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OPENSEQ.org
cI_G_cIII_isp_10
Genes: A B A+B
Length: 100 190 286
Sequences: 1241 1442 434
Seq/Len: 12.41 7.59 1.52
MirrorTree (Pazo et al. 2001) 0.63
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 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.02
100 0.01 0.01 0.10
∞ 0.02 0.02 1.50
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
19_L 122_A 1.24 0.69 0.01
17_L 96_Q 1.23 0.67 0.01
98_M 175_H 1.18 0.63 0.01
46_F 41_Q 1.16 0.60 0.01
2_I 48_V 1.15 0.60 0.01
75_I 56_V 1.15 0.60 0.01
20_T 79_R 1.15 0.59 0.01
19_L 163_G 1.15 0.59 0.01
84_H 47_D 1.13 0.58 0.01
54_G 184_D 1.12 0.57 0.01
56_T 93_D 1.12 0.57 0.01
60_V 74_K 1.10 0.55 0.01
88_Q 168_G 1.09 0.54 0.01
62_Y 24_A 1.09 0.53 0.01
30_F 184_D 1.06 0.51 0.01
80_L 98_I 1.05 0.50 0.01
98_M 153_P 1.04 0.48 0.00
80_L 62_E 1.02 0.47 0.00
38_M 23_T 1.01 0.46 0.00
42_S 25_G 1.00 0.45 0.00
46_F 66_Q 0.99 0.44 0.00
62_Y 138_V 0.99 0.44 0.00
17_L 186_T 0.99 0.44 0.00
78_A 174_L 0.97 0.42 0.00
91_N 25_G 0.95 0.39 0.00
10_L 140_I 0.94 0.39 0.00
45_A 173_N 0.94 0.39 0.00
75_I 131_V 0.94 0.38 0.00
38_M 34_A 0.94 0.38 0.00
50_G 187_I 0.93 0.38 0.00
45_A 165_I 0.92 0.37 0.00
23_V 151_F 0.92 0.37 0.00
10_L 66_Q 0.92 0.36 0.00
31_M 84_D 0.92 0.36 0.00
93_D 158_H 0.91 0.36 0.00
56_T 74_K 0.91 0.35 0.00
11_A 115_E 0.90 0.35 0.00
1_M 172_Q 0.90 0.34 0.00
93_D 13_A 0.90 0.34 0.00
3_P 127_V 0.89 0.33 0.00
20_T 65_T 0.88 0.33 0.00
61_M 27_G 0.88 0.33 0.00
75_I 187_I 0.88 0.33 0.00
75_I 35_A 0.88 0.33 0.00
23_V 131_V 0.87 0.32 0.00
54_G 40_N 0.87 0.32 0.00
41_A 96_Q 0.87 0.32 0.00
52_Y 189_L 0.87 0.32 0.00
28_L 159_Y 0.86 0.31 0.00
35_L 101_S 0.86 0.31 0.00
54_G 38_L 0.86 0.31 0.00
71_A 73_G 0.86 0.31 0.00
28_L 181_F 0.85 0.30 0.00
44_L 146_D 0.85 0.30 0.00
99_R 76_V 0.84 0.30 0.00
41_A 51_L 0.84 0.29 0.00
49_A 160_D 0.84 0.29 0.00
18_G 137_C 0.83 0.29 0.00
1_M 25_G 0.83 0.28 0.00
18_G 134_H 0.83 0.28 0.00
67_S 149_G 0.82 0.28 0.00
33_I 33_A 0.82 0.28 0.00
8_L 32_G 0.82 0.28 0.00
75_I 65_T 0.82 0.28 0.00
4_L 26_A 0.82 0.28 0.00
2_I 103_Q 0.82 0.27 0.00
11_A 32_G 0.82 0.27 0.00
6_H 143_G 0.81 0.27 0.00
29_L 78_I 0.81 0.27 0.00
41_A 84_D 0.81 0.27 0.00
65_A 115_E 0.81 0.27 0.00
99_R 23_T 0.81 0.27 0.00
18_G 132_C 0.81 0.27 0.00
2_I 128_M 0.81 0.26 0.00
98_M 9_G 0.81 0.26 0.00
5_Q 29_V 0.81 0.26 0.00
96_S 97_L 0.80 0.26 0.00
84_H 39_V 0.80 0.26 0.00
46_F 71_W 0.80 0.26 0.00
1_M 114_D 0.80 0.26 0.00
92_I 64_G 0.80 0.26 0.00
88_Q 114_D 0.79 0.25 0.00
46_F 38_L 0.79 0.25 0.00
8_L 31_A 0.79 0.25 0.00
17_L 60_G 0.79 0.25 0.00
60_V 40_N 0.78 0.24 0.00
51_S 189_L 0.78 0.24 0.00
46_F 163_G 0.78 0.24 0.00
59_Q 165_I 0.78 0.24 0.00
18_G 154_C 0.78 0.24 0.00
63_I 128_M 0.77 0.24 0.00
78_A 157_S 0.77 0.24 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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