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OPENSEQ.org
IscAHscB
Genes: A B A+B
Length: 107 171 276
Sequences: 2921 3234 374
Seq/Len: 27.3 18.91 1.36
MirrorTree (Pazo et al. 2001) 0.74
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 1.29
2 0.00 0.01 1.32
5 0.01 0.01 1.35
10 0.01 0.02 1.35
20 0.02 0.02 1.37
100 0.03 0.03 1.57
∞ 0.09 0.05 2.32
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
89_K 43_E 1.59 0.88 0.24
31_R 3_Y 1.42 0.79 0.16
3_I 15_L 1.40 0.78 0.15
26_L 44_Q 1.39 0.77 0.14
12_R 69_E 1.28 0.69 0.11
97_D 114_L 1.28 0.69 0.10
51_E 89_T 1.27 0.68 0.10
24_F 37_A 1.25 0.66 0.10
42_L 156_K 1.24 0.65 0.09
76_Q 44_Q 1.24 0.65 0.09
17_L 121_V 1.20 0.61 0.08
2_S 5_T 1.20 0.61 0.08
106_H 157_L 1.19 0.60 0.08
6_S 163_Q 1.16 0.58 0.07
81_K 50_Q 1.15 0.57 0.07
41_V 165_E 1.15 0.56 0.07
38_M 44_Q 1.14 0.56 0.07
14_N 44_Q 1.13 0.55 0.07
77_L 136_L 1.13 0.54 0.06
26_L 39_G 1.12 0.54 0.06
26_L 136_L 1.11 0.53 0.06
95_V 52_A 1.11 0.52 0.06
45_V 93_M 1.10 0.52 0.06
41_V 88_D 1.10 0.51 0.06
62_V 160_S 1.08 0.50 0.06
64_V 9_L 1.08 0.49 0.05
28_L 85_T 1.08 0.49 0.05
98_E 150_K 1.08 0.49 0.05
90_F 70_Y 1.07 0.48 0.05
65_D 64_P 1.06 0.48 0.05
79_F 113_R 1.06 0.47 0.05
98_E 52_A 1.06 0.47 0.05
44_F 157_L 1.04 0.46 0.05
80_V 65_L 1.04 0.45 0.05
51_E 24_F 1.03 0.45 0.05
12_R 45_L 1.03 0.44 0.04
85_N 28_Q 1.02 0.44 0.04
64_V 30_Q 1.02 0.44 0.04
15_T 152_R 1.02 0.44 0.04
80_V 39_G 1.02 0.43 0.04
80_V 97_E 1.00 0.42 0.04
16_F 150_K 0.99 0.41 0.04
89_K 53_T 0.99 0.41 0.04
80_V 155_D 0.99 0.41 0.04
30_V 129_H 0.99 0.41 0.04
67_K 64_P 0.99 0.40 0.04
81_K 72_L 0.98 0.39 0.04
38_M 75_H 0.97 0.39 0.04
95_V 78_D 0.97 0.38 0.04
14_N 63_H 0.97 0.38 0.04
28_L 98_L 0.97 0.38 0.04
44_F 72_L 0.96 0.38 0.04
38_M 155_D 0.96 0.38 0.04
72_L 103_D 0.95 0.37 0.03
53_I 161_A 0.95 0.37 0.03
12_R 152_R 0.95 0.37 0.03
17_L 36_F 0.95 0.37 0.03
19_N 45_L 0.95 0.36 0.03
81_K 150_K 0.94 0.36 0.03
96_K 52_A 0.94 0.36 0.03
97_D 152_R 0.94 0.36 0.03
30_V 163_Q 0.94 0.35 0.03
38_M 25_Q 0.94 0.35 0.03
72_L 5_T 0.94 0.35 0.03
41_V 87_R 0.93 0.35 0.03
39_A 37_A 0.93 0.35 0.03
82_E 95_Q 0.93 0.34 0.03
33_S 157_L 0.92 0.34 0.03
86_E 153_F 0.92 0.34 0.03
41_V 27_L 0.91 0.33 0.03
38_M 8_G 0.91 0.33 0.03
54_V 14_Q 0.91 0.33 0.03
64_V 142_D 0.91 0.33 0.03
18_A 29_R 0.91 0.33 0.03
57_D 31_Y 0.91 0.33 0.03
5_L 29_R 0.90 0.32 0.03
31_R 169_L 0.90 0.32 0.03
14_N 90_A 0.90 0.32 0.03
33_S 154_L 0.89 0.32 0.03
63_V 69_E 0.89 0.31 0.03
31_R 41_Q 0.88 0.31 0.03
42_L 139_E 0.88 0.30 0.03
2_S 89_T 0.87 0.30 0.03
54_V 85_T 0.87 0.29 0.02
26_L 69_E 0.87 0.29 0.02
6_S 124_M 0.86 0.29 0.02
45_V 159_S 0.86 0.29 0.02
79_F 52_A 0.86 0.28 0.02
98_E 165_E 0.85 0.28 0.02
45_V 45_L 0.85 0.28 0.02
49_T 62_R 0.85 0.28 0.02
14_N 156_K 0.84 0.27 0.02
79_F 145_A 0.84 0.27 0.02
24_F 167_K 0.84 0.27 0.02
12_R 87_R 0.84 0.27 0.02
26_L 24_F 0.84 0.27 0.02
39_A 59_Q 0.84 0.27 0.02
87_G 92_L 0.83 0.27 0.02
5_L 166_E 0.83 0.27 0.02
16_F 152_R 0.83 0.26 0.02
44_F 27_L 0.83 0.26 0.02
49_T 122_K 0.82 0.26 0.02
39_A 7_F 0.82 0.26 0.02
4_T 113_R 0.82 0.26 0.02
72_L 151_L 0.82 0.25 0.02
17_L 162_E 0.82 0.25 0.02
70_Q 50_Q 0.82 0.25 0.02
41_V 152_R 0.81 0.25 0.02
26_L 43_E 0.81 0.25 0.02
72_L 118_I 0.81 0.25 0.02
107_V 24_F 0.81 0.25 0.02
106_H 150_K 0.81 0.25 0.02
72_L 25_Q 0.81 0.25 0.02
66_G 167_K 0.81 0.24 0.02
98_E 78_D 0.81 0.24 0.02
3_I 9_L 0.80 0.24 0.02
54_V 36_F 0.80 0.24 0.02
72_L 158_R 0.80 0.24 0.02
30_V 164_L 0.80 0.24 0.02
11_A 127_T 0.80 0.24 0.02
83_G 95_Q 0.80 0.24 0.02
32_T 28_Q 0.79 0.23 0.02
31_R 135_Q 0.79 0.23 0.02
4_T 124_M 0.79 0.23 0.02
14_N 103_D 0.79 0.23 0.02
2_S 135_Q 0.78 0.23 0.02
7_D 112_A 0.78 0.23 0.02
80_V 104_E 0.78 0.23 0.02
23_G 91_F 0.78 0.22 0.02
65_D 149_R 0.78 0.22 0.02
81_K 45_L 0.78 0.22 0.02
76_Q 159_S 0.77 0.22 0.02
81_K 46_A 0.77 0.22 0.02
86_E 95_Q 0.77 0.22 0.02
23_G 95_Q 0.77 0.22 0.02
54_V 8_G 0.77 0.22 0.02
45_V 165_E 0.77 0.22 0.02
13_V 141_W 0.77 0.22 0.02
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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