| pgl_long |
| ID: | 1420734823 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 194 (194) | ||
| Sequences: | 3938 (2963.2) | ||
| Seq/Len: | 20.299 | ||
| Nf(neff/√len): | 212.7 |
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: 20.299).
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 |
| 36_Q | 44_L | 3.408 | 1.00 |
| 20_L | 99_L | 3.278 | 1.00 |
| 166_W | 170_N | 3.275 | 1.00 |
| 34_G | 46_P | 3.145 | 1.00 |
| 36_Q | 46_P | 3.049 | 1.00 |
| 23_K | 90_V | 3.013 | 1.00 |
| 108_V | 143_M | 2.890 | 1.00 |
| 52_S | 94_I | 2.687 | 1.00 |
| 26_R | 89_A | 2.686 | 1.00 |
| 93_F | 97_T | 2.660 | 1.00 |
| 10_L | 106_F | 2.419 | 1.00 |
| 159_T | 162_Y | 2.215 | 1.00 |
| 146_L | 150_S | 2.208 | 1.00 |
| 135_Y | 169_K | 2.195 | 1.00 |
| 178_A | 182_K | 2.118 | 1.00 |
| 1_F | 5_C | 2.047 | 1.00 |
| 116_V | 144_T | 2.045 | 1.00 |
| 21_W | 31_A | 1.951 | 1.00 |
| 39_G | 141_P | 1.928 | 1.00 |
| 2_D | 114_S | 1.915 | 1.00 |
| 48_Y | 107_N | 1.899 | 1.00 |
| 6_S | 10_L | 1.883 | 1.00 |
| 34_G | 48_Y | 1.838 | 1.00 |
| 20_L | 94_I | 1.811 | 1.00 |
| 7_I | 109_L | 1.785 | 1.00 |
| 146_L | 166_W | 1.768 | 1.00 |
| 30_P | 55_M | 1.766 | 1.00 |
| 32_I | 48_Y | 1.732 | 1.00 |
| 3_I | 6_S | 1.697 | 1.00 |
| 116_V | 180_L | 1.690 | 1.00 |
| 44_L | 123_S | 1.639 | 1.00 |
| 17_M | 50_F | 1.618 | 1.00 |
| 182_K | 186_V | 1.598 | 1.00 |
| 185_K | 189_R | 1.598 | 1.00 |
| 20_L | 50_F | 1.597 | 1.00 |
| 56_N | 60_V | 1.589 | 1.00 |
| 139_A | 168_V | 1.587 | 1.00 |
| 125_E | 129_Y | 1.570 | 1.00 |
| 19_Y | 23_K | 1.539 | 1.00 |
| 106_F | 110_K | 1.537 | 1.00 |
| 5_C | 115_L | 1.529 | 1.00 |
| 9_I | 13_A | 1.519 | 1.00 |
| 167_Y | 176_D | 1.486 | 1.00 |
| 13_A | 17_M | 1.483 | 1.00 |
| 98_S | 152_R | 1.478 | 1.00 |
| 166_W | 175_N | 1.474 | 1.00 |
| 24_V | 27_D | 1.471 | 1.00 |
| 38_V | 44_L | 1.458 | 1.00 |
| 54_V | 60_V | 1.457 | 1.00 |
| 3_I | 7_I | 1.423 | 1.00 |
| 151_G | 155_V | 1.405 | 0.99 |
| 6_S | 109_L | 1.397 | 0.99 |
| 90_V | 94_I | 1.396 | 0.99 |
| 121_I | 125_E | 1.362 | 0.99 |
| 156_D | 159_T | 1.360 | 0.99 |
| 40_R | 140_K | 1.350 | 0.99 |
| 135_Y | 138_M | 1.342 | 0.99 |
| 96_K | 190_R | 1.336 | 0.99 |
| 145_G | 148_Q | 1.335 | 0.99 |
| 10_L | 14_S | 1.325 | 0.99 |
| 9_I | 115_L | 1.323 | 0.99 |
| 11_I | 14_S | 1.301 | 0.99 |
| 115_L | 180_L | 1.288 | 0.99 |
| 63_E | 67_N | 1.269 | 0.99 |
| 146_L | 179_I | 1.263 | 0.99 |
| 105_L | 115_L | 1.241 | 0.98 |
| 9_I | 105_L | 1.227 | 0.98 |
| 33_Y | 58_Q | 1.225 | 0.98 |
| 173_L | 177_I | 1.211 | 0.98 |
| 150_S | 182_K | 1.195 | 0.98 |
| 42_G | 137_L | 1.187 | 0.98 |
| 145_G | 160_R | 1.186 | 0.98 |
| 72_R | 76_E | 1.177 | 0.98 |
| 146_L | 175_N | 1.170 | 0.97 |
| 3_I | 109_L | 1.160 | 0.97 |
| 126_L | 129_Y | 1.151 | 0.97 |
| 5_C | 9_I | 1.138 | 0.97 |
| 187_V | 192_G | 1.135 | 0.97 |
| 35_H | 47_C | 1.134 | 0.97 |
| 102_L | 105_L | 1.126 | 0.97 |
| 180_L | 184_A | 1.125 | 0.97 |
| 148_Q | 164_D | 1.122 | 0.97 |
| 146_L | 163_F | 1.116 | 0.96 |
| 144_T | 183_T | 1.086 | 0.96 |
| 14_S | 17_M | 1.081 | 0.95 |
| 107_N | 112_D | 1.076 | 0.95 |
| 121_I | 157_Y | 1.052 | 0.95 |
| 48_Y | 110_K | 1.044 | 0.94 |
| 54_V | 57_S | 1.044 | 0.94 |
| 94_I | 97_T | 1.043 | 0.94 |
| 123_S | 127_E | 1.032 | 0.94 |
| 82_K | 194_Y | 1.027 | 0.94 |
| 30_P | 51_R | 1.022 | 0.93 |
| 132_D | 162_Y | 1.018 | 0.93 |
| 7_I | 11_I | 1.018 | 0.93 |
| 83_N | 92_R | 1.014 | 0.93 |
| 121_I | 126_L | 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 | |
| 3wguG | 2 | 0.1804 | 3.9 | 0.969 | Contact Map |
| 4c48C | 1 | 0.232 | 2.5 | 0.972 | Contact Map |
| 4ld7A | 16 | 0.6907 | 2.1 | 0.973 | Contact Map |
| 3nd0A | 2 | 0.2113 | 1.9 | 0.973 | Contact Map |
| 1hywA | 1 | 0.2887 | 1.8 | 0.974 | Contact Map |
| 2bzwB | 1 | 0.1392 | 1.8 | 0.974 | Contact Map |
| 2k44A | 1 | 0.1392 | 1.7 | 0.974 | Contact Map |
| 3hinA | 2 | 0.3041 | 1.6 | 0.974 | Contact Map |
| 1ypxA | 1 | 0.6907 | 1.6 | 0.974 | Contact Map |
| 3j2wE | 4 | 0.1495 | 1.5 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)