| GP25 |
| ID: | 1400157382 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 134 (121) | ||
| Sequences: | 351 (298.3) | ||
| Seq/Len: | 2.901 | ||
| Nf(neff/√len): | 27.1 |
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: 2.901).
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 |
| 41_I | 55_F | 3.753 | 1.00 |
| 28_S | 36_N | 3.667 | 1.00 |
| 34_I | 114_V | 2.702 | 1.00 |
| 38_L | 83_V | 2.564 | 1.00 |
| 83_V | 90_I | 2.063 | 1.00 |
| 33_S | 40_G | 1.893 | 0.99 |
| 38_L | 41_I | 1.866 | 0.99 |
| 58_D | 97_V | 1.773 | 0.99 |
| 45_R | 48_S | 1.697 | 0.98 |
| 76_E | 80_E | 1.614 | 0.97 |
| 34_I | 90_I | 1.579 | 0.97 |
| 91_D | 113_S | 1.520 | 0.96 |
| 13_I | 16_E | 1.506 | 0.96 |
| 20_D | 55_F | 1.501 | 0.95 |
| 41_I | 82_A | 1.470 | 0.95 |
| 93_L | 113_S | 1.467 | 0.95 |
| 37_S | 89_R | 1.466 | 0.95 |
| 83_V | 92_K | 1.446 | 0.94 |
| 36_N | 55_F | 1.421 | 0.93 |
| 90_I | 112_F | 1.389 | 0.92 |
| 37_S | 87_E | 1.367 | 0.91 |
| 57_C | 82_A | 1.331 | 0.90 |
| 61_D | 110_I | 1.324 | 0.90 |
| 30_G | 34_I | 1.316 | 0.89 |
| 95_V | 115_I | 1.288 | 0.88 |
| 52_D | 86_Y | 1.284 | 0.88 |
| 55_F | 110_I | 1.277 | 0.87 |
| 121_I | 124_I | 1.274 | 0.87 |
| 42_I | 83_V | 1.225 | 0.84 |
| 46_K | 58_D | 1.215 | 0.83 |
| 92_K | 95_V | 1.197 | 0.82 |
| 45_R | 114_V | 1.159 | 0.79 |
| 15_P | 33_S | 1.139 | 0.78 |
| 72_A | 97_V | 1.138 | 0.78 |
| 42_I | 49_R | 1.125 | 0.76 |
| 31_L | 114_V | 1.121 | 0.76 |
| 15_P | 40_G | 1.116 | 0.76 |
| 39_L | 43_T | 1.115 | 0.76 |
| 59_L | 117_N | 1.114 | 0.75 |
| 62_Q | 65_E | 1.111 | 0.75 |
| 37_S | 88_P | 1.091 | 0.73 |
| 11_S | 14_D | 1.090 | 0.73 |
| 17_M | 28_S | 1.088 | 0.73 |
| 23_K | 86_Y | 1.085 | 0.73 |
| 97_V | 111_R | 1.083 | 0.72 |
| 32_R | 35_K | 1.075 | 0.72 |
| 62_Q | 66_N | 1.064 | 0.71 |
| 62_Q | 78_N | 1.062 | 0.70 |
| 52_D | 66_N | 1.033 | 0.67 |
| 53_P | 90_I | 1.033 | 0.67 |
| 18_K | 86_Y | 1.029 | 0.67 |
| 98_I | 109_E | 1.026 | 0.67 |
| 41_I | 83_V | 1.025 | 0.66 |
| 48_S | 64_F | 1.012 | 0.65 |
| 91_D | 107_I | 1.005 | 0.64 |
| 53_P | 82_A | 1.005 | 0.64 |
| 22_N | 59_L | 1.003 | 0.64 |
| 82_A | 86_Y | 1.000 | 0.64 |
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 | |
| 4hrzA | 2 | 0.9328 | 100 | 0.273 | Contact Map |
| 2ia7A | 1 | 0.806 | 99.9 | 0.38 | Contact Map |
| 3j2mU | 6 | 0.8806 | 19.7 | 0.926 | Contact Map |
| 2cvbA | 1 | 0.5299 | 15.9 | 0.929 | Contact Map |
| 4l7iA | 2 | 0.9478 | 10.9 | 0.934 | Contact Map |
| 3u5rE | 4 | 0.5149 | 10.6 | 0.935 | Contact Map |
| 2ywiA | 2 | 0.4776 | 10 | 0.935 | Contact Map |
| 4l4qA | 4 | 0.9478 | 9.5 | 0.936 | Contact Map |
| 1r6bX | 1 | 0.9776 | 9.2 | 0.936 | Contact Map |
| 4m4dA | 2 | 0.9179 | 6.3 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)