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OPENSEQ.org
PulE (A) - PulF (B)
Genes: A B A+B
Length: 497 401 876
Sequences: 3060 3592 2346
Seq/Len: 6.16 8.96 2.68
MirrorTree (Pazo et al. 2001) 0.88
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 2.01
2 0.01 0.00 2.45
5 0.01 0.00 2.53
10 0.01 0.00 2.60
20 0.01 0.01 2.61
100 0.04 0.05 2.65
∞ 0.14 0.15 2.74
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
322_L 388_I 1.22 0.82 0.09
286_I 174_L 1.00 0.61 0.05
179_A 343_L 0.98 0.59 0.04
337_Q 67_T 0.95 0.55 0.04
337_Q 152_T 0.95 0.55 0.04
135_I 153_E 0.93 0.53 0.04
322_L 209_L 0.92 0.51 0.04
346_L 209_L 0.87 0.46 0.03
339_S 378_A 0.86 0.45 0.03
212_R 191_V 0.85 0.43 0.03
207_S 377_M 0.83 0.41 0.03
363_D 389_L 0.83 0.41 0.03
305_T 161_R 0.81 0.39 0.03
309_G 389_L 0.81 0.39 0.03
278_N 206_T 0.80 0.38 0.02
212_R 179_V 0.80 0.37 0.02
369_F 28_A 0.79 0.37 0.02
292_G 385_V 0.79 0.37 0.02
340_L 145_L 0.79 0.37 0.02
244_I 158_L 0.79 0.36 0.02
135_I 115_E 0.79 0.36 0.02
277_R 283_L 0.79 0.36 0.02
322_L 294_L 0.78 0.35 0.02
177_D 214_D 0.78 0.35 0.02
212_R 389_L 0.78 0.35 0.02
278_N 191_V 0.78 0.35 0.02
129_K 319_A 0.77 0.34 0.02
133_I 290_S 0.77 0.34 0.02
170_I 7_Q 0.77 0.34 0.02
344_L 399_M 0.77 0.34 0.02
321_V 130_A 0.75 0.32 0.02
320_V 152_T 0.75 0.32 0.02
371_L 116_A 0.74 0.32 0.02
353_S 276_L 0.74 0.32 0.02
16_A 283_L 0.74 0.31 0.02
262_S 274_S 0.73 0.30 0.02
378_V 343_L 0.73 0.30 0.02
481_S 161_R 0.73 0.30 0.02
247_P 40_L 0.72 0.29 0.02
212_R 393_L 0.72 0.29 0.02
397_A 109_E 0.72 0.29 0.02
278_N 179_V 0.72 0.29 0.02
399_A 253_R 0.72 0.29 0.02
296_T 191_V 0.72 0.29 0.02
66_K 20_Q 0.72 0.29 0.02
278_N 387_A 0.72 0.29 0.02
363_D 393_L 0.72 0.29 0.02
219_D 188_V 0.71 0.28 0.02
314_L 69_Q 0.71 0.28 0.02
175_S 285_L 0.71 0.28 0.02
470_A 389_L 0.70 0.27 0.02
466_T 219_A 0.69 0.26 0.01
308_R 164_Q 0.69 0.26 0.01
340_L 164_Q 0.69 0.26 0.01
30_C 41_D 0.68 0.25 0.01
121_M 269_Y 0.68 0.25 0.01
399_A 174_L 0.68 0.25 0.01
333_Q 97_K 0.68 0.25 0.01
250_I 172_L 0.68 0.25 0.01
303_D 351_A 0.68 0.25 0.01
166_L 227_I 0.68 0.25 0.01
172_V 340_S 0.68 0.25 0.01
121_M 81_E 0.68 0.25 0.01
262_S 390_Q 0.68 0.25 0.01
166_L 333_M 0.67 0.25 0.01
278_N 391_P 0.67 0.25 0.01
172_V 285_L 0.67 0.24 0.01
240_V 333_M 0.67 0.24 0.01
475_A 340_S 0.67 0.24 0.01
375_L 103_V 0.67 0.24 0.01
358_I 295_S 0.67 0.24 0.01
279_I 62_D 0.67 0.24 0.01
113_P 374_V 0.66 0.24 0.01
346_L 83_A 0.66 0.24 0.01
164_A 35_K 0.66 0.24 0.01
456_L 228_L 0.66 0.23 0.01
174_A 204_F 0.66 0.23 0.01
204_T 356_R 0.65 0.23 0.01
227_L 131_M 0.65 0.23 0.01
372_S 258_G 0.65 0.23 0.01
170_I 376_A 0.65 0.23 0.01
321_V 65_L 0.65 0.23 0.01
339_S 191_V 0.65 0.22 0.01
292_G 72_T 0.65 0.22 0.01
208_S 310_V 0.65 0.22 0.01
415_Q 84_L 0.65 0.22 0.01
172_V 284_L 0.65 0.22 0.01
292_G 153_E 0.64 0.22 0.01
138_Y 78_I 0.64 0.22 0.01
296_T 279_S 0.64 0.22 0.01
427_Y 305_A 0.64 0.21 0.01
154_E 390_Q 0.64 0.21 0.01
466_T 166_M 0.64 0.21 0.01
32_V 221_P 0.64 0.21 0.01
304_M 393_L 0.64 0.21 0.01
121_M 2_A 0.64 0.21 0.01
267_A 351_A 0.63 0.21 0.01
267_A 140_H 0.63 0.21 0.01
278_N 69_Q 0.63 0.21 0.01
361_L 131_M 0.63 0.21 0.01
267_A 310_V 0.63 0.21 0.01
48_R 209_L 0.63 0.21 0.01
363_D 388_I 0.63 0.21 0.01
420_A 46_A 0.63 0.21 0.01
170_I 349_R 0.63 0.21 0.01
245_A 117_M 0.63 0.21 0.01
470_A 57_R 0.63 0.21 0.01
246_R 259_R 0.63 0.21 0.01
120_A 269_Y 0.63 0.21 0.01
85_D 23_D 0.63 0.21 0.01
204_T 222_W 0.62 0.20 0.01
438_L 187_V 0.62 0.20 0.01
481_S 304_E 0.62 0.20 0.01
444_R 194_Q 0.62 0.20 0.01
144_I 364_L 0.62 0.20 0.01
219_D 131_M 0.62 0.20 0.01
314_L 387_A 0.62 0.20 0.01
70_L 89_Q 0.62 0.20 0.01
273_D 73_L 0.62 0.20 0.01
212_R 206_T 0.62 0.20 0.01
181_K 315_S 0.62 0.20 0.01
177_D 142_D 0.61 0.20 0.01
127_K 117_M 0.61 0.20 0.01
299_N 391_P 0.61 0.20 0.01
373_T 161_R 0.61 0.20 0.01
309_G 109_E 0.61 0.20 0.01
379_M 128_Y 0.61 0.19 0.01
390_H 222_W 0.61 0.19 0.01
74_R 286_A 0.61 0.19 0.01
69_V 227_I 0.61 0.19 0.01
108_S 75_A 0.61 0.19 0.01
186_D 371_P 0.61 0.19 0.01
254_T 378_A 0.61 0.19 0.01
320_V 166_M 0.61 0.19 0.01
303_D 382_L 0.61 0.19 0.01
175_S 82_K 0.61 0.19 0.01
79_A 42_I 0.60 0.19 0.01
273_D 185_S 0.60 0.19 0.01
292_G 393_L 0.60 0.19 0.01
447_I 336_S 0.60 0.19 0.01
172_V 179_V 0.60 0.19 0.01
428_R 199_K 0.60 0.19 0.01
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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