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OPENSEQ.org
cI_K_cIV_cyoc_Pdenitr
Genes: A B A+B
Length: 101 273 354
Sequences: 4825 2888 2236
Seq/Len: 47.77 10.58 6.32
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 0.00 0.10
2 0.00 0.00 1.84
5 0.01 0.00 4.17
10 0.01 0.00 4.60
20 0.02 0.00 4.76
100 0.03 0.00 5.09
∞ 0.07 0.01 5.98
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
80_I 81_V 1.03 0.86 0.04
42_A 98_V 1.02 0.86 0.04
51_S 32_V 1.02 0.86 0.04
34_M 61_V 0.99 0.83 0.04
64_M 48_P 0.96 0.82 0.04
74_A 169_K 0.94 0.79 0.03
74_A 135_F 0.94 0.79 0.03
66_V 135_F 0.90 0.75 0.03
43_V 61_V 0.87 0.71 0.03
39_M 38_I 0.86 0.71 0.03
68_T 268_I 0.84 0.68 0.02
71_A 135_F 0.83 0.66 0.02
99_M 238_Q 0.82 0.64 0.02
13_I 183_V 0.81 0.63 0.02
25_N 134_T 0.80 0.62 0.02
74_A 147_I 0.80 0.62 0.02
79_A 186_T 0.80 0.61 0.02
32_I 125_G 0.79 0.60 0.02
47_F 208_A 0.79 0.60 0.02
93_V 87_Q 0.79 0.60 0.02
74_A 6_H 0.79 0.60 0.02
31_V 150_L 0.79 0.60 0.02
62_F 80_P 0.78 0.60 0.02
38_L 135_F 0.78 0.59 0.02
23_F 208_A 0.77 0.58 0.02
44_N 237_G 0.77 0.58 0.02
74_A 170_T 0.77 0.58 0.02
81_L 111_N 0.77 0.57 0.02
55_G 237_G 0.76 0.57 0.02
98_V 70_V 0.76 0.56 0.02
31_V 196_A 0.76 0.56 0.02
25_N 5_N 0.76 0.56 0.02
80_I 23_G 0.76 0.55 0.02
85_F 108_F 0.75 0.55 0.02
89_G 113_L 0.75 0.55 0.02
13_I 180_I 0.75 0.55 0.02
80_I 25_F 0.75 0.54 0.02
18_G 158_A 0.74 0.54 0.02
92_A 162_F 0.74 0.54 0.02
38_L 103_A 0.74 0.52 0.02
99_M 36_K 0.73 0.52 0.02
80_I 180_I 0.73 0.52 0.02
55_G 182_G 0.73 0.52 0.02
69_V 146_L 0.73 0.51 0.02
62_F 99_M 0.72 0.51 0.02
93_V 21_A 0.72 0.50 0.02
93_V 37_G 0.72 0.50 0.01
63_T 103_A 0.72 0.49 0.01
64_M 87_Q 0.71 0.49 0.01
39_M 83_R 0.71 0.48 0.01
19_I 132_I 0.71 0.48 0.01
12_A 121_P 0.71 0.48 0.01
68_T 205_Y 0.70 0.48 0.01
70_A 8_Y 0.70 0.47 0.01
34_M 221_I 0.70 0.47 0.01
87_N 98_V 0.69 0.46 0.01
25_N 125_G 0.69 0.46 0.01
45_I 84_I 0.69 0.46 0.01
64_M 24_A 0.69 0.45 0.01
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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