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OPENSEQ.org
cI_G_cIII_isp
Genes: A B A+B
Length: 100 195 285
Sequences: 1241 974 277
Seq/Len: 12.41 4.99 0.97
MirrorTree (Pazo et al. 2001) 0.43
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 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.08
∞ 0.02 0.02 0.94
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
56_T 98_D 1.56 0.80 0.04
80_L 67_E 1.32 0.62 0.02
98_M 180_H 1.29 0.59 0.02
80_L 103_I 1.26 0.57 0.02
30_F 189_D 1.23 0.54 0.01
11_A 136_V 1.23 0.54 0.01
19_L 127_A 1.20 0.51 0.01
2_I 53_V 1.19 0.50 0.01
30_F 192_I 1.14 0.46 0.01
3_P 132_V 1.11 0.43 0.01
38_M 28_T 1.10 0.42 0.01
20_T 84_R 1.09 0.41 0.01
62_Y 29_A 1.05 0.38 0.01
73_A 187_L 1.05 0.37 0.01
65_A 46_Q 1.05 0.37 0.01
41_A 56_L 1.04 0.36 0.01
65_A 120_E 1.04 0.36 0.01
60_V 181_I 1.03 0.36 0.01
1_M 30_G 1.02 0.35 0.01
38_M 78_G 1.01 0.35 0.01
88_Q 173_G 1.00 0.34 0.01
95_V 82_F 1.00 0.33 0.01
23_V 52_D 1.00 0.33 0.01
93_D 74_V 0.99 0.32 0.01
10_L 71_Q 0.98 0.32 0.01
17_L 75_K 0.97 0.31 0.01
20_T 70_T 0.97 0.31 0.01
2_I 39_A 0.96 0.30 0.01
46_F 46_Q 0.95 0.29 0.01
17_L 101_Q 0.95 0.29 0.01
10_L 91_I 0.95 0.29 0.01
38_M 25_Y 0.95 0.29 0.01
54_G 67_E 0.95 0.29 0.01
71_A 78_G 0.93 0.28 0.01
9_I 120_E 0.93 0.28 0.01
75_I 136_V 0.93 0.28 0.01
38_M 98_D 0.92 0.27 0.01
2_I 108_Q 0.92 0.27 0.01
95_V 164_Y 0.90 0.26 0.01
31_M 89_D 0.90 0.26 0.01
52_Y 191_T 0.90 0.26 0.01
2_I 29_A 0.90 0.25 0.01
16_V 192_I 0.88 0.24 0.01
91_N 98_D 0.88 0.24 0.01
98_M 158_P 0.88 0.24 0.01
60_V 45_N 0.87 0.24 0.01
84_H 52_D 0.87 0.24 0.01
75_I 73_T 0.87 0.24 0.01
78_A 169_R 0.87 0.24 0.01
75_I 192_I 0.86 0.23 0.01
51_S 155_W 0.86 0.23 0.01
63_I 152_F 0.86 0.23 0.01
60_V 106_S 0.86 0.23 0.01
31_M 120_E 0.85 0.23 0.00
46_F 27_A 0.85 0.23 0.00
23_V 68_T 0.85 0.22 0.00
28_L 164_Y 0.85 0.22 0.00
48_V 164_Y 0.84 0.22 0.00
17_L 119_D 0.84 0.22 0.00
95_V 145_I 0.84 0.22 0.00
54_G 189_D 0.84 0.22 0.00
87_R 20_R 0.84 0.21 0.00
78_A 178_N 0.84 0.21 0.00
47_V 125_D 0.83 0.21 0.00
9_I 33_T 0.83 0.21 0.00
87_R 102_L 0.83 0.21 0.00
73_A 26_Y 0.83 0.21 0.00
65_A 32_G 0.82 0.21 0.00
82_Q 43_L 0.82 0.20 0.00
71_A 86_R 0.82 0.20 0.00
52_Y 194_L 0.82 0.20 0.00
28_L 120_E 0.82 0.20 0.00
11_A 101_Q 0.82 0.20 0.00
60_V 74_V 0.81 0.20 0.00
20_T 163_H 0.81 0.20 0.00
44_L 151_D 0.81 0.20 0.00
56_T 58_S 0.81 0.20 0.00
23_V 156_F 0.81 0.20 0.00
86_R 194_L 0.81 0.20 0.00
17_L 12_H 0.81 0.20 0.00
83_L 32_G 0.80 0.20 0.00
93_D 90_E 0.80 0.20 0.00
73_A 61_V 0.80 0.19 0.00
55_Q 47_M 0.80 0.19 0.00
38_M 148_G 0.80 0.19 0.00
98_M 14_G 0.80 0.19 0.00
54_G 45_N 0.80 0.19 0.00
33_I 40_A 0.80 0.19 0.00
60_V 79_K 0.80 0.19 0.00
51_S 181_I 0.79 0.19 0.00
62_Y 118_T 0.79 0.19 0.00
23_V 134_I 0.79 0.19 0.00
7_G 95_R 0.79 0.19 0.00
26_R 114_D 0.79 0.19 0.00
65_A 185_E 0.79 0.19 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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