| 1t9z |
| ID: | 1452700406 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 191 (182) | ||
| Sequences: | 2004 (1233.7) | ||
| Seq/Len: | 11.011 | ||
| Nf(neff/√len): | 91.4 |
HHblits Results: (2015_06)
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: 11.011).
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 |
| 56_K | 61_D | 4.411 | 1.00 |
| 77_T | 84_A | 3.716 | 1.00 |
| 66_R | 167_E | 3.591 | 1.00 |
| 137_Y | 144_A | 3.341 | 1.00 |
| 16_I | 126_R | 2.814 | 1.00 |
| 59_H | 160_H | 2.780 | 1.00 |
| 81_A | 85_D | 2.501 | 1.00 |
| 89_D | 100_R | 2.408 | 1.00 |
| 24_E | 132_N | 2.362 | 1.00 |
| 18_V | 67_M | 2.152 | 1.00 |
| 60_V | 91_L | 1.991 | 1.00 |
| 70_L | 167_E | 1.947 | 1.00 |
| 129_I | 137_Y | 1.930 | 1.00 |
| 72_E | 122_R | 1.825 | 1.00 |
| 73_C | 97_F | 1.817 | 1.00 |
| 21_D | 25_T | 1.807 | 1.00 |
| 81_A | 104_E | 1.755 | 1.00 |
| 19_V | 120_L | 1.740 | 1.00 |
| 17_C | 74_V | 1.735 | 1.00 |
| 56_K | 60_V | 1.726 | 1.00 |
| 66_R | 69_E | 1.720 | 1.00 |
| 115_K | 131_D | 1.712 | 1.00 |
| 142_D | 180_R | 1.704 | 1.00 |
| 27_V | 87_V | 1.703 | 1.00 |
| 133_S | 136_S | 1.651 | 1.00 |
| 132_N | 149_S | 1.636 | 1.00 |
| 18_V | 166_F | 1.608 | 1.00 |
| 67_M | 73_C | 1.582 | 1.00 |
| 23_D | 83_Y | 1.564 | 1.00 |
| 20_I | 63_F | 1.546 | 1.00 |
| 75_L | 97_F | 1.535 | 1.00 |
| 137_Y | 146_P | 1.533 | 1.00 |
| 129_I | 140_H | 1.524 | 1.00 |
| 157_T | 161_D | 1.508 | 1.00 |
| 3_Y | 7_E | 1.503 | 1.00 |
| 148_A | 158_E | 1.492 | 1.00 |
| 75_L | 88_A | 1.485 | 1.00 |
| 160_H | 163_L | 1.482 | 1.00 |
| 125_R | 174_D | 1.444 | 1.00 |
| 63_F | 67_M | 1.439 | 1.00 |
| 21_D | 132_N | 1.348 | 0.99 |
| 67_M | 163_L | 1.343 | 0.99 |
| 130_M | 162_L | 1.328 | 0.99 |
| 168_Q | 178_V | 1.314 | 0.99 |
| 18_V | 71_F | 1.303 | 0.99 |
| 22_L | 88_A | 1.303 | 0.99 |
| 17_C | 122_R | 1.280 | 0.99 |
| 67_M | 71_F | 1.253 | 0.99 |
| 19_V | 127_V | 1.251 | 0.99 |
| 74_V | 99_A | 1.248 | 0.99 |
| 16_I | 71_F | 1.244 | 0.98 |
| 165_F | 179_L | 1.209 | 0.98 |
| 73_C | 96_A | 1.193 | 0.98 |
| 101_L | 122_R | 1.191 | 0.98 |
| 65_Q | 94_W | 1.191 | 0.98 |
| 24_E | 28_H | 1.187 | 0.98 |
| 25_T | 132_N | 1.183 | 0.98 |
| 22_L | 25_T | 1.183 | 0.98 |
| 116_D | 140_H | 1.180 | 0.98 |
| 8_A | 14_D | 1.177 | 0.98 |
| 129_I | 144_A | 1.161 | 0.97 |
| 156_D | 159_L | 1.154 | 0.97 |
| 86_P | 89_D | 1.140 | 0.97 |
| 158_E | 161_D | 1.134 | 0.97 |
| 128_L | 145_V | 1.128 | 0.97 |
| 15_K | 72_E | 1.112 | 0.96 |
| 66_R | 70_L | 1.109 | 0.96 |
| 24_E | 83_Y | 1.096 | 0.96 |
| 115_K | 132_N | 1.095 | 0.96 |
| 21_D | 24_E | 1.089 | 0.96 |
| 63_F | 159_L | 1.083 | 0.96 |
| 23_D | 136_S | 1.077 | 0.95 |
| 99_A | 122_R | 1.065 | 0.95 |
| 123_D | 126_R | 1.064 | 0.95 |
| 109_H | 114_V | 1.014 | 0.93 |
| 175_V | 179_L | 1.010 | 0.93 |
| 41_I | 44_E | 1.007 | 0.93 |
| 106_C | 158_E | 1.004 | 0.93 |
| 66_R | 163_L | 1.004 | 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 | |
| 3shqA | 1 | 0.8796 | 100 | 0.402 | Contact Map |
| 2ghtA | 2 | 0.9424 | 100 | 0.427 | Contact Map |
| 2hhlA | 4 | 0.9058 | 100 | 0.446 | Contact Map |
| 3qleA | 1 | 0.9005 | 100 | 0.456 | Contact Map |
| 3ef1A | 1 | 0.7853 | 99.9 | 0.522 | Contact Map |
| 4xpzA | 1 | 0.9476 | 99.9 | 0.527 | Contact Map |
| 2w43A | 2 | 0.8586 | 98.4 | 0.81 | Contact Map |
| 3ib6A | 4 | 0.8534 | 98.4 | 0.81 | Contact Map |
| 2no4A | 2 | 0.8953 | 98.4 | 0.81 | Contact Map |
| 3nuqA | 1 | 0.8848 | 98.3 | 0.815 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)