| CH_NDC80 1-115 |
| ID: | 1415900097 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (112) | ||
| Sequences: | 274 (209.5) | ||
| Seq/Len: | 2.446 | ||
| Nf(neff/√len): | 19.8 |
Jackhmmer Results: (2014_04_16)
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: 2.446).
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_L | 105_A | 3.883 | 1.00 |
| 43_S | 47_F | 1.958 | 0.99 |
| 42_P | 100_W | 1.901 | 0.99 |
| 7_P | 13_F | 1.860 | 0.99 |
| 39_L | 50_I | 1.799 | 0.98 |
| 21_L | 111_I | 1.610 | 0.96 |
| 51_F | 55_Y | 1.556 | 0.95 |
| 11_K | 14_I | 1.526 | 0.94 |
| 93_T | 96_A | 1.515 | 0.94 |
| 101_P | 109_W | 1.490 | 0.93 |
| 65_P | 72_E | 1.449 | 0.92 |
| 77_F | 106_A | 1.424 | 0.91 |
| 28_N | 53_F | 1.418 | 0.91 |
| 88_K | 105_A | 1.358 | 0.88 |
| 24_F | 57_F | 1.354 | 0.88 |
| 55_Y | 76_I | 1.354 | 0.88 |
| 69_F | 73_V | 1.321 | 0.86 |
| 16_Q | 111_I | 1.320 | 0.86 |
| 4_D | 54_L | 1.302 | 0.85 |
| 14_I | 110_L | 1.299 | 0.85 |
| 44_V | 103_I | 1.244 | 0.82 |
| 100_W | 109_W | 1.242 | 0.81 |
| 3_K | 7_P | 1.241 | 0.81 |
| 4_D | 8_L | 1.229 | 0.81 |
| 3_K | 15_Q | 1.204 | 0.79 |
| 35_S | 104_V | 1.201 | 0.78 |
| 77_F | 105_A | 1.196 | 0.78 |
| 35_S | 45_K | 1.190 | 0.77 |
| 50_I | 77_F | 1.154 | 0.74 |
| 32_H | 46_D | 1.147 | 0.74 |
| 68_K | 71_E | 1.138 | 0.73 |
| 55_Y | 73_V | 1.138 | 0.73 |
| 68_K | 101_P | 1.126 | 0.72 |
| 59_C | 64_L | 1.125 | 0.72 |
| 77_F | 108_V | 1.117 | 0.71 |
| 46_D | 62_Y | 1.114 | 0.71 |
| 95_G | 107_L | 1.111 | 0.70 |
| 47_F | 82_Y | 1.107 | 0.70 |
| 37_K | 87_S | 1.107 | 0.70 |
| 43_S | 97_P | 1.102 | 0.69 |
| 51_F | 114_I | 1.101 | 0.69 |
| 45_K | 80_L | 1.089 | 0.68 |
| 25_L | 53_F | 1.082 | 0.67 |
| 51_F | 107_L | 1.082 | 0.67 |
| 10_D | 53_F | 1.079 | 0.67 |
| 59_C | 109_W | 1.071 | 0.66 |
| 53_F | 57_F | 1.069 | 0.66 |
| 68_K | 88_K | 1.061 | 0.65 |
| 30_Y | 53_F | 1.049 | 0.64 |
| 21_L | 113_C | 1.046 | 0.64 |
| 76_I | 80_L | 1.043 | 0.63 |
| 49_K | 73_V | 1.030 | 0.62 |
| 41_A | 95_G | 1.027 | 0.61 |
| 89_S | 114_I | 1.024 | 0.61 |
| 43_S | 61_S | 1.023 | 0.61 |
| 26_T | 94_V | 1.018 | 0.60 |
| 55_Y | 72_E | 1.003 | 0.59 |
| 46_D | 73_V | 1.002 | 0.59 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2ve7A | 2 | 1 | 100 | 0.018 | Contact Map |
| 2igpA | 1 | 0.9739 | 100 | 0.053 | Contact Map |
| 4lvpA | 1 | 0.8435 | 57.4 | 0.909 | Contact Map |
| 2lbcA | 1 | 0.8261 | 42.3 | 0.917 | Contact Map |
| 1ua4A | 1 | 0.8609 | 32.1 | 0.922 | Contact Map |
| 1l2lA | 1 | 0.8522 | 28.6 | 0.924 | Contact Map |
| 2nppB | 2 | 0.7652 | 24.4 | 0.927 | Contact Map |
| 3fgaB | 1 | 0.7652 | 21.5 | 0.929 | Contact Map |
| 3drwA | 2 | 0.8696 | 20.7 | 0.929 | Contact Map |
| 2jakA | 1 | 0.6522 | 20.5 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)