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OPENSEQ.org
IscRHscA
Genes: A B A+B
Length: 162 616 766
Sequences: 5205 5112 358
Seq/Len: 32.13 8.3 0.47
MirrorTree (Pazo et al. 2001) 0.85
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 0.01 0.02 0.00
2 0.01 0.02 0.01
5 0.01 0.02 0.36
10 0.02 0.03 0.46
20 0.02 0.03 0.50
100 0.03 0.04 0.78
∞ 0.10 0.08 1.97
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
51_K 310_R 1.50 0.54 0.00
69_K 18_R 1.37 0.45 0.00
119_G 47_H 1.34 0.42 0.00
17_V 128_R 1.33 0.42 0.00
78_E 205_V 1.32 0.41 0.00
17_V 167_G 1.29 0.39 0.00
51_K 152_V 1.29 0.39 0.00
5_S 488_K 1.28 0.38 0.00
51_K 22_A 1.28 0.38 0.00
120_F 314_A 1.27 0.38 0.00
127_G 286_V 1.22 0.34 0.00
74_I 445_V 1.21 0.33 0.00
125_T 496_I 1.18 0.31 0.00
139_S 611_H 1.16 0.30 0.00
108_A 468_H 1.16 0.30 0.00
66_L 537_A 1.16 0.30 0.00
9_Y 341_V 1.16 0.30 0.00
124_I 297_R 1.15 0.29 0.00
26_V 359_S 1.14 0.28 0.00
75_A 611_H 1.13 0.28 0.00
96_G 7_S 1.13 0.28 0.00
69_K 13_A 1.13 0.28 0.00
125_T 217_I 1.09 0.26 0.00
114_S 413_T 1.08 0.25 0.00
24_G 334_M 1.07 0.25 0.00
69_K 458_G 1.07 0.24 0.00
5_S 167_G 1.06 0.24 0.00
5_S 486_M 1.06 0.24 0.00
143_H 484_T 1.06 0.24 0.00
24_G 506_D 1.05 0.23 0.00
9_Y 304_I 1.04 0.23 0.00
48_R 588_V 1.03 0.22 0.00
123_N 50_R 1.03 0.22 0.00
5_S 468_H 1.03 0.22 0.00
68_G 486_M 1.02 0.22 0.00
87_V 41_A 1.02 0.22 0.00
17_V 92_S 1.02 0.22 0.00
80_I 113_G 1.02 0.22 0.00
116_R 525_K 1.02 0.22 0.00
48_R 484_T 1.01 0.21 0.00
68_G 11_L 1.00 0.21 0.00
144_T 279_S 1.00 0.21 0.00
73_S 266_E 1.00 0.21 0.00
76_V 320_K 1.00 0.21 0.00
9_Y 331_E 0.99 0.20 0.00
30_D 315_C 0.98 0.20 0.00
127_G 279_S 0.98 0.20 0.00
54_L 473_F 0.98 0.20 0.00
140_G 167_G 0.98 0.20 0.00
17_V 125_N 0.98 0.20 0.00
55_V 374_A 0.97 0.20 0.00
113_L 161_D 0.97 0.19 0.00
39_L 334_M 0.97 0.19 0.00
47_S 331_E 0.96 0.19 0.00
131_N 152_V 0.96 0.19 0.00
9_Y 413_T 0.96 0.19 0.00
21_S 383_D 0.96 0.19 0.00
108_A 488_K 0.96 0.19 0.00
130_V 398_L 0.95 0.18 0.00
94_G 593_Q 0.95 0.18 0.00
68_G 324_V 0.94 0.18 0.00
80_I 177_L 0.94 0.18 0.00
40_S 334_M 0.94 0.18 0.00
14_M 480_L 0.93 0.18 0.00
62_G 475_V 0.93 0.17 0.00
22_E 285_T 0.93 0.17 0.00
68_G 345_R 0.93 0.17 0.00
125_T 41_A 0.92 0.17 0.00
75_A 18_R 0.92 0.17 0.00
69_K 91_R 0.92 0.17 0.00
141_R 562_I 0.92 0.17 0.00
125_T 566_A 0.92 0.17 0.00
135_V 543_L 0.91 0.17 0.00
100_G 252_Q 0.91 0.17 0.00
5_S 197_S 0.91 0.17 0.00
9_Y 386_M 0.91 0.16 0.00
4_T 151_G 0.91 0.16 0.00
17_V 468_H 0.90 0.16 0.00
146_D 435_I 0.90 0.16 0.00
125_T 526_A 0.90 0.16 0.00
32_S 408_V 0.89 0.16 0.00
75_A 13_A 0.89 0.16 0.00
52_N 310_R 0.89 0.16 0.00
136_L 51_H 0.89 0.16 0.00
127_G 295_I 0.89 0.16 0.00
33_E 407_K 0.89 0.16 0.00
84_D 234_S 0.89 0.16 0.00
118_T 167_G 0.89 0.16 0.00
18_A 169_K 0.88 0.15 0.00
12_T 164_Q 0.88 0.15 0.00
134_E 245_L 0.88 0.15 0.00
69_K 434_S 0.88 0.15 0.00
58_V 422_D 0.88 0.15 0.00
14_M 478_D 0.88 0.15 0.00
119_G 299_Q 0.88 0.15 0.00
19_L 279_S 0.88 0.15 0.00
29_A 333_V 0.87 0.15 0.00
80_I 507_S 0.87 0.15 0.00
9_Y 543_L 0.87 0.15 0.00
119_G 88_L 0.87 0.15 0.00
69_K 229_A 0.87 0.15 0.00
91_R 589_D 0.86 0.15 0.00
128_E 73_N 0.86 0.15 0.00
27_P 384_S 0.86 0.15 0.00
2_R 455_A 0.86 0.15 0.00
136_L 548_A 0.86 0.15 0.00
77_G 455_A 0.86 0.15 0.00
87_V 386_M 0.86 0.15 0.00
120_F 203_I 0.86 0.15 0.00
74_I 317_R 0.86 0.15 0.00
17_V 383_D 0.86 0.15 0.00
125_T 559_R 0.86 0.14 0.00
5_S 199_Q 0.86 0.14 0.00
36_G 508_E 0.85 0.14 0.00
29_A 545_G 0.85 0.14 0.00
130_V 310_R 0.85 0.14 0.00
6_K 429_G 0.85 0.14 0.00
103_K 435_I 0.85 0.14 0.00
110_W 406_E 0.85 0.14 0.00
103_K 310_R 0.85 0.14 0.00
112_D 345_R 0.85 0.14 0.00
124_I 446_Q 0.84 0.14 0.00
132_N 435_I 0.84 0.14 0.00
8_R 421_Q 0.84 0.14 0.00
6_K 225_F 0.84 0.14 0.00
76_V 615_E 0.84 0.14 0.00
48_R 513_I 0.84 0.14 0.00
112_D 368_I 0.84 0.14 0.00
125_T 576_D 0.84 0.14 0.00
73_S 288_V 0.84 0.14 0.00
95_K 514_K 0.83 0.14 0.00
2_R 595_F 0.83 0.14 0.00
81_S 117_I 0.83 0.14 0.00
17_V 89_M 0.83 0.14 0.00
71_A 143_E 0.83 0.13 0.00
107_H 406_E 0.83 0.13 0.00
101_G 562_I 0.83 0.13 0.00
133_Q 279_S 0.83 0.13 0.00
17_V 437_V 0.82 0.13 0.00
11_V 433_M 0.82 0.13 0.00
25_P 333_V 0.82 0.13 0.00
50_R 200_E 0.82 0.13 0.00
138_V 615_E 0.82 0.13 0.00
46_F 427_K 0.82 0.13 0.00
48_R 269_D 0.82 0.13 0.00
58_V 361_D 0.82 0.13 0.00
2_R 597_A 0.82 0.13 0.00
39_L 478_D 0.82 0.13 0.00
86_S 559_R 0.82 0.13 0.00
68_G 111_E 0.82 0.13 0.00
32_S 7_S 0.82 0.13 0.00
116_R 202_V 0.81 0.13 0.00
52_N 233_D 0.81 0.13 0.00
5_S 114_L 0.81 0.13 0.00
128_E 372_I 0.81 0.13 0.00
122_N 540_L 0.81 0.13 0.00
53_G 446_Q 0.81 0.13 0.00
88_D 53_L 0.81 0.13 0.00
71_A 515_D 0.81 0.13 0.00
9_Y 539_V 0.81 0.13 0.00
46_F 200_E 0.81 0.13 0.00
54_L 66_V 0.81 0.13 0.00
105_L 338_S 0.81 0.13 0.00
139_S 615_E 0.81 0.13 0.00
108_A 138_A 0.80 0.13 0.00
27_P 444_L 0.80 0.13 0.00
118_T 13_A 0.80 0.12 0.00
76_V 346_E 0.80 0.12 0.00
100_G 295_I 0.80 0.12 0.00
88_D 164_Q 0.80 0.12 0.00
140_G 283_S 0.80 0.12 0.00
72_S 533_K 0.80 0.12 0.00
100_G 298_E 0.80 0.12 0.00
107_H 499_K 0.80 0.12 0.00
125_T 435_I 0.80 0.12 0.00
25_P 470_R 0.80 0.12 0.00
32_S 474_Q 0.80 0.12 0.00
62_G 478_D 0.80 0.12 0.00
102_D 329_V 0.79 0.12 0.00
145_H 606_R 0.79 0.12 0.00
69_K 49_G 0.79 0.12 0.00
5_S 128_R 0.79 0.12 0.00
27_P 612_S 0.79 0.12 0.00
123_N 247_D 0.79 0.12 0.00
138_V 267_L 0.79 0.12 0.00
27_P 463_P 0.79 0.12 0.00
35_Q 161_D 0.79 0.12 0.00
33_E 408_V 0.79 0.12 0.00
127_G 592_T 0.79 0.12 0.00
74_I 473_F 0.79 0.12 0.00
71_A 588_V 0.79 0.12 0.00
21_S 279_S 0.79 0.12 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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