| gpJ2gap-tolerant |
| ID: | 1479768775 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 106 (101) | ||
| Sequences: | 203 (160) | ||
| Seq/Len: | 2.010 | ||
| Nf(neff/√len): | 15.9 |
HHblits Results: (2016_02)
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: 2.010).
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 |
| 8_N | 15_C | 3.091 | 1.00 |
| 8_N | 17_I | 2.677 | 1.00 |
| 11_I | 15_C | 2.395 | 1.00 |
| 9_V | 15_C | 2.365 | 1.00 |
| 17_I | 21_L | 2.119 | 0.99 |
| 8_N | 11_I | 2.048 | 0.99 |
| 2_N | 5_T | 1.947 | 0.99 |
| 10_T | 15_C | 1.943 | 0.99 |
| 11_I | 17_I | 1.923 | 0.99 |
| 10_T | 17_I | 1.826 | 0.98 |
| 6_L | 15_C | 1.817 | 0.98 |
| 20_K | 25_Q | 1.750 | 0.97 |
| 12_N | 18_K | 1.734 | 0.97 |
| 26_I | 30_I | 1.734 | 0.97 |
| 9_V | 14_N | 1.679 | 0.96 |
| 9_V | 17_I | 1.647 | 0.95 |
| 6_L | 17_I | 1.634 | 0.95 |
| 2_N | 7_N | 1.589 | 0.94 |
| 55_D | 59_F | 1.573 | 0.93 |
| 7_N | 11_I | 1.525 | 0.92 |
| 6_L | 10_T | 1.494 | 0.91 |
| 16_Q | 22_S | 1.482 | 0.90 |
| 22_S | 26_I | 1.466 | 0.90 |
| 8_N | 13_E | 1.434 | 0.88 |
| 101_E | 104_X | 1.430 | 0.88 |
| 10_T | 13_E | 1.388 | 0.86 |
| 55_D | 61_R | 1.386 | 0.86 |
| 6_L | 11_I | 1.310 | 0.82 |
| 20_K | 26_I | 1.230 | 0.76 |
| 7_N | 15_C | 1.222 | 0.75 |
| 8_N | 12_N | 1.209 | 0.74 |
| 65_I | 68_V | 1.199 | 0.73 |
| 6_L | 13_E | 1.187 | 0.72 |
| 48_T | 63_V | 1.183 | 0.71 |
| 23_A | 26_I | 1.158 | 0.69 |
| 20_K | 27_E | 1.152 | 0.69 |
| 13_E | 17_I | 1.149 | 0.68 |
| 9_V | 13_E | 1.144 | 0.68 |
| 7_N | 12_N | 1.132 | 0.67 |
| 7_N | 13_E | 1.128 | 0.66 |
| 20_K | 30_I | 1.120 | 0.65 |
| 2_N | 14_N | 1.082 | 0.61 |
| 53_I | 61_R | 1.042 | 0.57 |
| 26_I | 31_V | 1.041 | 0.57 |
| 95_V | 99_G | 1.039 | 0.57 |
| 22_S | 30_I | 1.016 | 0.54 |
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 | |
| 3rwxA | 1 | 0.4057 | 2.1 | 0.925 | Contact Map |
| 2lw3A | 1 | 0.7075 | 1.8 | 0.927 | Contact Map |
| 3fcgA | 2 | 0.3208 | 1.5 | 0.931 | Contact Map |
| 4x5pA | 1 | 0 | 1.3 | 0.933 | Contact Map |
| 4ellA | 2 | 0.4528 | 1.2 | 0.935 | Contact Map |
| 3wnoA | 2 | 0.8113 | 1.2 | 0.935 | Contact Map |
| 3zm8A | 1 | 0.7736 | 1.2 | 0.935 | Contact Map |
| 4qs4A | 1 | 0 | 1.1 | 0.936 | Contact Map |
| 1yp2A | 4 | 0.4906 | 1.1 | 0.936 | Contact Map |
| 4r7pA | 4 | 0 | 1 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)