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OPENSEQ.org
GI
Genes: A B A+B
Length: 140 121 256
Sequences: 1248 694 538
Seq/Len: 8.91 5.74 2.1
MirrorTree (Pazo et al. 2001) 0.65
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.08 0.00 0.21
2 0.09 0.00 2.02
5 0.09 0.00 2.03
10 0.09 0.00 2.05
20 0.09 0.00 2.06
100 0.09 0.00 2.08
∞ 0.13 0.04 2.12
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
54_D 35_R 1.64 0.95 0.75
44_S 13_M 1.32 0.83 0.48
31_M 48_W 1.31 0.83 0.47
8_T 64_P 1.28 0.81 0.45
32_G 84_W 1.24 0.78 0.41
93_R 23_G 1.20 0.74 0.36
51_G 31_L 1.17 0.71 0.34
25_L 95_R 1.11 0.66 0.29
65_T 83_R 1.08 0.63 0.26
54_D 94_L 1.08 0.62 0.26
93_R 19_F 1.07 0.61 0.25
50_E 82_I 1.06 0.60 0.24
3_R 76_A 1.02 0.56 0.21
26_V 53_Q 1.00 0.54 0.20
8_T 20_A 1.00 0.54 0.20
65_T 96_A 0.98 0.52 0.19
57_K 38_G 0.97 0.50 0.18
19_L 69_S 0.96 0.49 0.17
97_Q 7_M 0.96 0.49 0.17
44_S 26_V 0.96 0.49 0.17
124_G 16_L 0.93 0.46 0.15
42_V 97_L 0.93 0.46 0.15
49_L 55_V 0.92 0.45 0.15
20_G 76_A 0.92 0.45 0.15
57_K 5_A 0.92 0.44 0.15
119_S 97_L 0.92 0.44 0.15
52_A 99_V 0.91 0.44 0.14
37_A 64_P 0.91 0.44 0.14
51_G 34_T 0.91 0.44 0.14
45_D 52_N 0.91 0.44 0.14
48_A 63_W 0.91 0.43 0.14
108_S 34_T 0.91 0.43 0.14
5_R 69_S 0.90 0.43 0.14
24_S 45_L 0.90 0.42 0.14
68_Q 12_V 0.89 0.41 0.13
30_L 115_R 0.88 0.41 0.13
55_M 10_I 0.88 0.41 0.13
137_I 119_T 0.88 0.40 0.12
41_K 82_I 0.88 0.40 0.12
30_L 26_V 0.87 0.40 0.12
129_N 86_G 0.87 0.39 0.12
103_D 58_R 0.86 0.39 0.12
16_I 8_T 0.86 0.39 0.12
16_I 71_T 0.86 0.39 0.12
26_V 17_A 0.86 0.38 0.12
55_M 94_L 0.85 0.38 0.11
81_P 48_W 0.84 0.37 0.11
122_P 99_V 0.84 0.36 0.11
65_T 93_Q 0.84 0.36 0.10
80_E 80_W 0.83 0.35 0.10
4_Q 59_L 0.83 0.35 0.10
60_N 49_L 0.83 0.35 0.10
86_Y 24_L 0.82 0.34 0.10
119_S 64_P 0.82 0.34 0.10
49_L 61_N 0.82 0.34 0.10
12_I 50_A 0.81 0.34 0.10
102_S 21_L 0.81 0.33 0.09
55_M 13_M 0.81 0.33 0.09
61_S 118_V 0.80 0.32 0.09
118_F 99_V 0.80 0.32 0.09
58_L 14_V 0.80 0.32 0.09
66_T 77_G 0.79 0.30 0.08
57_K 33_Q 0.78 0.30 0.08
17_V 27_M 0.78 0.30 0.08
120_L 30_T 0.78 0.30 0.08
16_I 112_S 0.78 0.30 0.08
30_L 67_S 0.77 0.29 0.08
63_Y 56_Q 0.77 0.29 0.08
62_R 14_V 0.77 0.29 0.08
118_F 29_A 0.77 0.29 0.08
78_S 118_V 0.76 0.28 0.07
12_I 117_Y 0.76 0.28 0.07
74_V 104_A 0.76 0.28 0.07
107_L 22_A 0.76 0.28 0.07
89_G 71_T 0.76 0.28 0.07
106_L 7_M 0.75 0.27 0.07
112_H 72_T 0.75 0.27 0.07
80_E 100_E 0.75 0.27 0.07
19_L 75_A 0.74 0.27 0.07
130_D 96_A 0.74 0.27 0.07
89_G 7_M 0.74 0.26 0.07
65_T 12_V 0.74 0.26 0.07
117_I 36_Q 0.73 0.25 0.06
67_E 70_E 0.73 0.25 0.06
22_L 112_S 0.73 0.25 0.06
92_I 18_V 0.73 0.25 0.06
136_T 117_Y 0.73 0.25 0.06
24_S 57_L 0.72 0.25 0.06
101_G 114_L 0.72 0.25 0.06
66_T 17_A 0.72 0.25 0.06
67_E 60_E 0.72 0.25 0.06
66_T 40_M 0.72 0.25 0.06
56_Y 18_V 0.71 0.24 0.06
37_A 70_E 0.71 0.24 0.06
38_D 14_V 0.71 0.24 0.06
33_N 29_A 0.71 0.24 0.06
134_N 12_V 0.71 0.24 0.06
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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