| CcsBA_6 |
| ID: | 1509672755 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 935 (302) | ||
| Sequences: | 6190 (3334.7) | ||
| Seq/Len: | 20.497 | ||
| Nf(neff/√len): | 191.9 |
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: 20.497).
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 |
| 679_T | 706_W | 3.714 | 1.00 |
| 772_L | 853_Y | 3.048 | 1.00 |
| 765_I | 821_G | 2.976 | 1.00 |
| 852_V | 878_G | 2.908 | 1.00 |
| 819_S | 850_I | 2.861 | 1.00 |
| 815_L | 854_A | 2.741 | 1.00 |
| 675_F | 710_L | 2.411 | 1.00 |
| 835_R | 838_G | 2.400 | 1.00 |
| 922_I | 926_R | 2.334 | 1.00 |
| 776_F | 876_V | 2.187 | 1.00 |
| 731_G | 735_F | 2.116 | 1.00 |
| 775_C | 811_M | 1.983 | 1.00 |
| 680_C | 684_L | 1.952 | 1.00 |
| 881_S | 884_M | 1.928 | 1.00 |
| 852_V | 881_S | 1.923 | 1.00 |
| 638_Y | 642_S | 1.880 | 1.00 |
| 773_G | 879_F | 1.856 | 1.00 |
| 642_S | 645_L | 1.829 | 1.00 |
| 675_F | 679_T | 1.818 | 1.00 |
| 675_F | 706_W | 1.761 | 1.00 |
| 679_T | 693_P | 1.754 | 1.00 |
| 664_H | 667_F | 1.723 | 1.00 |
| 912_E | 916_G | 1.680 | 1.00 |
| 691_H | 696_N | 1.679 | 1.00 |
| 661_P | 665_K | 1.676 | 1.00 |
| 645_L | 648_I | 1.658 | 1.00 |
| 642_S | 678_H | 1.658 | 1.00 |
| 734_L | 738_N | 1.635 | 1.00 |
| 771_F | 814_G | 1.547 | 1.00 |
| 731_G | 734_L | 1.533 | 1.00 |
| 865_K | 870_I | 1.513 | 1.00 |
| 793_R | 796_V | 1.480 | 1.00 |
| 729_L | 733_T | 1.473 | 1.00 |
| 726_S | 730_A | 1.472 | 1.00 |
| 764_V | 820_V | 1.460 | 1.00 |
| 674_L | 709_I | 1.459 | 1.00 |
| 672_F | 706_W | 1.454 | 1.00 |
| 804_S | 860_R | 1.446 | 1.00 |
| 676_I | 680_C | 1.409 | 1.00 |
| 645_L | 649_V | 1.406 | 0.99 |
| 735_F | 738_N | 1.401 | 0.99 |
| 675_F | 693_P | 1.399 | 0.99 |
| 739_L | 742_M | 1.390 | 0.99 |
| 647_I | 651_V | 1.388 | 0.99 |
| 729_L | 732_M | 1.354 | 0.99 |
| 668_Y | 672_F | 1.352 | 0.99 |
| 907_V | 911_V | 1.349 | 0.99 |
| 682_L | 706_W | 1.340 | 0.99 |
| 722_A | 726_S | 1.340 | 0.99 |
| 855_I | 859_L | 1.319 | 0.99 |
| 829_A | 837_W | 1.315 | 0.99 |
| 642_S | 649_V | 1.280 | 0.99 |
| 851_G | 855_I | 1.280 | 0.99 |
| 727_S | 731_G | 1.280 | 0.99 |
| 778_L | 803_L | 1.277 | 0.99 |
| 772_L | 878_G | 1.274 | 0.99 |
| 812_I | 857_L | 1.274 | 0.99 |
| 709_I | 732_M | 1.274 | 0.99 |
| 740_G | 743_D | 1.273 | 0.99 |
| 638_Y | 645_L | 1.271 | 0.99 |
| 914_M | 917_I | 1.266 | 0.99 |
| 764_V | 824_L | 1.258 | 0.99 |
| 756_Y | 760_I | 1.258 | 0.99 |
| 776_F | 879_F | 1.257 | 0.99 |
| 769_Y | 818_L | 1.246 | 0.98 |
| 757_W | 831_E | 1.239 | 0.98 |
| 731_G | 738_N | 1.239 | 0.98 |
| 732_M | 735_F | 1.229 | 0.98 |
| 726_S | 729_L | 1.229 | 0.98 |
| 779_G | 807_N | 1.227 | 0.98 |
| 732_M | 736_V | 1.225 | 0.98 |
| 919_L | 924_A | 1.225 | 0.98 |
| 913_L | 917_I | 1.218 | 0.98 |
| 641_I | 670_L | 1.214 | 0.98 |
| 724_C | 731_G | 1.213 | 0.98 |
| 722_A | 725_A | 1.212 | 0.98 |
| 671_L | 729_L | 1.209 | 0.98 |
| 859_L | 871_F | 1.208 | 0.98 |
| 728_F | 732_M | 1.193 | 0.98 |
| 722_A | 731_G | 1.191 | 0.98 |
| 678_H | 702_L | 1.191 | 0.98 |
| 911_V | 914_M | 1.191 | 0.98 |
| 642_S | 653_I | 1.188 | 0.98 |
| 771_F | 813_L | 1.186 | 0.98 |
| 923_I | 927_K | 1.185 | 0.98 |
| 675_F | 709_I | 1.183 | 0.98 |
| 683_G | 687_Y | 1.181 | 0.98 |
| 663_I | 667_F | 1.180 | 0.98 |
| 782_T | 872_A | 1.178 | 0.98 |
| 829_A | 833_W | 1.174 | 0.98 |
| 672_F | 713_V | 1.173 | 0.98 |
| 671_L | 709_I | 1.173 | 0.98 |
| 815_L | 850_I | 1.171 | 0.98 |
| 686_W | 692_A | 1.167 | 0.97 |
| 641_I | 645_L | 1.161 | 0.97 |
| 909_L | 913_L | 1.159 | 0.97 |
| 730_A | 734_L | 1.156 | 0.97 |
| 787_L | 791_E | 1.154 | 0.97 |
| 725_A | 735_F | 1.151 | 0.97 |
| 675_F | 678_H | 1.149 | 0.97 |
| 906_P | 910_W | 1.139 | 0.97 |
| 789_R | 792_K | 1.137 | 0.97 |
| 632_Y | 636_Y | 1.134 | 0.97 |
| 811_M | 875_S | 1.134 | 0.97 |
| 693_P | 699_E | 1.130 | 0.97 |
| 767_A | 817_L | 1.124 | 0.97 |
| 717_R | 720_N | 1.123 | 0.97 |
| 727_S | 730_A | 1.122 | 0.97 |
| 786_F | 868_P | 1.115 | 0.96 |
| 780_L | 876_V | 1.111 | 0.96 |
| 725_A | 729_L | 1.107 | 0.96 |
| 725_A | 734_L | 1.103 | 0.96 |
| 885_T | 888_G | 1.101 | 0.96 |
| 772_L | 814_G | 1.095 | 0.96 |
| 725_A | 732_M | 1.092 | 0.96 |
| 727_S | 734_L | 1.085 | 0.96 |
| 853_Y | 878_G | 1.083 | 0.96 |
| 815_L | 819_S | 1.079 | 0.95 |
| 722_A | 732_M | 1.079 | 0.95 |
| 905_E | 908_P | 1.073 | 0.95 |
| 693_P | 696_N | 1.069 | 0.95 |
| 707_A | 770_G | 1.069 | 0.95 |
| 779_G | 875_S | 1.068 | 0.95 |
| 660_R | 663_I | 1.059 | 0.95 |
| 660_R | 665_K | 1.058 | 0.95 |
| 649_V | 653_I | 1.054 | 0.95 |
| 919_L | 922_I | 1.054 | 0.95 |
| 814_G | 853_Y | 1.052 | 0.95 |
| 848_I | 852_V | 1.052 | 0.95 |
| 849_S | 882_V | 1.050 | 0.94 |
| 642_S | 646_F | 1.050 | 0.94 |
| 708_A | 773_G | 1.049 | 0.94 |
| 914_M | 922_I | 1.047 | 0.94 |
| 907_V | 912_E | 1.044 | 0.94 |
| 822_N | 846_A | 1.038 | 0.94 |
| 901_A | 904_A | 1.033 | 0.94 |
| 691_H | 699_E | 1.032 | 0.94 |
| 894_T | 898_S | 1.031 | 0.94 |
| 807_N | 875_S | 1.031 | 0.94 |
| 645_L | 652_G | 1.030 | 0.94 |
| 649_V | 725_A | 1.029 | 0.94 |
| 724_C | 728_F | 1.028 | 0.94 |
| 639_I | 642_S | 1.028 | 0.94 |
| 730_A | 738_N | 1.026 | 0.94 |
| 901_A | 908_P | 1.025 | 0.93 |
| 724_C | 729_L | 1.022 | 0.93 |
| 733_T | 737_A | 1.018 | 0.93 |
| 818_L | 822_N | 1.014 | 0.93 |
| 729_L | 735_F | 1.014 | 0.93 |
| 859_L | 865_K | 1.012 | 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 | |
| 2wswA | 1 | 0.2278 | 39 | 0.985 | Contact Map |
| 1zcdA | 2 | 0.1294 | 24.1 | 0.986 | Contact Map |
| 2yevA | 2 | 0.2439 | 15 | 0.988 | Contact Map |
| 2m20A | 2 | 0.0374 | 12.5 | 0.988 | Contact Map |
| 1q16C | 1 | 0.1861 | 11.9 | 0.988 | Contact Map |
| 4ev6A | 5 | 0.0663 | 11 | 0.988 | Contact Map |
| 1v54A | 2 | 0.2385 | 10.4 | 0.989 | Contact Map |
| 3b5dA | 2 | 0.0043 | 9.9 | 0.989 | Contact Map |
| 1fftA | 2 | 0.2139 | 9.8 | 0.989 | Contact Map |
| 4o6yA | 2 | 0.2128 | 9.8 | 0.989 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)