| 1tlv |
| ID: | 1448614035 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (217) | ||
| Sequences: | 3017 (2499.5) | ||
| Seq/Len: | 13.903 | ||
| Nf(neff/√len): | 169.7 |
HHblits Results: (2015_06)
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: 13.903).
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 |
| 88_K | 94_S | 3.174 | 1.00 |
| 31_Q | 82_E | 3.107 | 1.00 |
| 198_E | 204_K | 2.816 | 1.00 |
| 176_L | 211_L | 2.783 | 1.00 |
| 180_K | 187_Y | 2.726 | 1.00 |
| 186_A | 218_E | 2.680 | 1.00 |
| 190_T | 214_T | 2.470 | 1.00 |
| 136_H | 192_K | 2.443 | 1.00 |
| 134_K | 140_E | 2.382 | 1.00 |
| 180_K | 207_S | 2.333 | 1.00 |
| 53_Q | 57_K | 2.189 | 1.00 |
| 23_E | 90_K | 2.028 | 1.00 |
| 81_K | 100_A | 2.018 | 1.00 |
| 161_R | 209_E | 1.971 | 1.00 |
| 186_A | 190_T | 1.946 | 1.00 |
| 47_H | 106_H | 1.936 | 1.00 |
| 141_F | 217_I | 1.871 | 1.00 |
| 154_H | 216_H | 1.833 | 1.00 |
| 4_E | 7_K | 1.803 | 1.00 |
| 194_Q | 210_L | 1.794 | 1.00 |
| 132_I | 196_Y | 1.716 | 1.00 |
| 29_K | 36_L | 1.688 | 1.00 |
| 137_F | 189_C | 1.626 | 1.00 |
| 128_E | 200_E | 1.626 | 1.00 |
| 133_V | 217_I | 1.602 | 1.00 |
| 81_K | 97_E | 1.587 | 1.00 |
| 190_T | 210_L | 1.580 | 1.00 |
| 191_K | 207_S | 1.574 | 1.00 |
| 28_A | 83_A | 1.510 | 1.00 |
| 133_V | 189_C | 1.507 | 1.00 |
| 27_Y | 86_M | 1.496 | 1.00 |
| 76_E | 104_A | 1.489 | 1.00 |
| 24_I | 83_A | 1.464 | 1.00 |
| 127_Q | 148_Y | 1.457 | 1.00 |
| 188_E | 191_K | 1.450 | 1.00 |
| 55_N | 96_P | 1.422 | 1.00 |
| 178_T | 182_K | 1.419 | 1.00 |
| 20_V | 90_K | 1.403 | 0.99 |
| 66_L | 101_G | 1.398 | 0.99 |
| 43_S | 47_H | 1.393 | 0.99 |
| 173_D | 211_L | 1.385 | 0.99 |
| 186_A | 217_I | 1.382 | 0.99 |
| 78_A | 81_K | 1.371 | 0.99 |
| 134_K | 144_E | 1.369 | 0.99 |
| 191_K | 210_L | 1.363 | 0.99 |
| 43_S | 106_H | 1.358 | 0.99 |
| 130_L | 148_Y | 1.342 | 0.99 |
| 158_F | 162_L | 1.328 | 0.99 |
| 194_Q | 213_L | 1.312 | 0.99 |
| 3_M | 7_K | 1.310 | 0.99 |
| 131_S | 135_Y | 1.301 | 0.99 |
| 22_E | 26_S | 1.292 | 0.99 |
| 48_I | 103_I | 1.285 | 0.99 |
| 148_Y | 152_V | 1.284 | 0.99 |
| 187_Y | 207_S | 1.264 | 0.99 |
| 155_L | 158_F | 1.250 | 0.99 |
| 190_T | 193_I | 1.246 | 0.98 |
| 129_I | 193_I | 1.235 | 0.98 |
| 133_V | 151_F | 1.235 | 0.98 |
| 128_E | 196_Y | 1.230 | 0.98 |
| 179_V | 214_T | 1.222 | 0.98 |
| 187_Y | 191_K | 1.220 | 0.98 |
| 190_T | 194_Q | 1.218 | 0.98 |
| 80_G | 100_A | 1.210 | 0.98 |
| 41_Y | 45_T | 1.209 | 0.98 |
| 20_V | 91_T | 1.208 | 0.98 |
| 158_F | 205_L | 1.205 | 0.98 |
| 165_G | 203_H | 1.197 | 0.98 |
| 84_L | 100_A | 1.193 | 0.98 |
| 96_P | 99_E | 1.192 | 0.98 |
| 84_L | 88_K | 1.178 | 0.98 |
| 32_L | 82_E | 1.168 | 0.97 |
| 24_I | 28_A | 1.167 | 0.97 |
| 176_L | 207_S | 1.166 | 0.97 |
| 200_E | 203_H | 1.163 | 0.97 |
| 172_D | 208_D | 1.153 | 0.97 |
| 133_V | 190_T | 1.147 | 0.97 |
| 77_F | 81_K | 1.147 | 0.97 |
| 87_V | 95_L | 1.144 | 0.97 |
| 17_C | 21_S | 1.143 | 0.97 |
| 55_N | 95_L | 1.130 | 0.97 |
| 80_G | 83_A | 1.126 | 0.97 |
| 124_K | 200_E | 1.109 | 0.96 |
| 151_F | 213_L | 1.106 | 0.96 |
| 77_F | 104_A | 1.103 | 0.96 |
| 186_A | 214_T | 1.102 | 0.96 |
| 158_F | 161_R | 1.100 | 0.96 |
| 54_R | 61_I | 1.089 | 0.96 |
| 27_Y | 31_Q | 1.083 | 0.96 |
| 4_E | 8_T | 1.081 | 0.95 |
| 20_V | 24_I | 1.081 | 0.95 |
| 75_D | 78_A | 1.074 | 0.95 |
| 77_F | 100_A | 1.069 | 0.95 |
| 27_Y | 82_E | 1.065 | 0.95 |
| 88_K | 95_L | 1.047 | 0.94 |
| 211_L | 214_T | 1.045 | 0.94 |
| 77_F | 101_G | 1.044 | 0.94 |
| 174_F | 208_D | 1.042 | 0.94 |
| 158_F | 206_T | 1.036 | 0.94 |
| 80_G | 104_A | 1.025 | 0.93 |
| 62_K | 98_D | 1.020 | 0.93 |
| 25_I | 45_T | 1.019 | 0.93 |
| 196_Y | 200_E | 1.018 | 0.93 |
| 39_S | 43_S | 1.018 | 0.93 |
| 189_C | 193_I | 1.018 | 0.93 |
| 88_K | 91_T | 1.005 | 0.93 |
| 187_Y | 214_T | 1.000 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1h99A | 1 | 0.991 | 100 | 0.119 | Contact Map |
| 4r6iA | 2 | 0.9774 | 100 | 0.266 | Contact Map |
| 3sqnA | 2 | 0.9276 | 99.8 | 0.438 | Contact Map |
| 3ufeA | 2 | 0.4796 | 99.6 | 0.55 | Contact Map |
| 3rioA | 1 | 0.7466 | 99.5 | 0.585 | Contact Map |
| 3nufA | 2 | 0.4932 | 92.3 | 0.851 | Contact Map |
| 2p0tA | 1 | 0.2489 | 21.4 | 0.918 | Contact Map |
| 2pyqA | 4 | 0.457 | 9.5 | 0.93 | Contact Map |
| 1w99A | 1 | 0.4299 | 4.6 | 0.94 | Contact Map |
| 3nw0A | 1 | 0.4842 | 4 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)