| d4msva_ |
| ID: | 1450012477 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (139) | ||
| Sequences: | 541 (314.9) | ||
| Seq/Len: | 3.892 | ||
| Nf(neff/√len): | 26.7 |
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: 3.892).
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 |
| 38_G | 114_H | 2.833 | 1.00 |
| 32_V | 136_L | 2.261 | 1.00 |
| 51_S | 67_H | 2.117 | 1.00 |
| 49_V | 115_L | 1.991 | 1.00 |
| 31_G | 48_F | 1.981 | 1.00 |
| 51_S | 91_C | 1.776 | 0.99 |
| 48_F | 105_A | 1.768 | 0.99 |
| 4_V | 9_G | 1.628 | 0.99 |
| 37_G | 110_T | 1.611 | 0.99 |
| 70_Y | 81_V | 1.558 | 0.98 |
| 69_V | 99_R | 1.550 | 0.98 |
| 9_G | 87_M | 1.460 | 0.97 |
| 135_G | 139_L | 1.448 | 0.97 |
| 67_H | 103_L | 1.436 | 0.96 |
| 67_H | 101_S | 1.413 | 0.96 |
| 6_H | 50_Y | 1.381 | 0.95 |
| 42_N | 138_K | 1.368 | 0.95 |
| 5_A | 8_T | 1.361 | 0.95 |
| 20_W | 34_Y | 1.346 | 0.94 |
| 82_M | 107_F | 1.341 | 0.94 |
| 52_K | 101_S | 1.297 | 0.93 |
| 60_C | 91_C | 1.294 | 0.93 |
| 46_L | 106_V | 1.282 | 0.92 |
| 21_E | 25_G | 1.264 | 0.91 |
| 88_M | 105_A | 1.258 | 0.91 |
| 5_A | 117_V | 1.244 | 0.91 |
| 37_G | 109_L | 1.237 | 0.90 |
| 10_K | 13_S | 1.223 | 0.90 |
| 94_G | 97_W | 1.213 | 0.89 |
| 34_Y | 37_G | 1.210 | 0.89 |
| 2_R | 10_K | 1.209 | 0.89 |
| 51_S | 107_F | 1.209 | 0.89 |
| 33_K | 111_S | 1.206 | 0.89 |
| 65_L | 107_F | 1.202 | 0.88 |
| 25_G | 129_E | 1.175 | 0.87 |
| 117_V | 124_L | 1.165 | 0.86 |
| 48_F | 60_C | 1.154 | 0.86 |
| 52_K | 107_F | 1.153 | 0.86 |
| 4_V | 46_L | 1.141 | 0.85 |
| 74_S | 114_H | 1.139 | 0.85 |
| 36_K | 133_F | 1.109 | 0.82 |
| 102_Y | 133_F | 1.104 | 0.82 |
| 98_A | 126_N | 1.104 | 0.82 |
| 26_I | 49_V | 1.104 | 0.82 |
| 4_V | 10_K | 1.104 | 0.82 |
| 40_V | 113_D | 1.103 | 0.82 |
| 72_R | 126_N | 1.089 | 0.81 |
| 80_L | 125_V | 1.081 | 0.80 |
| 24_Y | 39_L | 1.080 | 0.80 |
| 65_L | 119_V | 1.077 | 0.80 |
| 4_V | 28_L | 1.072 | 0.79 |
| 48_F | 104_G | 1.056 | 0.78 |
| 55_F | 119_V | 1.051 | 0.77 |
| 48_F | 137_Y | 1.050 | 0.77 |
| 67_H | 102_Y | 1.043 | 0.77 |
| 125_V | 132_T | 1.041 | 0.77 |
| 68_K | 130_S | 1.039 | 0.76 |
| 80_L | 112_A | 1.035 | 0.76 |
| 37_G | 69_V | 1.033 | 0.76 |
| 68_K | 94_G | 1.025 | 0.75 |
| 119_V | 124_L | 1.025 | 0.75 |
| 7_L | 32_V | 1.023 | 0.75 |
| 48_F | 90_Y | 1.023 | 0.75 |
| 76_Y | 136_L | 1.021 | 0.75 |
| 13_S | 111_S | 1.021 | 0.75 |
| 11_S | 15_S | 1.014 | 0.74 |
| 28_L | 133_F | 1.010 | 0.73 |
| 5_A | 29_L | 1.005 | 0.73 |
| 58_Q | 114_H | 1.005 | 0.73 |
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 | |
| 4msvA | 1 | 1 | 100 | 0.085 | Contact Map |
| 1tnrA | 1 | 0.9784 | 100 | 0.113 | Contact Map |
| 2rjlA | 1 | 0.964 | 100 | 0.124 | Contact Map |
| 1s55A | 3 | 0.9928 | 100 | 0.126 | Contact Map |
| 4kg8A | 3 | 0.9065 | 100 | 0.132 | Contact Map |
| 4mxwY | 4 | 0.9065 | 100 | 0.136 | Contact Map |
| 2tnfA | 3 | 0.9856 | 100 | 0.136 | Contact Map |
| 1dg6A | 1 | 0.9568 | 100 | 0.136 | Contact Map |
| 2x29A | 1 | 0.9281 | 100 | 0.151 | Contact Map |
| 1alyA | 1 | 0.9784 | 100 | 0.174 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)