| 1CCWA |
| ID: | 1411602977 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 137 (124) | ||
| Sequences: | 76859 (60312) | ||
| Seq/Len: | 619.831 | ||
| Nf(neff/√len): | 5416.2 |
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: 619.831).
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 |
| 35_V | 55_A | 2.594 | 1.00 |
| 20_N | 36_N | 2.523 | 1.00 |
| 42_P | 66_Q | 2.448 | 1.00 |
| 20_N | 41_S | 2.399 | 1.00 |
| 44_E | 66_Q | 2.310 | 1.00 |
| 60_V | 74_L | 2.124 | 1.00 |
| 51_I | 81_A | 2.057 | 1.00 |
| 68_E | 73_G | 2.045 | 1.00 |
| 9_G | 46_F | 1.983 | 1.00 |
| 41_S | 45_L | 1.961 | 1.00 |
| 43_Q | 67_G | 1.949 | 1.00 |
| 5_T | 33_N | 1.915 | 1.00 |
| 115_R | 129_D | 1.897 | 1.00 |
| 67_G | 77_K | 1.842 | 1.00 |
| 63_L | 94_I | 1.727 | 1.00 |
| 90_V | 113_Y | 1.709 | 1.00 |
| 79_D | 114_D | 1.698 | 1.00 |
| 42_P | 45_L | 1.686 | 1.00 |
| 30_A | 127_I | 1.671 | 1.00 |
| 24_D | 36_N | 1.671 | 1.00 |
| 77_K | 80_E | 1.657 | 1.00 |
| 24_D | 28_T | 1.632 | 1.00 |
| 26_A | 123_P | 1.601 | 1.00 |
| 47_I | 77_K | 1.537 | 1.00 |
| 5_T | 35_V | 1.500 | 1.00 |
| 20_N | 39_V | 1.469 | 1.00 |
| 75_R | 88_L | 1.442 | 1.00 |
| 37_I | 49_A | 1.403 | 0.99 |
| 47_I | 74_L | 1.389 | 0.99 |
| 60_V | 75_R | 1.346 | 0.99 |
| 35_V | 49_A | 1.342 | 0.99 |
| 44_E | 48_K | 1.288 | 0.99 |
| 67_G | 73_G | 1.286 | 0.99 |
| 7_V | 37_I | 1.280 | 0.99 |
| 62_S | 90_V | 1.271 | 0.99 |
| 77_K | 81_A | 1.264 | 0.99 |
| 43_Q | 74_L | 1.260 | 0.99 |
| 75_R | 90_V | 1.253 | 0.99 |
| 50_A | 78_C | 1.245 | 0.98 |
| 58_I | 86_I | 1.238 | 0.98 |
| 60_V | 88_L | 1.190 | 0.98 |
| 27_F | 130_L | 1.160 | 0.97 |
| 24_D | 39_V | 1.159 | 0.97 |
| 49_A | 55_A | 1.145 | 0.97 |
| 37_I | 46_F | 1.138 | 0.97 |
| 49_A | 52_E | 1.126 | 0.97 |
| 49_A | 53_T | 1.124 | 0.97 |
| 73_G | 76_Q | 1.124 | 0.97 |
| 15_C | 61_S | 1.118 | 0.96 |
| 35_V | 53_T | 1.111 | 0.96 |
| 76_Q | 107_R | 1.104 | 0.96 |
| 57_A | 130_L | 1.100 | 0.96 |
| 7_V | 46_F | 1.097 | 0.96 |
| 47_I | 67_G | 1.093 | 0.96 |
| 62_S | 72_K | 1.089 | 0.96 |
| 106_K | 110_D | 1.081 | 0.95 |
| 72_K | 107_R | 1.079 | 0.95 |
| 83_L | 86_I | 1.077 | 0.95 |
| 44_E | 67_G | 1.071 | 0.95 |
| 6_I | 32_F | 1.065 | 0.95 |
| 105_E | 125_V | 1.054 | 0.95 |
| 48_K | 52_E | 1.054 | 0.95 |
| 16_H | 19_G | 1.044 | 0.94 |
| 125_V | 129_D | 1.034 | 0.94 |
| 114_D | 133_D | 1.023 | 0.93 |
| 9_G | 64_Y | 1.011 | 0.93 |
| 45_L | 49_A | 1.005 | 0.93 |
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 | |
| 4l4uA | 1 | 0.8905 | 99.4 | 0.014 | Contact Map |
| 3rqiA | 1 | 0.8686 | 99.4 | 0.021 | Contact Map |
| 3q9sA | 1 | 0.8686 | 99.4 | 0.026 | Contact Map |
| 1ys7A | 2 | 0.8759 | 99.4 | 0.03 | Contact Map |
| 3r0jA | 2 | 0.8832 | 99.4 | 0.032 | Contact Map |
| 3eq2A | 2 | 0.8759 | 99.4 | 0.034 | Contact Map |
| 1kgsA | 1 | 0.8759 | 99.4 | 0.036 | Contact Map |
| 2ayxA | 1 | 0.8905 | 99.4 | 0.038 | Contact Map |
| 1yioA | 1 | 0.8759 | 99.4 | 0.04 | Contact Map |
| 1ccwA | 2 | 1 | 99.4 | 0.046 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)