| IBPA_coli |
| ID: | 1402325315 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 137 (132) | ||
| Sequences: | 5914 (4554.5) | ||
| Seq/Len: | 44.803 | ||
| Nf(neff/√len): | 396.4 |
Jackhmmer Results: (2014_04_16)
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: 44.803).
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 |
| 46_H | 120_D | 3.121 | 1.00 |
| 62_E | 133_R | 2.968 | 1.00 |
| 51_I | 72_V | 2.940 | 1.00 |
| 41_L | 123_R | 2.800 | 1.00 |
| 37_Y | 51_I | 2.470 | 1.00 |
| 37_Y | 99_F | 2.378 | 1.00 |
| 75_A | 94_N | 2.353 | 1.00 |
| 57_A | 114_N | 2.279 | 1.00 |
| 74_G | 95_F | 2.272 | 1.00 |
| 109_G | 137_N | 2.251 | 1.00 |
| 42_V | 46_H | 2.199 | 1.00 |
| 73_K | 96_E | 2.170 | 1.00 |
| 57_A | 60_E | 2.152 | 1.00 |
| 48_R | 118_Y | 2.009 | 1.00 |
| 53_V | 112_L | 2.007 | 1.00 |
| 89_G | 97_R | 1.999 | 1.00 |
| 52_A | 90_I | 1.995 | 1.00 |
| 52_A | 116_L | 1.968 | 1.00 |
| 61_L | 112_L | 1.929 | 1.00 |
| 50_A | 118_Y | 1.925 | 1.00 |
| 38_N | 90_I | 1.896 | 1.00 |
| 85_Y | 88_Q | 1.818 | 1.00 |
| 53_V | 61_L | 1.779 | 1.00 |
| 65_A | 101_L | 1.739 | 1.00 |
| 69_L | 98_K | 1.688 | 1.00 |
| 62_E | 73_K | 1.675 | 1.00 |
| 106_H | 124_V | 1.617 | 1.00 |
| 41_L | 44_E | 1.584 | 1.00 |
| 73_K | 94_N | 1.553 | 1.00 |
| 42_V | 45_N | 1.530 | 1.00 |
| 40_E | 48_R | 1.523 | 1.00 |
| 105_I | 121_L | 1.521 | 1.00 |
| 71_V | 98_K | 1.496 | 1.00 |
| 43_D | 46_H | 1.428 | 1.00 |
| 69_L | 100_Q | 1.393 | 0.99 |
| 35_P | 95_F | 1.388 | 0.99 |
| 40_E | 50_A | 1.345 | 0.99 |
| 39_V | 49_I | 1.340 | 0.99 |
| 38_N | 50_A | 1.304 | 0.99 |
| 64_T | 133_R | 1.275 | 0.99 |
| 18_R | 21_N | 1.270 | 0.99 |
| 63_I | 110_A | 1.225 | 0.98 |
| 56_F | 74_G | 1.209 | 0.98 |
| 58_E | 114_N | 1.197 | 0.98 |
| 38_N | 88_Q | 1.181 | 0.98 |
| 60_E | 77_A | 1.146 | 0.97 |
| 64_T | 71_V | 1.127 | 0.97 |
| 15_G | 18_R | 1.126 | 0.97 |
| 42_V | 48_R | 1.126 | 0.97 |
| 102_A | 105_I | 1.116 | 0.96 |
| 48_R | 120_D | 1.114 | 0.96 |
| 60_E | 76_H | 1.103 | 0.96 |
| 38_N | 52_A | 1.089 | 0.96 |
| 57_A | 113_V | 1.061 | 0.95 |
| 39_V | 47_Y | 1.041 | 0.94 |
| 13_A | 17_D | 1.041 | 0.94 |
| 33_G | 74_G | 1.033 | 0.94 |
| 90_I | 116_L | 1.013 | 0.93 |
| 53_V | 74_G | 1.003 | 0.93 |
| 108_R | 132_R | 1.002 | 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
- 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 | |
| 3w1zA | 4 | 0.9635 | 99.9 | 0.204 | Contact Map |
| 4eldA | 2 | 0.7883 | 99.9 | 0.213 | Contact Map |
| 1gmeA | 4 | 0.9854 | 99.9 | 0.256 | Contact Map |
| 3aabA | 2 | 0.8102 | 99.9 | 0.281 | Contact Map |
| 2bolA | 2 | 0.927 | 99.9 | 0.32 | Contact Map |
| 3glaA | 2 | 0.7007 | 99.8 | 0.358 | Contact Map |
| 4feiA | 1 | 0.7299 | 99.8 | 0.367 | Contact Map |
| 3l1eA | 1 | 0.7153 | 99.8 | 0.372 | Contact Map |
| 2klrA | 2 | 0.5766 | 99.8 | 0.374 | Contact Map |
| 2wj5A | 1 | 0.6788 | 99.8 | 0.387 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)