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OPENSEQ.org
IscUHscB
Genes: A B A+B
Length: 128 171 296
Sequences: 2384 3234 329
Seq/Len: 18.62 18.91 1.11
MirrorTree (Pazo et al. 2001) 0.60
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 0.03
2 0.00 0.01 1.04
5 0.00 0.01 1.09
10 0.00 0.02 1.10
20 0.01 0.02 1.10
100 0.01 0.03 1.21
∞ 0.02 0.05 1.68
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
61_Y 153_F 1.40 0.73 0.01
61_Y 95_Q 1.39 0.71 0.01
87_A 166_E 1.30 0.64 0.01
124_K 44_Q 1.29 0.64 0.01
81_S 134_E 1.26 0.61 0.01
50_E 62_R 1.26 0.61 0.01
28_G 167_K 1.25 0.59 0.01
22_N 132_M 1.22 0.57 0.01
29_S 98_L 1.21 0.56 0.01
28_G 152_R 1.20 0.55 0.01
84_E 5_T 1.19 0.55 0.01
8_I 165_E 1.18 0.54 0.01
61_Y 91_F 1.18 0.53 0.01
108_I 152_R 1.16 0.51 0.01
31_M 153_F 1.16 0.51 0.01
125_R 126_D 1.15 0.51 0.01
20_F 145_A 1.15 0.51 0.01
45_I 114_L 1.15 0.50 0.01
57_R 43_E 1.14 0.50 0.01
123_S 89_T 1.13 0.49 0.01
31_M 95_Q 1.13 0.48 0.01
27_V 39_G 1.12 0.48 0.01
45_I 152_R 1.11 0.47 0.01
31_M 6_L 1.09 0.45 0.00
52_I 41_Q 1.09 0.45 0.00
92_D 167_K 1.08 0.44 0.00
45_I 1_M 1.08 0.43 0.00
84_E 112_A 1.07 0.42 0.00
5_E 127_T 1.06 0.42 0.00
5_E 89_T 1.06 0.42 0.00
61_Y 6_L 1.05 0.41 0.00
42_K 145_A 1.05 0.41 0.00
48_N 126_D 1.05 0.41 0.00
98_E 71_L 1.05 0.41 0.00
92_D 15_L 1.05 0.41 0.00
86_Q 164_L 1.04 0.40 0.00
119_A 90_A 1.04 0.40 0.00
108_I 136_L 1.04 0.40 0.00
122_K 38_S 1.03 0.39 0.00
108_I 145_A 1.03 0.39 0.00
81_S 135_Q 1.03 0.39 0.00
48_N 66_M 1.00 0.37 0.00
19_S 51_S 1.00 0.37 0.00
73_V 145_A 0.99 0.36 0.00
86_Q 31_Y 0.99 0.35 0.00
26_N 150_K 0.99 0.35 0.00
49_D 44_Q 0.98 0.35 0.00
89_K 97_E 0.97 0.34 0.00
8_I 121_V 0.97 0.34 0.00
49_D 158_R 0.97 0.34 0.00
57_R 89_T 0.97 0.34 0.00
73_V 44_Q 0.97 0.34 0.00
25_E 44_Q 0.96 0.33 0.00
49_D 78_D 0.96 0.33 0.00
120_D 70_Y 0.96 0.33 0.00
98_E 76_G 0.95 0.32 0.00
87_A 163_Q 0.95 0.32 0.00
81_S 139_E 0.94 0.31 0.00
29_S 124_M 0.94 0.31 0.00
122_K 62_R 0.93 0.31 0.00
45_I 154_L 0.92 0.30 0.00
50_E 39_G 0.92 0.30 0.00
24_D 166_E 0.92 0.30 0.00
125_R 31_Y 0.92 0.30 0.00
24_D 125_F 0.92 0.29 0.00
57_R 5_T 0.92 0.29 0.00
22_N 136_L 0.92 0.29 0.00
45_I 81_S 0.91 0.29 0.00
45_I 79_L 0.91 0.29 0.00
125_R 43_E 0.91 0.29 0.00
50_E 104_E 0.91 0.29 0.00
23_N 150_K 0.91 0.29 0.00
27_V 167_K 0.91 0.28 0.00
52_I 42_A 0.90 0.28 0.00
2_A 27_L 0.90 0.28 0.00
19_S 2_D 0.90 0.28 0.00
118_I 31_Y 0.90 0.28 0.00
8_I 29_R 0.90 0.28 0.00
104_I 86_V 0.90 0.28 0.00
123_S 90_A 0.90 0.28 0.00
118_I 161_A 0.89 0.28 0.00
77_V 46_A 0.89 0.27 0.00
47_V 152_R 0.89 0.27 0.00
31_M 91_F 0.89 0.27 0.00
84_E 160_S 0.88 0.27 0.00
47_V 154_L 0.88 0.27 0.00
77_V 157_L 0.87 0.26 0.00
81_S 60_T 0.87 0.26 0.00
122_K 126_D 0.87 0.26 0.00
8_I 23_R 0.87 0.26 0.00
61_Y 54_I 0.86 0.26 0.00
73_V 151_L 0.86 0.25 0.00
118_I 30_Q 0.86 0.25 0.00
5_E 7_F 0.86 0.25 0.00
28_G 63_H 0.85 0.25 0.00
73_V 149_R 0.85 0.25 0.00
87_A 63_H 0.85 0.25 0.00
52_I 5_T 0.85 0.24 0.00
25_E 39_G 0.84 0.24 0.00
91_T 60_T 0.83 0.23 0.00
123_S 135_Q 0.83 0.23 0.00
118_I 107_Q 0.83 0.23 0.00
23_N 44_Q 0.83 0.23 0.00
23_N 104_E 0.83 0.23 0.00
89_K 114_L 0.82 0.23 0.00
73_V 136_L 0.82 0.23 0.00
51_G 100_E 0.82 0.23 0.00
95_E 144_A 0.82 0.22 0.00
118_I 98_L 0.82 0.22 0.00
22_N 77_F 0.82 0.22 0.00
126_E 127_T 0.82 0.22 0.00
57_R 38_S 0.81 0.22 0.00
124_K 8_G 0.81 0.22 0.00
125_R 12_R 0.81 0.22 0.00
88_I 162_E 0.81 0.22 0.00
92_D 46_A 0.81 0.22 0.00
123_S 12_R 0.81 0.21 0.00
55_D 64_P 0.80 0.21 0.00
124_K 75_H 0.80 0.21 0.00
42_K 48_V 0.80 0.21 0.00
81_S 83_Q 0.80 0.21 0.00
51_G 68_A 0.80 0.21 0.00
83_D 113_R 0.79 0.20 0.00
126_E 90_A 0.79 0.20 0.00
42_K 70_Y 0.79 0.20 0.00
2_A 102_L 0.79 0.20 0.00
45_I 167_K 0.78 0.20 0.00
86_Q 29_R 0.78 0.20 0.00
122_K 80_A 0.78 0.20 0.00
61_Y 49_Q 0.78 0.20 0.00
60_T 99_R 0.77 0.19 0.00
9_D 121_V 0.77 0.19 0.00
84_E 126_D 0.77 0.19 0.00
45_I 161_A 0.77 0.19 0.00
50_E 131_L 0.77 0.19 0.00
118_I 81_S 0.77 0.19 0.00
81_S 141_W 0.76 0.19 0.00
123_S 15_L 0.76 0.19 0.00
49_D 110_D 0.76 0.19 0.00
82_L 47_A 0.76 0.19 0.00
28_G 161_A 0.76 0.18 0.00
27_V 80_A 0.75 0.18 0.00
88_I 159_S 0.75 0.18 0.00
87_A 46_A 0.75 0.18 0.00
22_N 164_L 0.75 0.18 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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