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OPENSEQ.org
B_c
Genes: A B A+B
Length: 164 226 350
Sequences: 56 132 56
Seq/Len: 0.34 0.58 0.16
MirrorTree (Pazo et al. 2001) 0.59
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 0.01 0.00 0.15
2 0.01 0.00 0.14
5 0.01 0.00 0.14
10 0.01 0.00 0.14
20 0.01 0.00 0.14
100 0.01 0.00 0.14
∞ 0.01 0.00 0.14
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
95_I 44_G 1.55 0.30 0.00
92_A 145_A 1.52 0.28 0.00
92_A 163_A 1.45 0.26 0.00
56_D 71_I 1.39 0.23 0.00
60_N 113_N 1.39 0.23 0.00
62_S 109_N 1.37 0.22 0.00
79_V 83_A 1.36 0.22 0.00
143_V 26_S 1.35 0.21 0.00
72_N 14_G 1.29 0.19 0.00
156_A 45_S 1.29 0.19 0.00
63_A 185_N 1.28 0.19 0.00
86_N 66_D 1.24 0.17 0.00
56_D 48_N 1.22 0.17 0.00
60_N 126_Q 1.20 0.16 0.00
69_A 25_V 1.18 0.16 0.00
106_V 39_N 1.17 0.15 0.00
56_D 34_T 1.16 0.15 0.00
76_I 120_V 1.14 0.14 0.00
59_L 7_K 1.14 0.14 0.00
114_L 45_S 1.13 0.14 0.00
156_A 105_A 1.13 0.14 0.00
82_S 182_N 1.11 0.14 0.00
160_G 100_G 1.10 0.13 0.00
69_A 156_D 1.09 0.13 0.00
58_S 104_N 1.09 0.13 0.00
87_N 61_S 1.08 0.13 0.00
111_N 62_G 1.07 0.12 0.00
106_V 50_K 1.07 0.12 0.00
78_G 62_G 1.05 0.12 0.00
163_I 150_T 1.05 0.12 0.00
95_I 91_S 1.05 0.12 0.00
66_Q 10_P 1.04 0.12 0.00
106_V 73_S 1.04 0.12 0.00
117_D 59_A 1.04 0.12 0.00
106_V 188_S 1.04 0.12 0.00
69_A 12_P 1.03 0.12 0.00
97_T 138_T 1.03 0.12 0.00
120_S 79_A 1.03 0.12 0.00
77_L 36_T 1.02 0.11 0.00
94_R 70_A 1.02 0.11 0.00
90_I 39_N 1.02 0.11 0.00
56_D 110_S 1.02 0.11 0.00
122_S 175_V 1.02 0.11 0.00
63_A 149_N 1.01 0.11 0.00
64_A 95_K 1.00 0.11 0.00
68_S 78_A 1.00 0.11 0.00
143_V 175_V 0.99 0.11 0.00
83_A 149_N 0.99 0.11 0.00
101_S 77_D 0.98 0.11 0.00
108_S 79_A 0.98 0.10 0.00
70_F 189_G 0.98 0.10 0.00
161_V 25_V 0.97 0.10 0.00
122_S 149_N 0.97 0.10 0.00
92_A 8_P 0.96 0.10 0.00
76_I 88_Y 0.95 0.10 0.00
122_S 147_A 0.94 0.10 0.00
98_G 80_T 0.94 0.10 0.00
107_L 52_N 0.94 0.10 0.00
89_M 10_P 0.94 0.10 0.00
62_S 7_K 0.94 0.10 0.00
63_A 7_K 0.94 0.10 0.00
59_L 100_G 0.93 0.10 0.00
49_Q 183_S 0.93 0.09 0.00
123_T 145_A 0.92 0.09 0.00
72_N 154_S 0.92 0.09 0.00
109_Q 64_Q 0.92 0.09 0.00
92_A 7_K 0.92 0.09 0.00
155_M 54_G 0.92 0.09 0.00
108_S 91_S 0.92 0.09 0.00
95_I 83_A 0.92 0.09 0.00
98_G 39_N 0.91 0.09 0.00
108_S 75_A 0.91 0.09 0.00
124_T 105_A 0.91 0.09 0.00
93_V 17_A 0.91 0.09 0.00
128_Q 136_I 0.91 0.09 0.00
108_S 55_A 0.91 0.09 0.00
108_S 76_G 0.91 0.09 0.00
119_R 124_A 0.91 0.09 0.00
108_S 118_V 0.91 0.09 0.00
107_L 131_K 0.91 0.09 0.00
36_A 28_D 0.90 0.09 0.00
162_T 139_A 0.90 0.09 0.00
98_G 44_G 0.90 0.09 0.00
134_Q 136_I 0.90 0.09 0.00
32_I 16_V 0.90 0.09 0.00
39_L 88_Y 0.89 0.09 0.00
123_T 110_S 0.89 0.09 0.00
133_D 22_D 0.88 0.09 0.00
122_S 160_L 0.88 0.09 0.00
155_M 50_K 0.88 0.09 0.00
155_M 122_V 0.88 0.09 0.00
68_S 91_S 0.88 0.09 0.00
161_V 110_S 0.88 0.09 0.00
44_S 175_V 0.88 0.09 0.00
74_N 114_S 0.88 0.09 0.00
107_L 192_G 0.88 0.09 0.00
45_D 126_Q 0.87 0.08 0.00
96_S 73_S 0.87 0.08 0.00
132_S 62_G 0.87 0.08 0.00
101_S 50_K 0.87 0.08 0.00
63_A 126_Q 0.87 0.08 0.00
79_V 19_A 0.87 0.08 0.00
96_S 147_A 0.86 0.08 0.00
89_M 111_A 0.86 0.08 0.00
145_V 6_W 0.86 0.08 0.00
92_A 110_S 0.86 0.08 0.00
47_L 164_S 0.86 0.08 0.00
55_V 20_V 0.86 0.08 0.00
162_T 137_V 0.86 0.08 0.00
142_V 105_A 0.86 0.08 0.00
55_V 81_V 0.85 0.08 0.00
126_S 47_S 0.85 0.08 0.00
74_N 97_T 0.85 0.08 0.00
35_R 113_N 0.85 0.08 0.00
106_V 37_L 0.84 0.08 0.00
156_A 66_D 0.84 0.08 0.00
78_G 114_S 0.84 0.08 0.00
69_A 185_N 0.84 0.08 0.00
53_G 26_S 0.84 0.08 0.00
102_V 42_A 0.84 0.08 0.00
62_S 5_K 0.83 0.08 0.00
56_D 109_N 0.83 0.08 0.00
72_N 26_S 0.83 0.08 0.00
73_G 22_D 0.83 0.08 0.00
40_G 119_G 0.83 0.08 0.00
64_A 28_D 0.82 0.08 0.00
102_V 183_S 0.82 0.08 0.00
47_L 111_A 0.82 0.08 0.00
47_L 31_F 0.82 0.08 0.00
69_A 111_A 0.82 0.07 0.00
68_S 75_A 0.82 0.07 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)
ID Seq/Len Name Options I_Prob Status
8301 0.39 BC noSS jack Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.01 Done
4709 0.16 B_c Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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