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OPENSEQ.org
cI_BctermL_G
Genes: A B A+B
Length: 170 100 268
Sequences: 2039 1241 1723
Seq/Len: 11.99 12.41 6.43
MirrorTree (Pazo et al. 2001) 0.81
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 5.18
2 0.00 0.00 5.26
5 0.00 0.00 5.83
10 0.00 0.00 6.05
20 0.00 0.00 6.14
100 0.01 0.01 6.25
∞ 0.01 0.02 6.38
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
153_A 81_L 1.27 0.97 0.46
19_I 7_G 1.14 0.93 0.34
40_T 17_L 1.10 0.91 0.32
56_V 92_I 1.03 0.87 0.26
126_M 83_L 1.03 0.87 0.26
116_L 60_V 1.02 0.86 0.25
134_R 17_L 1.00 0.85 0.23
149_R 40_N 0.99 0.84 0.23
160_V 16_V 0.97 0.83 0.21
16_V 59_Q 0.96 0.82 0.21
9_T 81_L 0.95 0.81 0.20
10_H 18_G 0.95 0.81 0.20
3_H 6_H 0.95 0.81 0.20
131_V 47_V 0.95 0.81 0.20
34_G 98_M 0.94 0.80 0.19
149_R 45_A 0.94 0.80 0.19
137_G 29_L 0.93 0.79 0.19
33_Q 98_M 0.93 0.78 0.18
3_H 56_T 0.92 0.78 0.18
50_L 38_M 0.92 0.77 0.18
54_S 40_N 0.92 0.77 0.18
141_L 64_L 0.90 0.75 0.17
103_D 64_L 0.90 0.75 0.17
53_T 10_L 0.87 0.72 0.15
7_G 44_L 0.86 0.71 0.14
58_A 41_A 0.85 0.69 0.14
63_L 99_R 0.84 0.68 0.14
65_A 7_G 0.84 0.67 0.13
95_A 31_M 0.84 0.67 0.13
157_I 35_L 0.83 0.66 0.13
153_A 31_M 0.82 0.66 0.12
24_V 34_G 0.82 0.65 0.12
24_V 21_G 0.82 0.65 0.12
8_V 98_M 0.82 0.65 0.12
26_A 12_A 0.81 0.65 0.12
149_R 93_D 0.81 0.64 0.12
7_G 98_M 0.80 0.63 0.12
101_L 31_M 0.80 0.62 0.11
119_R 50_G 0.80 0.62 0.11
4_A 41_A 0.79 0.62 0.11
139_G 16_V 0.79 0.60 0.11
128_I 80_L 0.79 0.60 0.11
78_S 73_A 0.79 0.60 0.11
53_T 38_M 0.78 0.60 0.11
62_I 49_A 0.78 0.60 0.11
15_I 65_A 0.77 0.59 0.10
158_G 13_I 0.77 0.58 0.10
124_S 83_L 0.77 0.58 0.10
70_L 100_G 0.77 0.58 0.10
130_A 99_R 0.77 0.57 0.10
6_K 99_R 0.75 0.56 0.09
24_V 73_A 0.75 0.55 0.09
141_L 98_M 0.75 0.55 0.09
60_V 60_V 0.75 0.55 0.09
56_V 90_L 0.74 0.54 0.09
114_A 42_S 0.74 0.54 0.09
155_M 25_R 0.74 0.53 0.09
135_F 13_I 0.74 0.53 0.09
71_G 75_I 0.73 0.53 0.09
94_N 65_A 0.73 0.53 0.09
137_G 66_I 0.73 0.52 0.09
28_I 46_F 0.73 0.52 0.08
145_N 83_L 0.73 0.52 0.08
129_P 8_L 0.73 0.52 0.08
18_L 39_I 0.72 0.51 0.08
2_A 28_L 0.72 0.51 0.08
166_L 50_G 0.72 0.51 0.08
138_K 46_F 0.72 0.51 0.08
72_K 11_A 0.72 0.50 0.08
96_W 51_S 0.71 0.50 0.08
122_L 20_T 0.71 0.50 0.08
113_I 8_L 0.71 0.50 0.08
13_P 71_A 0.71 0.50 0.08
25_G 21_G 0.71 0.50 0.08
46_S 83_L 0.71 0.50 0.08
70_L 26_R 0.71 0.49 0.08
31_P 46_F 0.71 0.49 0.08
18_L 63_I 0.71 0.49 0.08
141_L 63_I 0.70 0.48 0.07
12_L 81_L 0.70 0.48 0.07
123_N 73_A 0.70 0.47 0.07
77_T 26_R 0.70 0.47 0.07
156_S 32_L 0.70 0.47 0.07
57_V 35_L 0.70 0.47 0.07
61_G 87_R 0.70 0.47 0.07
48_L 79_L 0.70 0.47 0.07
164_A 9_I 0.69 0.47 0.07
119_R 94_S 0.69 0.47 0.07
125_M 60_V 0.69 0.47 0.07
113_I 98_M 0.69 0.46 0.07
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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