| T0847 |
| ID: | 1404840924 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (165) | ||
| Sequences: | 4747 (3251.2) | ||
| Seq/Len: | 28.770 | ||
| Nf(neff/√len): | 253.1 |
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: 28.770).
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 |
| 55_A | 59_R | 4.160 | 1.00 |
| 37_V | 64_C | 3.628 | 1.00 |
| 126_V | 156_F | 3.140 | 1.00 |
| 93_S | 169_P | 3.112 | 1.00 |
| 62_F | 93_S | 3.022 | 1.00 |
| 30_T | 54_E | 2.872 | 1.00 |
| 30_T | 51_D | 2.862 | 1.00 |
| 28_C | 127_L | 2.492 | 1.00 |
| 123_W | 157_D | 2.453 | 1.00 |
| 36_L | 121_S | 2.403 | 1.00 |
| 126_V | 153_V | 2.372 | 1.00 |
| 64_C | 93_S | 2.368 | 1.00 |
| 29_I | 51_D | 2.255 | 1.00 |
| 26_R | 51_D | 2.190 | 1.00 |
| 37_V | 62_F | 2.165 | 1.00 |
| 35_V | 123_W | 2.078 | 1.00 |
| 28_C | 147_K | 2.077 | 1.00 |
| 37_V | 157_D | 1.953 | 1.00 |
| 35_V | 157_D | 1.943 | 1.00 |
| 66_L | 167_S | 1.900 | 1.00 |
| 64_C | 164_Y | 1.877 | 1.00 |
| 56_A | 92_I | 1.873 | 1.00 |
| 28_C | 121_S | 1.857 | 1.00 |
| 51_D | 55_A | 1.853 | 1.00 |
| 120_I | 153_V | 1.806 | 1.00 |
| 29_I | 36_L | 1.805 | 1.00 |
| 39_L | 114_I | 1.723 | 1.00 |
| 157_D | 161_R | 1.679 | 1.00 |
| 127_L | 145_L | 1.658 | 1.00 |
| 53_L | 58_K | 1.616 | 1.00 |
| 53_L | 90_K | 1.563 | 1.00 |
| 32_T | 121_S | 1.555 | 1.00 |
| 67_L | 96_S | 1.546 | 1.00 |
| 39_L | 118_F | 1.520 | 1.00 |
| 53_L | 86_D | 1.517 | 1.00 |
| 54_E | 59_R | 1.472 | 1.00 |
| 25_V | 119_I | 1.439 | 1.00 |
| 28_C | 125_F | 1.439 | 1.00 |
| 160_F | 164_Y | 1.438 | 1.00 |
| 43_F | 65_V | 1.400 | 0.99 |
| 36_L | 52_I | 1.393 | 0.99 |
| 95_R | 164_Y | 1.346 | 0.99 |
| 137_C | 143_N | 1.337 | 0.99 |
| 37_V | 161_R | 1.316 | 0.99 |
| 85_S | 89_L | 1.301 | 0.99 |
| 34_Q | 124_R | 1.301 | 0.99 |
| 71_G | 77_E | 1.298 | 0.99 |
| 159_E | 163_L | 1.291 | 0.99 |
| 115_R | 132_S | 1.280 | 0.99 |
| 148_F | 152_A | 1.278 | 0.99 |
| 27_R | 31_R | 1.275 | 0.99 |
| 124_R | 149_T | 1.265 | 0.99 |
| 35_V | 62_F | 1.262 | 0.99 |
| 32_T | 36_L | 1.253 | 0.99 |
| 117_K | 132_S | 1.236 | 0.98 |
| 87_S | 92_I | 1.219 | 0.98 |
| 64_C | 161_R | 1.217 | 0.98 |
| 41_D | 68_D | 1.217 | 0.98 |
| 49_F | 53_L | 1.199 | 0.98 |
| 118_F | 156_F | 1.195 | 0.98 |
| 125_F | 147_K | 1.193 | 0.98 |
| 36_L | 55_A | 1.186 | 0.98 |
| 22_R | 45_D | 1.178 | 0.98 |
| 131_Y | 145_L | 1.176 | 0.98 |
| 37_V | 160_F | 1.153 | 0.97 |
| 127_L | 147_K | 1.143 | 0.97 |
| 134_T | 141_H | 1.141 | 0.97 |
| 95_R | 169_P | 1.137 | 0.97 |
| 51_D | 54_E | 1.112 | 0.96 |
| 25_V | 127_L | 1.103 | 0.96 |
| 69_Q | 96_S | 1.077 | 0.95 |
| 21_I | 131_Y | 1.069 | 0.95 |
| 136_L | 140_V | 1.061 | 0.95 |
| 24_L | 147_K | 1.051 | 0.94 |
| 155_L | 158_E | 1.034 | 0.94 |
| 66_L | 163_L | 1.029 | 0.94 |
| 29_I | 55_A | 1.020 | 0.93 |
| 134_T | 137_C | 1.008 | 0.93 |
| 24_L | 27_R | 1.005 | 0.93 |
| 96_S | 170_V | 1.005 | 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 | |
| 4gelA | 2 | 0.858 | 99.9 | 0.355 | Contact Map |
| 1byrA | 1 | 0.8523 | 99.9 | 0.363 | Contact Map |
| 3hsiA | 3 | 0.9261 | 99.9 | 0.371 | Contact Map |
| 4ggjA | 1 | 0.7955 | 99.9 | 0.399 | Contact Map |
| 1v0wA | 1 | 0.9432 | 99.9 | 0.409 | Contact Map |
| 2c1lA | 2 | 0.9091 | 99.9 | 0.411 | Contact Map |
| 1xdpA | 2 | 0.9034 | 99.9 | 0.415 | Contact Map |
| 2o8rA | 2 | 0.892 | 99.9 | 0.438 | Contact Map |
| 3qphA | 1 | 0.8068 | 98.2 | 0.767 | Contact Map |
| 2f5tX | 1 | 0.7159 | 97.6 | 0.793 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)