| IBPB_coli |
| ID: | 1402325373 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (132) | ||
| Sequences: | 5603 (4251.9) | ||
| Seq/Len: | 42.447 | ||
| Nf(neff/√len): | 370.1 |
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: 42.447).
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 |
| 44_H | 118_D | 2.983 | 1.00 |
| 60_E | 131_R | 2.968 | 1.00 |
| 107_G | 135_S | 2.899 | 1.00 |
| 49_L | 70_V | 2.839 | 1.00 |
| 39_K | 121_R | 2.666 | 1.00 |
| 35_Y | 49_L | 2.527 | 1.00 |
| 73_T | 92_P | 2.427 | 1.00 |
| 35_Y | 97_F | 2.377 | 1.00 |
| 55_R | 112_N | 2.360 | 1.00 |
| 87_G | 95_L | 2.159 | 1.00 |
| 71_K | 94_S | 2.156 | 1.00 |
| 55_R | 58_D | 2.107 | 1.00 |
| 72_G | 93_F | 2.083 | 1.00 |
| 48_T | 116_H | 2.044 | 1.00 |
| 46_R | 116_H | 2.014 | 1.00 |
| 41_D | 44_H | 2.000 | 1.00 |
| 50_A | 88_L | 1.983 | 1.00 |
| 59_L | 110_F | 1.933 | 1.00 |
| 36_N | 88_L | 1.884 | 1.00 |
| 50_A | 114_L | 1.866 | 1.00 |
| 51_L | 110_F | 1.833 | 1.00 |
| 51_L | 59_L | 1.810 | 1.00 |
| 83_W | 86_Q | 1.766 | 1.00 |
| 104_E | 122_N | 1.764 | 1.00 |
| 71_K | 92_P | 1.697 | 1.00 |
| 39_K | 42_D | 1.681 | 1.00 |
| 67_R | 96_S | 1.657 | 1.00 |
| 60_E | 71_K | 1.649 | 1.00 |
| 63_L | 99_L | 1.632 | 1.00 |
| 41_D | 46_R | 1.631 | 1.00 |
| 38_E | 46_R | 1.600 | 1.00 |
| 67_R | 98_T | 1.511 | 1.00 |
| 103_M | 119_L | 1.510 | 1.00 |
| 109_T | 135_S | 1.500 | 1.00 |
| 69_S | 96_S | 1.427 | 1.00 |
| 33_P | 93_F | 1.379 | 0.99 |
| 40_S | 44_H | 1.376 | 0.99 |
| 38_E | 48_T | 1.329 | 0.99 |
| 62_Q | 131_R | 1.307 | 0.99 |
| 36_N | 48_T | 1.288 | 0.99 |
| 58_D | 74_P | 1.282 | 0.99 |
| 62_Q | 69_S | 1.238 | 0.98 |
| 13_W | 17_D | 1.200 | 0.98 |
| 54_F | 72_G | 1.199 | 0.98 |
| 37_I | 47_I | 1.193 | 0.98 |
| 38_E | 81_K | 1.184 | 0.98 |
| 46_R | 118_D | 1.178 | 0.98 |
| 36_N | 86_Q | 1.177 | 0.98 |
| 125_E | 128_A | 1.162 | 0.97 |
| 36_N | 50_A | 1.128 | 0.97 |
| 18_K | 21_N | 1.117 | 0.96 |
| 61_I | 108_A | 1.077 | 0.95 |
| 45_Y | 101_E | 1.072 | 0.95 |
| 56_Q | 136_E | 1.070 | 0.95 |
| 58_D | 75_E | 1.056 | 0.95 |
| 100_A | 103_M | 1.051 | 0.94 |
| 55_R | 111_V | 1.037 | 0.94 |
| 68_L | 117_I | 1.035 | 0.94 |
| 72_G | 91_Q | 1.034 | 0.94 |
| 78_K | 81_K | 1.030 | 0.94 |
| 56_Q | 112_N | 1.029 | 0.94 |
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 | 0.9155 | 99.9 | 0.253 | Contact Map |
| 4eldA | 2 | 0.7465 | 99.9 | 0.262 | Contact Map |
| 1gmeA | 4 | 0.9437 | 99.9 | 0.294 | Contact Map |
| 3aabA | 2 | 0.7817 | 99.9 | 0.323 | Contact Map |
| 2bolA | 2 | 0.9296 | 99.9 | 0.356 | Contact Map |
| 3glaA | 2 | 0.6761 | 99.8 | 0.391 | Contact Map |
| 4feiA | 1 | 0.7042 | 99.8 | 0.397 | Contact Map |
| 3l1eA | 1 | 0.6972 | 99.8 | 0.397 | Contact Map |
| 2klrA | 2 | 0.5563 | 99.8 | 0.405 | Contact Map |
| 2wj5A | 1 | 0.6549 | 99.8 | 0.416 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)