| Sim |
| ID: | 1431559956 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 976 (976) | ||
| Sequences: | 10000 (9914.9) | ||
| Seq/Len: | 10.246 | ||
| Nf(neff/√len): | 317.4 |
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: 10.246).
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 |
| 392_A | 491_A | 36.279 | 1.00 |
| 491_A | 589_A | 34.950 | 1.00 |
| 392_A | 589_A | 25.215 | 1.00 |
| 589_A | 782_A | 20.247 | 1.00 |
| 197_A | 392_A | 20.100 | 1.00 |
| 491_A | 782_A | 17.634 | 1.00 |
| 197_A | 491_A | 17.253 | 1.00 |
| 99_A | 197_A | 15.564 | 1.00 |
| 782_A | 879_A | 14.626 | 1.00 |
| 197_A | 589_A | 13.141 | 1.00 |
| 392_A | 782_A | 12.012 | 1.00 |
| 99_A | 392_A | 9.716 | 1.00 |
| 589_A | 879_A | 9.600 | 1.00 |
| 99_A | 491_A | 8.304 | 1.00 |
| 491_A | 879_A | 8.246 | 1.00 |
| 392_A | 879_A | 5.623 | 1.00 |
| 99_A | 589_A | 5.614 | 1.00 |
| 197_A | 782_A | 5.440 | 1.00 |
| 99_A | 782_A | 2.678 | 1.00 |
| 197_A | 879_A | 2.219 | 1.00 |
| 423_C | 564_T | 1.365 | 0.99 |
| 19_C | 635_A | 1.231 | 0.98 |
| 183_A | 810_C | 1.223 | 0.98 |
| 635_A | 867_C | 1.193 | 0.98 |
| 249_T | 495_G | 1.183 | 0.98 |
| 407_G | 815_T | 1.181 | 0.98 |
| 471_T | 588_T | 1.178 | 0.98 |
| 212_C | 948_T | 1.176 | 0.98 |
| 48_G | 95_T | 1.170 | 0.97 |
| 79_A | 158_G | 1.166 | 0.97 |
| 27_C | 320_T | 1.157 | 0.97 |
| 335_T | 670_G | 1.147 | 0.97 |
| 610_G | 960_G | 1.146 | 0.97 |
| 17_G | 35_C | 1.144 | 0.97 |
| 55_C | 870_A | 1.138 | 0.97 |
| 161_A | 408_G | 1.126 | 0.97 |
| 187_T | 335_T | 1.125 | 0.97 |
| 487_A | 571_C | 1.122 | 0.97 |
| 665_A | 927_T | 1.122 | 0.97 |
| 65_C | 452_A | 1.110 | 0.96 |
| 315_T | 627_A | 1.110 | 0.96 |
| 472_C | 940_C | 1.108 | 0.96 |
| 394_T | 571_C | 1.100 | 0.96 |
| 23_G | 724_T | 1.093 | 0.96 |
| 409_T | 684_G | 1.090 | 0.96 |
| 800_C | 841_T | 1.086 | 0.96 |
| 516_A | 658_T | 1.085 | 0.96 |
| 489_A | 956_G | 1.079 | 0.95 |
| 440_G | 878_T | 1.077 | 0.95 |
| 54_G | 915_G | 1.073 | 0.95 |
| 243_G | 849_T | 1.072 | 0.95 |
| 109_T | 626_A | 1.070 | 0.95 |
| 378_A | 893_C | 1.066 | 0.95 |
| 206_A | 957_T | 1.065 | 0.95 |
| 263_T | 544_T | 1.064 | 0.95 |
| 212_C | 564_T | 1.056 | 0.95 |
| 109_T | 439_T | 1.056 | 0.95 |
| 284_T | 799_G | 1.056 | 0.95 |
| 83_C | 584_G | 1.056 | 0.95 |
| 658_T | 843_T | 1.056 | 0.95 |
| 711_T | 878_T | 1.055 | 0.95 |
| 64_A | 366_C | 1.053 | 0.95 |
| 70_C | 772_A | 1.053 | 0.95 |
| 319_A | 821_T | 1.050 | 0.94 |
| 141_T | 282_T | 1.047 | 0.94 |
| 206_A | 674_G | 1.044 | 0.94 |
| 243_G | 595_G | 1.038 | 0.94 |
| 204_G | 406_T | 1.037 | 0.94 |
| 108_T | 877_G | 1.034 | 0.94 |
| 247_G | 414_G | 1.034 | 0.94 |
| 178_A | 966_G | 1.034 | 0.94 |
| 522_T | 762_T | 1.033 | 0.94 |
| 533_C | 813_T | 1.032 | 0.94 |
| 356_G | 521_A | 1.031 | 0.94 |
| 797_C | 891_T | 1.030 | 0.94 |
| 725_G | 958_T | 1.025 | 0.93 |
| 470_T | 818_T | 1.025 | 0.93 |
| 239_G | 752_A | 1.025 | 0.93 |
| 63_T | 620_A | 1.024 | 0.93 |
| 360_C | 649_C | 1.022 | 0.93 |
| 725_G | 795_A | 1.020 | 0.93 |
| 413_G | 821_T | 1.019 | 0.93 |
| 132_A | 625_G | 1.017 | 0.93 |
| 381_G | 615_C | 1.014 | 0.93 |
| 275_C | 316_A | 1.013 | 0.93 |
| 21_C | 26_G | 1.013 | 0.93 |
| 263_T | 731_G | 1.013 | 0.93 |
| 410_C | 588_T | 1.011 | 0.93 |
| 14_A | 296_G | 1.008 | 0.93 |
| 481_C | 751_T | 1.007 | 0.93 |
| 259_G | 465_T | 1.003 | 0.93 |
| 121_A | 940_C | 1.002 | 0.92 |
| 46_G | 265_T | 1.000 | 0.92 |
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 | |
| 1t2yA | 1 | 0.0143 | 0.2 | 0.995 | Contact Map |
| 1zpxA | 1 | 0.0143 | 0.2 | 0.995 | Contact Map |
| 2otnA | 2 | 0.0564 | 0.1 | 0.996 | Contact Map |
| 1qjlA | 1 | 0.0102 | 0.1 | 0.996 | Contact Map |
| 3c8xA | 1 | 0.0379 | 0.1 | 0.997 | Contact Map |
| 1f5qB | 2 | 0.0451 | 0.1 | 0.997 | Contact Map |
| 1al0B | 1 | 0.0277 | 0.1 | 0.997 | Contact Map |
| 2y8tB | 2 | 0.0123 | 0.1 | 0.997 | Contact Map |
| 2oq9A | 1 | 0.0143 | 0.1 | 0.997 | Contact Map |
| 2pq5A | 4 | 0.0318 | 0.1 | 0.997 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)