| Muscle_without_TAT |
| ID: | 1416332673 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (129) | ||
| Sequences: | 290 (233.4) | ||
| Seq/Len: | 2.248 | ||
| Nf(neff/√len): | 20.5 |
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: 2.248).
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 |
| 111_S | 114_D | 3.009 | 1.00 |
| 49_K | 55_T | 2.397 | 1.00 |
| 51_I | 57_E | 2.308 | 1.00 |
| 22_K | 26_S | 2.145 | 1.00 |
| 27_S | 98_R | 2.111 | 1.00 |
| 26_S | 84_D | 1.936 | 0.99 |
| 100_T | 104_L | 1.859 | 0.99 |
| 52_D | 61_K | 1.793 | 0.98 |
| 102_G | 106_Q | 1.777 | 0.98 |
| 29_E | 95_S | 1.775 | 0.98 |
| 125_Y | 129_R | 1.661 | 0.96 |
| 51_I | 55_T | 1.609 | 0.95 |
| 27_S | 99_E | 1.558 | 0.94 |
| 33_L | 37_L | 1.496 | 0.93 |
| 79_F | 95_S | 1.466 | 0.92 |
| 32_D | 82_L | 1.445 | 0.91 |
| 27_S | 102_G | 1.412 | 0.89 |
| 30_F | 91_I | 1.328 | 0.85 |
| 49_K | 57_E | 1.313 | 0.84 |
| 42_L | 92_I | 1.312 | 0.84 |
| 23_G | 98_R | 1.292 | 0.83 |
| 34_D | 75_I | 1.289 | 0.83 |
| 121_L | 126_Y | 1.252 | 0.80 |
| 30_F | 34_D | 1.251 | 0.80 |
| 122_I | 127_Y | 1.251 | 0.80 |
| 34_D | 39_A | 1.246 | 0.80 |
| 21_E | 29_E | 1.196 | 0.76 |
| 77_T | 80_R | 1.171 | 0.74 |
| 37_L | 83_N | 1.150 | 0.72 |
| 21_E | 25_D | 1.136 | 0.70 |
| 26_S | 94_N | 1.132 | 0.70 |
| 23_G | 55_T | 1.123 | 0.69 |
| 31_R | 34_D | 1.116 | 0.68 |
| 7_S | 128_V | 1.092 | 0.66 |
| 27_S | 75_I | 1.091 | 0.66 |
| 42_L | 46_W | 1.090 | 0.66 |
| 10_N | 15_Q | 1.089 | 0.66 |
| 37_L | 80_R | 1.084 | 0.65 |
| 70_A | 74_N | 1.069 | 0.63 |
| 117_L | 121_L | 1.068 | 0.63 |
| 18_S | 121_L | 1.065 | 0.63 |
| 57_E | 76_N | 1.064 | 0.63 |
| 65_P | 69_S | 1.060 | 0.62 |
| 8_I | 129_R | 1.056 | 0.62 |
| 55_T | 83_N | 1.053 | 0.62 |
| 42_L | 68_Q | 1.052 | 0.62 |
| 110_N | 113_R | 1.051 | 0.62 |
| 34_D | 95_S | 1.040 | 0.60 |
| 34_D | 69_S | 1.040 | 0.60 |
| 3_R | 127_Y | 1.039 | 0.60 |
| 45_P | 79_F | 1.039 | 0.60 |
| 22_K | 29_E | 1.036 | 0.60 |
| 47_F | 55_T | 1.034 | 0.60 |
| 65_P | 84_D | 1.011 | 0.57 |
| 3_R | 6_S | 1.010 | 0.57 |
| 5_H | 9_S | 1.005 | 0.56 |
| 122_I | 128_V | 1.005 | 0.56 |
| 84_D | 92_I | 1.004 | 0.56 |
| 5_H | 8_I | 1.001 | 0.56 |
| 22_K | 25_D | 1.001 | 0.56 |
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 | |
| 2lndA | 1 | 0.3643 | 21.5 | 0.934 | Contact Map |
| 1f07A | 4 | 0.4574 | 15 | 0.939 | Contact Map |
| 1z69A | 4 | 0.4961 | 12.1 | 0.941 | Contact Map |
| 2wjnC | 1 | 0.6202 | 11.8 | 0.941 | Contact Map |
| 1x1nA | 1 | 0.9612 | 10.3 | 0.943 | Contact Map |
| 4mjkA | 2 | 0.4109 | 9.5 | 0.944 | Contact Map |
| 1q16B | 1 | 0.7364 | 8.3 | 0.945 | Contact Map |
| 1lucA | 1 | 0.5039 | 7.1 | 0.947 | Contact Map |
| 1ezwA | 1 | 0.5116 | 6.7 | 0.948 | Contact Map |
| 3dmyA | 2 | 0.2868 | 6.3 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)