| pglC_cjejuni_nonTM |
| ID: | 1423775815 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (151) | ||
| Sequences: | 3573 (2497.5) | ||
| Seq/Len: | 23.662 | ||
| Nf(neff/√len): | 203.2 |
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: 23.662).
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 |
| 12_N | 20_I | 3.463 | 1.00 |
| 10_T | 22_K | 3.385 | 1.00 |
| 125_Y | 129_N | 3.360 | 1.00 |
| 12_N | 22_K | 3.059 | 1.00 |
| 52_I | 56_L | 2.893 | 1.00 |
| 28_T | 53_V | 2.807 | 1.00 |
| 67_V | 102_I | 2.722 | 1.00 |
| 118_K | 121_E | 2.496 | 1.00 |
| 105_W | 109_N | 2.484 | 1.00 |
| 15_G | 100_P | 2.390 | 1.00 |
| 94_L | 128_K | 2.363 | 1.00 |
| 137_K | 141_L | 2.350 | 1.00 |
| 75_V | 103_T | 2.170 | 1.00 |
| 105_W | 125_Y | 2.019 | 1.00 |
| 24_Y | 66_N | 2.004 | 1.00 |
| 80_L | 84_Y | 1.896 | 1.00 |
| 98_V | 127_V | 1.875 | 1.00 |
| 75_V | 139_M | 1.845 | 1.00 |
| 10_T | 24_Y | 1.818 | 1.00 |
| 64_L | 74_F | 1.773 | 1.00 |
| 57_S | 111_R | 1.764 | 1.00 |
| 104_G | 107_Q | 1.743 | 1.00 |
| 65_F | 69_K | 1.737 | 1.00 |
| 6_S | 31_D | 1.700 | 1.00 |
| 20_I | 82_V | 1.698 | 1.00 |
| 14_P | 20_I | 1.696 | 1.00 |
| 49_F | 53_V | 1.673 | 1.00 |
| 8_I | 24_Y | 1.627 | 1.00 |
| 141_L | 145_K | 1.594 | 1.00 |
| 6_S | 27_K | 1.514 | 1.00 |
| 16_L | 99_R | 1.506 | 1.00 |
| 105_W | 138_I | 1.497 | 1.00 |
| 144_L | 148_K | 1.485 | 1.00 |
| 110_G | 114_I | 1.471 | 1.00 |
| 126_Y | 135_D | 1.460 | 1.00 |
| 125_Y | 134_L | 1.440 | 1.00 |
| 7_V | 26_F | 1.425 | 1.00 |
| 104_G | 119_K | 1.411 | 1.00 |
| 61_L | 64_L | 1.411 | 1.00 |
| 74_F | 139_M | 1.393 | 0.99 |
| 30_S | 33_R | 1.377 | 0.99 |
| 132_F | 136_L | 1.328 | 0.99 |
| 94_L | 97_K | 1.325 | 0.99 |
| 55_S | 149_R | 1.307 | 0.99 |
| 14_P | 85_L | 1.284 | 0.99 |
| 84_Y | 88_Y | 1.282 | 0.99 |
| 106_A | 119_K | 1.269 | 0.99 |
| 11_Q | 23_I | 1.268 | 0.99 |
| 115_S | 118_K | 1.247 | 0.99 |
| 80_L | 116_W | 1.233 | 0.98 |
| 95_R | 123_D | 1.218 | 0.98 |
| 24_Y | 69_K | 1.202 | 0.98 |
| 18_E | 96_H | 1.199 | 0.98 |
| 107_Q | 123_D | 1.197 | 0.98 |
| 105_W | 134_L | 1.183 | 0.98 |
| 82_V | 86_S | 1.182 | 0.98 |
| 53_V | 56_L | 1.170 | 0.97 |
| 146_V | 151_G | 1.160 | 0.97 |
| 105_W | 122_L | 1.156 | 0.97 |
| 109_N | 141_L | 1.151 | 0.97 |
| 81_L | 84_Y | 1.144 | 0.97 |
| 9_F | 81_L | 1.144 | 0.97 |
| 66_N | 71_D | 1.140 | 0.97 |
| 80_L | 119_K | 1.137 | 0.97 |
| 139_M | 143_A | 1.132 | 0.97 |
| 103_T | 142_T | 1.129 | 0.97 |
| 24_Y | 65_F | 1.124 | 0.97 |
| 9_F | 34_D | 1.121 | 0.97 |
| 32_E | 36_K | 1.105 | 0.96 |
| 57_S | 119_K | 1.104 | 0.96 |
| 80_L | 85_L | 1.101 | 0.96 |
| 81_L | 88_Y | 1.073 | 0.95 |
| 112_N | 119_K | 1.066 | 0.95 |
| 42_D | 51_K | 1.045 | 0.94 |
| 95_R | 119_K | 1.016 | 0.93 |
| 65_F | 71_D | 1.015 | 0.93 |
| 89_N | 92_Q | 1.007 | 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 | |
| 2clyA | 2 | 0.0898 | 5.4 | 0.963 | Contact Map |
| 4djdC | 2 | 0.4731 | 5.4 | 0.963 | Contact Map |
| 2h9aA | 1 | 0.491 | 5.2 | 0.963 | Contact Map |
| 4pw8A | 8 | 0.3593 | 5.1 | 0.963 | Contact Map |
| 3wguG | 2 | 0.2096 | 4.8 | 0.964 | Contact Map |
| 3zuaA | 1 | 0.4192 | 4.3 | 0.965 | Contact Map |
| 3o2uA | 2 | 0.8263 | 3.8 | 0.965 | Contact Map |
| 3floA | 4 | 0.7425 | 2.3 | 0.969 | Contact Map |
| 3pffA | 1 | 0.3952 | 2.2 | 0.969 | Contact Map |
| 4q0wA | 2 | 0.3473 | 2.2 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)