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OPENSEQ.org
cI_G_cIII_cyt1_Pdenitr
Genes: A B A+B
Length: 674 263 901
Sequences: 1936 973 354
Seq/Len: 2.87 3.7 0.39
MirrorTree (Pazo et al. 2001) 0.26
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.03 0.01 0.04
∞ 0.09 0.01 0.38
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
220_F 216_L 1.41 0.42 0.00
90_M 249_N 1.33 0.37 0.00
443_S 201_T 1.31 0.36 0.00
292_N 213_A 1.28 0.33 0.00
336_V 250_K 1.26 0.33 0.00
28_M 63_G 1.26 0.32 0.00
316_I 201_T 1.15 0.26 0.00
90_M 246_Y 1.12 0.24 0.00
14_I 246_Y 1.09 0.23 0.00
332_L 124_S 1.08 0.22 0.00
534_G 129_A 1.07 0.22 0.00
604_L 96_D 1.07 0.22 0.00
377_L 247_L 1.04 0.20 0.00
25_A 108_T 1.04 0.20 0.00
489_D 101_E 1.03 0.20 0.00
290_R 46_Q 1.01 0.19 0.00
23_I 64_L 0.98 0.18 0.00
498_L 46_Q 0.97 0.17 0.00
98_V 124_S 0.97 0.17 0.00
263_V 82_E 0.97 0.17 0.00
269_S 129_A 0.96 0.17 0.00
135_Y 125_L 0.96 0.17 0.00
189_T 76_G 0.96 0.17 0.00
403_V 82_E 0.95 0.16 0.00
530_H 124_S 0.95 0.16 0.00
96_E 84_Q 0.94 0.16 0.00
387_P 48_Q 0.94 0.16 0.00
171_V 249_N 0.93 0.16 0.00
125_A 44_Q 0.92 0.15 0.00
289_I 63_G 0.92 0.15 0.00
135_Y 100_E 0.92 0.15 0.00
130_V 163_G 0.91 0.15 0.00
216_K 216_L 0.91 0.15 0.00
551_S 242_A 0.91 0.15 0.00
169_T 230_V 0.90 0.14 0.00
266_E 154_I 0.89 0.14 0.00
33_V 193_D 0.89 0.14 0.00
378_I 195_V 0.89 0.14 0.00
5_R 143_Q 0.89 0.14 0.00
570_A 74_D 0.89 0.14 0.00
290_R 67_V 0.89 0.14 0.00
487_A 132_G 0.89 0.14 0.00
546_C 219_T 0.88 0.14 0.00
377_L 126_M 0.88 0.14 0.00
529_S 158_L 0.88 0.14 0.00
135_Y 59_S 0.88 0.14 0.00
216_K 159_T 0.88 0.14 0.00
364_A 125_L 0.87 0.13 0.00
239_L 221_E 0.86 0.13 0.00
535_A 157_V 0.86 0.13 0.00
335_L 130_R 0.86 0.13 0.00
232_S 241_L 0.86 0.13 0.00
570_A 240_V 0.86 0.13 0.00
232_S 220_A 0.86 0.13 0.00
429_L 206_D 0.86 0.13 0.00
558_E 72_L 0.85 0.13 0.00
313_G 113_T 0.85 0.13 0.00
239_L 47_L 0.85 0.13 0.00
500_A 46_Q 0.85 0.13 0.00
201_Q 115_S 0.85 0.13 0.00
501_A 256_I 0.85 0.13 0.00
368_D 158_L 0.84 0.13 0.00
314_K 236_I 0.84 0.12 0.00
207_L 157_V 0.84 0.12 0.00
201_Q 128_K 0.84 0.12 0.00
519_D 95_T 0.84 0.12 0.00
355_G 196_T 0.84 0.12 0.00
96_E 69_L 0.84 0.12 0.00
26_C 137_Y 0.84 0.12 0.00
160_S 80_L 0.84 0.12 0.00
316_I 66_Y 0.84 0.12 0.00
382_P 230_V 0.83 0.12 0.00
540_I 224_M 0.83 0.12 0.00
507_V 250_K 0.83 0.12 0.00
299_S 18_E 0.83 0.12 0.00
25_A 96_D 0.82 0.12 0.00
443_S 33_F 0.82 0.12 0.00
377_L 130_R 0.82 0.12 0.00
239_L 220_A 0.82 0.12 0.00
176_Q 81_P 0.82 0.12 0.00
561_P 76_G 0.82 0.12 0.00
646_N 213_A 0.82 0.12 0.00
14_I 131_A 0.82 0.12 0.00
403_V 49_R 0.82 0.12 0.00
525_I 171_A 0.82 0.12 0.00
188_I 92_F 0.82 0.12 0.00
444_I 236_I 0.82 0.12 0.00
590_A 22_S 0.82 0.12 0.00
232_S 182_N 0.82 0.12 0.00
525_I 195_V 0.82 0.12 0.00
470_N 256_I 0.81 0.12 0.00
505_A 244_L 0.81 0.12 0.00
253_M 84_Q 0.81 0.12 0.00
287_P 222_P 0.81 0.12 0.00
151_V 241_L 0.81 0.12 0.00
445_V 236_I 0.81 0.12 0.00
216_K 202_P 0.81 0.12 0.00
443_S 200_G 0.81 0.12 0.00
552_G 38_P 0.81 0.12 0.00
194_Q 243_A 0.81 0.11 0.00
14_I 84_Q 0.81 0.11 0.00
487_A 250_K 0.80 0.11 0.00
292_N 119_M 0.80 0.11 0.00
353_P 101_E 0.80 0.11 0.00
13_I 64_L 0.80 0.11 0.00
299_S 101_E 0.80 0.11 0.00
363_T 172_V 0.80 0.11 0.00
430_S 256_I 0.80 0.11 0.00
171_V 238_L 0.80 0.11 0.00
371_D 167_E 0.80 0.11 0.00
527_Q 249_N 0.80 0.11 0.00
484_R 249_N 0.79 0.11 0.00
274_F 24_A 0.79 0.11 0.00
156_T 63_G 0.79 0.11 0.00
471_S 242_A 0.79 0.11 0.00
325_P 128_K 0.79 0.11 0.00
190_S 52_Q 0.79 0.11 0.00
179_Q 63_G 0.79 0.11 0.00
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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