
| 53_L | 143_G | 1.316 | 0.96 |
| 140_M | 178_G | 1.305 | 0.96 |
| 160_I | 218_S | 1.299 | 0.95 |
| 44_R | 48_H | 1.296 | 0.95 |
| 148_A | 152_G | 1.288 | 0.95 |
| 45_K | 148_A | 1.270 | 0.95 |
| 19_L | 24_A | 1.262 | 0.94 |
| 174_M | 210_S | 1.252 | 0.94 |
| 118_L | 122_F | 1.242 | 0.94 |
| 123_S | 137_S | 1.242 | 0.94 |
| 127_F | 236_I | 1.237 | 0.94 |
| 149_D | 174_M | 1.234 | 0.93 |
| 47_V | 112_G | 1.232 | 0.93 |
| 13_G | 17_A | 1.226 | 0.93 |
| 41_S | 112_G | 1.220 | 0.93 |
| 140_M | 181_I | 1.220 | 0.93 |
| 167_S | 171_S | 1.190 | 0.92 |
| 217_E | 227_D | 1.189 | 0.92 |
| 116_Y | 141_M | 1.184 | 0.92 |
| 140_M | 235_T | 1.176 | 0.91 |
| 24_A | 32_L | 1.168 | 0.91 |
| 148_A | 167_S | 1.162 | 0.91 |
| 16_V | 23_Y | 1.160 | 0.90 |
| 144_G | 178_G | 1.158 | 0.90 |
| 158_T | 172_I | 1.151 | 0.90 |
| 151_M | 154_K | 1.142 | 0.89 |
| 15_T | 19_L | 1.139 | 0.89 |
| 56_V | 167_S | 1.138 | 0.89 |
| 136_I | 182_S | 1.136 | 0.89 |
| 115_F | 229_I | 1.131 | 0.89 |
| 148_A | 170_G | 1.129 | 0.89 |
| 15_T | 18_V | 1.121 | 0.88 |
| 28_S | 31_S | 1.117 | 0.88 |
| 39_Q | 42_L | 1.113 | 0.88 |
| 179_F | 207_A | 1.112 | 0.88 |
| 25_L | 29_F | 1.103 | 0.87 |
| 141_M | 228_N | 1.097 | 0.87 |
| 95_M | 207_A | 1.090 | 0.86 |
| 41_S | 153_R | 1.090 | 0.86 |
| 174_M | 214_T | 1.090 | 0.86 |
| 116_Y | 146_G | 1.080 | 0.86 |
| 131_S | 231_V | 1.080 | 0.86 |
| 102_R | 112_G | 1.079 | 0.86 |
| 47_V | 141_M | 1.073 | 0.85 |
| 13_G | 19_L | 1.072 | 0.85 |
| 13_G | 16_V | 1.070 | 0.85 |
| 127_F | 142_C | 1.062 | 0.84 |
| 11_D | 15_T | 1.057 | 0.84 |
| 105_R | 111_K | 1.057 | 0.84 |
| 119_A | 141_M | 1.056 | 0.84 |
| 143_G | 147_I | 1.054 | 0.84 |
| 17_A | 27_L | 1.053 | 0.84 |
| 208_M | 212_V | 1.049 | 0.83 |
| 26_V | 29_F | 1.047 | 0.83 |
| 52_G | 235_T | 1.046 | 0.83 |
| 151_M | 242_S | 1.043 | 0.83 |
| 45_K | 146_G | 1.042 | 0.83 |
| 70_Y | 215_V | 1.038 | 0.82 |
| 112_G | 116_Y | 1.031 | 0.82 |
| 12_V | 17_A | 1.028 | 0.82 |
| 93_N | 100_V | 1.022 | 0.81 |
| 182_S | 206_V | 1.022 | 0.81 |
| 116_Y | 142_C | 1.018 | 0.81 |
| 18_V | 21_G | 1.015 | 0.80 |
| 25_L | 31_S | 1.015 | 0.80 |
| 168_W | 172_I | 1.011 | 0.80 |
| 16_V | 20_G | 1.005 | 0.80 |
| 206_V | 212_V | 1.004 | 0.79 |
| 19_L | 23_Y | 1.003 | 0.79 |
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 | |
| 4q2eA | 2 | 0.9388 | 97.9 | 0.834 | Contact Map |
| 4lz6A | 1 | 0.6571 | 3.6 | 0.959 | Contact Map |
| 2mofA | 1 | 0.0939 | 3.1 | 0.96 | Contact Map |
| 3w5aC | 1 | 0.1143 | 2.9 | 0.961 | Contact Map |
| 4xtlA | 1 | 0.3633 | 2.9 | 0.961 | Contact Map |
| 3ddlA | 2 | 0.4204 | 2.2 | 0.963 | Contact Map |
| 3wajA | 1 | 0.7429 | 2.2 | 0.963 | Contact Map |
| 4fbzA | 1 | 0.4245 | 2.1 | 0.964 | Contact Map |
| 4tq3A | 4 | 0.2694 | 2.1 | 0.964 | Contact Map |
| 4n7wA | 2 | 0.6327 | 2 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)