| 2mtz_peptidoglycan_his_removed |
| ID: | 1505504917 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 169 (164) | ||
| Sequences: | 1046 (595.9) | ||
| Seq/Len: | 6.378 | ||
| Nf(neff/√len): | 46.5 |
HHblits Results: (2016_02)
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: 6.378).
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 |
| 82_Y | 152_E | 3.253 | 1.00 |
| 102_N | 117_S | 2.996 | 1.00 |
| 73_S | 78_V | 2.499 | 1.00 |
| 98_F | 119_S | 2.375 | 1.00 |
| 115_W | 124_G | 2.335 | 1.00 |
| 111_F | 124_G | 2.117 | 1.00 |
| 113_A | 151_I | 2.066 | 1.00 |
| 64_S | 67_A | 1.987 | 1.00 |
| 100_I | 116_L | 1.876 | 1.00 |
| 68_K | 137_A | 1.786 | 1.00 |
| 7_Y | 22_F | 1.751 | 1.00 |
| 117_S | 124_G | 1.731 | 1.00 |
| 67_A | 71_T | 1.696 | 1.00 |
| 70_L | 84_I | 1.694 | 1.00 |
| 90_L | 139_S | 1.686 | 1.00 |
| 71_T | 78_V | 1.673 | 1.00 |
| 97_E | 162_R | 1.636 | 1.00 |
| 139_S | 142_C | 1.624 | 1.00 |
| 60_H | 73_S | 1.590 | 1.00 |
| 127_G | 153_L | 1.485 | 0.99 |
| 103_R | 159_N | 1.465 | 0.99 |
| 69_T | 81_T | 1.453 | 0.99 |
| 85_A | 139_S | 1.419 | 0.99 |
| 24_I | 49_P | 1.407 | 0.99 |
| 112_G | 127_G | 1.378 | 0.98 |
| 70_L | 125_I | 1.365 | 0.98 |
| 29_L | 46_I | 1.344 | 0.98 |
| 54_P | 166_N | 1.338 | 0.98 |
| 151_I | 155_S | 1.332 | 0.98 |
| 62_A | 73_S | 1.326 | 0.98 |
| 87_G | 142_C | 1.324 | 0.98 |
| 91_T | 140_K | 1.292 | 0.97 |
| 61_I | 157_V | 1.291 | 0.97 |
| 88_K | 91_T | 1.281 | 0.97 |
| 103_R | 116_L | 1.280 | 0.97 |
| 9_V | 12_G | 1.273 | 0.97 |
| 105_R | 114_Y | 1.272 | 0.97 |
| 133_S | 137_A | 1.270 | 0.97 |
| 63_V | 84_I | 1.263 | 0.96 |
| 97_E | 164_T | 1.253 | 0.96 |
| 7_Y | 13_D | 1.243 | 0.96 |
| 143_I | 165_I | 1.242 | 0.96 |
| 152_E | 156_I | 1.227 | 0.96 |
| 158_P | 161_T | 1.217 | 0.95 |
| 116_L | 159_N | 1.204 | 0.95 |
| 62_A | 166_N | 1.196 | 0.95 |
| 64_S | 166_N | 1.190 | 0.95 |
| 19_A | 29_L | 1.184 | 0.94 |
| 9_V | 46_I | 1.179 | 0.94 |
| 88_K | 92_Q | 1.177 | 0.94 |
| 128_T | 131_P | 1.149 | 0.93 |
| 126_H | 142_C | 1.145 | 0.93 |
| 80_K | 152_E | 1.143 | 0.93 |
| 72_L | 153_L | 1.121 | 0.92 |
| 10_K | 13_D | 1.121 | 0.92 |
| 61_I | 153_L | 1.120 | 0.92 |
| 20_A | 148_K | 1.120 | 0.92 |
| 145_M | 150_V | 1.106 | 0.91 |
| 36_L | 49_P | 1.096 | 0.91 |
| 91_T | 120_K | 1.092 | 0.91 |
| 106_N | 113_A | 1.092 | 0.91 |
| 20_A | 29_L | 1.086 | 0.90 |
| 89_I | 139_S | 1.074 | 0.90 |
| 87_G | 93_T | 1.054 | 0.89 |
| 73_S | 166_N | 1.054 | 0.89 |
| 16_N | 20_A | 1.053 | 0.88 |
| 116_L | 125_I | 1.052 | 0.88 |
| 103_R | 154_A | 1.050 | 0.88 |
| 107_P | 112_G | 1.049 | 0.88 |
| 134_I | 144_R | 1.039 | 0.88 |
| 114_Y | 150_V | 1.030 | 0.87 |
| 98_F | 120_K | 1.016 | 0.86 |
| 85_A | 150_V | 1.014 | 0.86 |
| 139_S | 144_R | 1.013 | 0.86 |
| 41_T | 44_Q | 1.001 | 0.85 |
| 117_S | 122_H | 1.001 | 0.85 |
| 110_P | 128_T | 1.000 | 0.85 |
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 | |
| 4lzhA | 1 | 0.9408 | 100 | 0.227 | Contact Map |
| 4a1kA | 1 | 0.9704 | 100 | 0.233 | Contact Map |
| 4jmnA | 1 | 0.9822 | 100 | 0.382 | Contact Map |
| 4xvoA | 3 | 0.9763 | 100 | 0.383 | Contact Map |
| 1zatA | 1 | 0.9645 | 100 | 0.429 | Contact Map |
| 4k73A | 1 | 0.9586 | 100 | 0.445 | Contact Map |
| 3vypA | 2 | 0.9822 | 100 | 0.449 | Contact Map |
| 4qtfA | 1 | 0 | 100 | 0.45 | Contact Map |
| 5bmqA | 1 | 0 | 100 | 0.456 | Contact Map |
| 4xxtA | 1 | 0.9349 | 100 | 0.475 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)