| consensus_DUF |
| ID: | 1424770053 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (143) | ||
| Sequences: | 607 (516.7) | ||
| Seq/Len: | 4.245 | ||
| Nf(neff/√len): | 43.2 |
Jackhmmer Results: (2015_01_07)
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: 4.245).
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 |
| 103_F | 108_G | 4.214 | 1.00 |
| 31_C | 69_C | 4.109 | 1.00 |
| 10_L | 97_V | 3.156 | 1.00 |
| 13_F | 110_I | 3.031 | 1.00 |
| 109_M | 128_A | 2.824 | 1.00 |
| 128_A | 135_I | 2.673 | 1.00 |
| 98_S | 103_F | 2.557 | 1.00 |
| 17_T | 135_I | 2.423 | 1.00 |
| 98_S | 108_G | 2.365 | 1.00 |
| 95_L | 133_L | 2.231 | 1.00 |
| 111_C | 122_E | 1.847 | 1.00 |
| 121_F | 142_L | 1.845 | 1.00 |
| 12_N | 15_K | 1.831 | 1.00 |
| 2_E | 6_K | 1.633 | 0.99 |
| 6_K | 99_D | 1.613 | 0.99 |
| 9_Y | 13_F | 1.576 | 0.99 |
| 104_C | 111_C | 1.568 | 0.99 |
| 17_T | 133_L | 1.560 | 0.98 |
| 71_V | 97_V | 1.556 | 0.98 |
| 31_C | 111_C | 1.500 | 0.98 |
| 122_E | 144_R | 1.489 | 0.98 |
| 109_M | 131_S | 1.487 | 0.98 |
| 138_K | 141_R | 1.452 | 0.97 |
| 19_W | 133_L | 1.420 | 0.97 |
| 20_P | 93_P | 1.392 | 0.96 |
| 121_F | 143_A | 1.382 | 0.96 |
| 39_A | 59_R | 1.368 | 0.96 |
| 14_A | 50_V | 1.353 | 0.95 |
| 71_V | 95_L | 1.352 | 0.95 |
| 29_R | 58_R | 1.338 | 0.95 |
| 89_L | 94_V | 1.321 | 0.94 |
| 17_T | 123_I | 1.281 | 0.93 |
| 27_P | 53_R | 1.275 | 0.93 |
| 34_G | 128_A | 1.269 | 0.93 |
| 28_L | 53_R | 1.261 | 0.93 |
| 10_L | 73_Y | 1.240 | 0.92 |
| 31_C | 60_L | 1.235 | 0.91 |
| 39_A | 43_S | 1.227 | 0.91 |
| 112_L | 142_L | 1.223 | 0.91 |
| 58_R | 68_G | 1.209 | 0.90 |
| 29_R | 70_H | 1.201 | 0.90 |
| 8_A | 121_F | 1.198 | 0.90 |
| 23_A | 70_H | 1.191 | 0.89 |
| 115_E | 144_R | 1.185 | 0.89 |
| 14_A | 71_V | 1.158 | 0.88 |
| 9_Y | 110_I | 1.151 | 0.87 |
| 17_T | 95_L | 1.151 | 0.87 |
| 36_D | 59_R | 1.136 | 0.86 |
| 14_A | 17_T | 1.135 | 0.86 |
| 123_I | 135_I | 1.131 | 0.86 |
| 17_T | 139_L | 1.122 | 0.85 |
| 60_L | 66_A | 1.096 | 0.83 |
| 110_I | 133_L | 1.093 | 0.83 |
| 16_F | 108_G | 1.061 | 0.81 |
| 80_A | 83_Q | 1.041 | 0.79 |
| 98_S | 111_C | 1.041 | 0.79 |
| 123_I | 140_L | 1.039 | 0.79 |
| 27_P | 56_R | 1.033 | 0.78 |
| 11_Y | 138_K | 1.023 | 0.77 |
| 82_L | 139_L | 1.017 | 0.76 |
| 126_D | 130_R | 1.009 | 0.76 |
| 7_A | 86_L | 1.009 | 0.76 |
| 38_F | 99_D | 1.001 | 0.75 |
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 | |
| 3uw3A | 2 | 0.7724 | 19.9 | 0.927 | Contact Map |
| 2yyyA | 2 | 0.9517 | 12.9 | 0.933 | Contact Map |
| 2r00A | 2 | 0.7655 | 11.6 | 0.935 | Contact Map |
| 2e44A | 1 | 0.4621 | 10.8 | 0.936 | Contact Map |
| 1t4bA | 2 | 0.8828 | 10.8 | 0.936 | Contact Map |
| 3pzrA | 2 | 0.7586 | 10.2 | 0.936 | Contact Map |
| 2kt5A | 1 | 0.5034 | 7 | 0.941 | Contact Map |
| 1jmtA | 1 | 0.4207 | 6.8 | 0.941 | Contact Map |
| 2ywkA | 1 | 0.4276 | 6.4 | 0.942 | Contact Map |
| 3nzzA | 2 | 0.4966 | 6.3 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)