| z15-seqchecked-jck |
| ID: | 1487816118 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (115) | ||
| Sequences: | 395 (264.9) | ||
| Seq/Len: | 3.435 | ||
| Nf(neff/√len): | 24.7 |
Jackhmmer Results: (2016_04)
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: 3.435).
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 |
| 3_M | 6_E | 2.300 | 1.00 |
| 10_A | 96_I | 2.177 | 1.00 |
| 14_I | 69_V | 1.846 | 0.99 |
| 42_Y | 78_G | 1.705 | 0.99 |
| 61_H | 91_D | 1.684 | 0.99 |
| 97_D | 104_Q | 1.628 | 0.98 |
| 6_E | 67_D | 1.614 | 0.98 |
| 109_G | 112_K | 1.461 | 0.96 |
| 7_I | 11_L | 1.426 | 0.95 |
| 45_H | 57_F | 1.419 | 0.95 |
| 6_E | 89_P | 1.402 | 0.95 |
| 7_I | 39_K | 1.381 | 0.94 |
| 83_D | 96_I | 1.344 | 0.93 |
| 30_F | 67_D | 1.328 | 0.92 |
| 55_S | 103_Y | 1.323 | 0.92 |
| 45_H | 48_P | 1.320 | 0.92 |
| 97_D | 102_S | 1.318 | 0.92 |
| 14_I | 66_V | 1.308 | 0.92 |
| 3_M | 67_D | 1.259 | 0.89 |
| 24_R | 27_V | 1.253 | 0.89 |
| 60_I | 99_F | 1.250 | 0.89 |
| 6_E | 84_V | 1.228 | 0.88 |
| 109_G | 114_L | 1.224 | 0.87 |
| 54_G | 58_R | 1.219 | 0.87 |
| 23_P | 33_E | 1.198 | 0.86 |
| 89_P | 103_Y | 1.182 | 0.85 |
| 47_Y | 53_K | 1.179 | 0.85 |
| 21_K | 24_R | 1.176 | 0.84 |
| 4_Q | 39_K | 1.176 | 0.84 |
| 111_V | 115_Y | 1.170 | 0.84 |
| 95_W | 104_Q | 1.170 | 0.84 |
| 59_C | 91_D | 1.161 | 0.83 |
| 47_Y | 57_F | 1.152 | 0.83 |
| 63_G | 91_D | 1.142 | 0.82 |
| 23_P | 29_I | 1.141 | 0.82 |
| 61_H | 93_S | 1.131 | 0.81 |
| 42_Y | 111_V | 1.128 | 0.81 |
| 45_H | 67_D | 1.128 | 0.81 |
| 40_K | 43_E | 1.125 | 0.81 |
| 63_G | 93_S | 1.121 | 0.80 |
| 74_S | 112_K | 1.115 | 0.80 |
| 4_Q | 60_I | 1.104 | 0.79 |
| 57_F | 95_W | 1.104 | 0.79 |
| 18_L | 87_N | 1.090 | 0.78 |
| 14_I | 79_L | 1.088 | 0.78 |
| 50_K | 53_K | 1.085 | 0.77 |
| 41_K | 62_I | 1.078 | 0.77 |
| 27_V | 83_D | 1.071 | 0.76 |
| 102_S | 111_V | 1.068 | 0.76 |
| 64_E | 94_V | 1.067 | 0.76 |
| 8_Q | 12_N | 1.062 | 0.75 |
| 105_I | 111_V | 1.060 | 0.75 |
| 52_Y | 94_V | 1.057 | 0.75 |
| 56_G | 95_W | 1.054 | 0.74 |
| 24_R | 82_D | 1.051 | 0.74 |
| 62_I | 79_L | 1.050 | 0.74 |
| 24_R | 80_D | 1.037 | 0.73 |
| 14_I | 33_E | 1.028 | 0.72 |
| 90_Q | 94_V | 1.024 | 0.71 |
| 8_Q | 88_L | 1.013 | 0.70 |
| 7_I | 87_N | 1.010 | 0.70 |
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 | |
| 2z15A | 4 | 1 | 100 | 0.045 | Contact Map |
| 3e9vA | 1 | 0.9916 | 100 | 0.05 | Contact Map |
| 3shrA | 2 | 0.5294 | 27.1 | 0.926 | Contact Map |
| 2yskA | 1 | 0.8319 | 20.7 | 0.93 | Contact Map |
| 2kmfA | 1 | 0.3782 | 17.7 | 0.933 | Contact Map |
| 4o5vA | 1 | 0.9664 | 16.9 | 0.933 | Contact Map |
| 2j0pA | 1 | 0.563 | 14.3 | 0.935 | Contact Map |
| 1lngA | 1 | 0.6303 | 13.2 | 0.936 | Contact Map |
| 4mf9A | 2 | 0.5378 | 12.4 | 0.937 | Contact Map |
| 3ky9A | 2 | 0.8824 | 12.2 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)