| ompa |
| ID: | 1446860962 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (112) | ||
| Sequences: | 12775 (8900.6) | ||
| Seq/Len: | 114.062 | ||
| Nf(neff/√len): | 841.0 |
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: 114.062).
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 |
| 48_V | 91_G | 3.428 | 1.00 |
| 18_N | 61_Y | 2.777 | 1.00 |
| 66_S | 90_R | 2.680 | 1.00 |
| 64_G | 68_K | 2.613 | 1.00 |
| 16_N | 23_K | 2.539 | 1.00 |
| 17_F | 54_D | 2.490 | 1.00 |
| 91_G | 95_S | 2.440 | 1.00 |
| 74_V | 88_S | 2.282 | 1.00 |
| 100_G | 105_N | 2.243 | 1.00 |
| 31_D | 80_K | 2.193 | 1.00 |
| 54_D | 106_V | 2.178 | 1.00 |
| 20_S | 68_K | 2.168 | 1.00 |
| 67_E | 71_Q | 2.152 | 1.00 |
| 98_V | 108_P | 2.103 | 1.00 |
| 98_V | 105_N | 2.055 | 1.00 |
| 63_Q | 67_E | 1.918 | 1.00 |
| 31_D | 76_Y | 1.905 | 1.00 |
| 30_L | 76_Y | 1.878 | 1.00 |
| 48_V | 115_C | 1.818 | 1.00 |
| 59_D | 93_G | 1.665 | 1.00 |
| 74_V | 78_I | 1.639 | 1.00 |
| 71_Q | 74_V | 1.630 | 1.00 |
| 59_D | 94_E | 1.587 | 1.00 |
| 63_Q | 94_E | 1.548 | 1.00 |
| 50_L | 95_S | 1.536 | 1.00 |
| 46_S | 87_I | 1.477 | 1.00 |
| 76_Y | 80_K | 1.442 | 1.00 |
| 47_V | 112_L | 1.436 | 1.00 |
| 53_T | 106_V | 1.408 | 1.00 |
| 55_R | 62_N | 1.376 | 0.99 |
| 29_A | 32_Q | 1.340 | 0.99 |
| 46_S | 89_A | 1.338 | 0.99 |
| 61_Y | 64_G | 1.320 | 0.99 |
| 52_F | 62_N | 1.316 | 0.99 |
| 99_T | 105_N | 1.304 | 0.99 |
| 22_L | 76_Y | 1.270 | 0.99 |
| 27_Q | 76_Y | 1.251 | 0.99 |
| 16_N | 19_K | 1.217 | 0.98 |
| 46_S | 117_A | 1.172 | 0.98 |
| 74_V | 86_K | 1.171 | 0.98 |
| 71_Q | 75_D | 1.162 | 0.97 |
| 75_D | 79_S | 1.155 | 0.97 |
| 48_V | 89_A | 1.148 | 0.97 |
| 102_T | 105_N | 1.144 | 0.97 |
| 101_N | 105_N | 1.084 | 0.96 |
| 71_Q | 88_S | 1.073 | 0.95 |
| 100_G | 106_V | 1.056 | 0.95 |
| 50_L | 113_I | 1.048 | 0.94 |
| 78_I | 86_K | 1.042 | 0.94 |
| 44_D | 87_I | 1.036 | 0.94 |
| 102_T | 106_V | 1.028 | 0.94 |
| 76_Y | 79_S | 1.026 | 0.94 |
| 17_F | 52_F | 1.018 | 0.93 |
| 67_E | 90_R | 1.013 | 0.93 |
| 24_P | 27_Q | 1.012 | 0.93 |
| 20_S | 72_S | 1.007 | 0.93 |
| 47_V | 74_V | 1.006 | 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 | |
| 2l26A | 1 | 0.9583 | 99.9 | 0.017 | Contact Map |
| 1r1mA | 1 | 0.9833 | 99.8 | 0.021 | Contact Map |
| 3ldtA | 1 | 0.9583 | 99.8 | 0.023 | Contact Map |
| 2hqsH | 4 | 0.8917 | 99.8 | 0.023 | Contact Map |
| 2k1sA | 1 | 0.9833 | 99.8 | 0.034 | Contact Map |
| 3td3A | 8 | 0.9833 | 99.8 | 0.036 | Contact Map |
| 2zf8A | 1 | 0.775 | 99.8 | 0.039 | Contact Map |
| 3s0yA | 2 | 0.9833 | 99.8 | 0.041 | Contact Map |
| 3nb3A | 3 | 0 | 99.8 | 0.045 | Contact Map |
| 2kgwA | 1 | 0.9583 | 99.8 | 0.048 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)