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OPENSEQ.org
BC noSS jack
Genes: A B A+B
Length: 164 226 370
Sequences: 150 272 144
Seq/Len: 0.91 1.2 0.39
MirrorTree (Pazo et al. 2001) 0.55
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 0.04 0.37
2 0.00 0.04 0.37
5 0.00 0.04 0.37
10 0.00 0.04 0.37
20 0.00 0.04 0.37
100 0.00 0.04 0.37
∞ 0.00 0.04 0.37
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
163_I 159_F 1.78 0.69 0.01
87_N 61_S 1.41 0.42 0.00
87_N 103_N 1.38 0.41 0.00
98_G 73_S 1.38 0.40 0.00
92_A 145_A 1.27 0.33 0.00
66_Q 12_P 1.26 0.33 0.00
108_S 153_V 1.25 0.32 0.00
162_T 139_A 1.22 0.30 0.00
87_N 144_V 1.14 0.25 0.00
72_N 14_G 1.14 0.25 0.00
87_N 154_S 1.12 0.24 0.00
92_A 155_L 1.11 0.24 0.00
163_I 16_V 1.10 0.23 0.00
117_D 123_A 1.09 0.23 0.00
108_S 20_V 1.08 0.22 0.00
143_V 110_S 1.08 0.22 0.00
76_I 109_N 1.06 0.21 0.00
106_V 159_F 1.06 0.21 0.00
131_T 150_T 1.05 0.21 0.00
79_V 71_I 1.05 0.21 0.00
163_I 150_T 1.05 0.20 0.00
123_T 109_N 1.02 0.19 0.00
156_A 88_Y 1.01 0.19 0.00
95_I 110_S 1.01 0.19 0.00
137_T 136_I 1.00 0.18 0.00
90_I 41_G 0.99 0.18 0.00
161_V 71_I 0.99 0.18 0.00
92_A 90_E 0.98 0.17 0.00
69_A 23_T 0.96 0.17 0.00
90_I 177_N 0.96 0.17 0.00
130_V 39_N 0.95 0.16 0.00
92_A 72_T 0.95 0.16 0.00
98_G 186_N 0.93 0.16 0.00
115_L 93_D 0.93 0.15 0.00
44_S 123_A 0.93 0.15 0.00
95_I 35_K 0.92 0.15 0.00
95_I 44_G 0.92 0.15 0.00
97_T 91_S 0.92 0.15 0.00
59_L 118_V 0.92 0.15 0.00
156_A 159_F 0.92 0.15 0.00
82_S 74_S 0.91 0.15 0.00
60_N 136_I 0.90 0.15 0.00
93_V 100_G 0.90 0.14 0.00
56_D 110_S 0.90 0.14 0.00
126_S 134_L 0.90 0.14 0.00
41_G 34_T 0.89 0.14 0.00
111_N 101_T 0.89 0.14 0.00
114_L 45_S 0.88 0.14 0.00
46_A 134_L 0.87 0.13 0.00
160_G 172_Q 0.87 0.13 0.00
145_V 109_N 0.87 0.13 0.00
130_V 20_V 0.87 0.13 0.00
148_S 64_Q 0.86 0.13 0.00
143_V 148_S 0.86 0.13 0.00
126_S 87_I 0.85 0.13 0.00
161_V 74_S 0.85 0.13 0.00
162_T 137_V 0.85 0.13 0.00
46_A 104_N 0.85 0.13 0.00
106_V 77_D 0.85 0.13 0.00
128_Q 136_I 0.85 0.13 0.00
143_V 12_P 0.84 0.13 0.00
155_M 50_K 0.84 0.12 0.00
94_R 136_I 0.84 0.12 0.00
90_I 153_V 0.83 0.12 0.00
69_A 46_L 0.83 0.12 0.00
116_P 87_I 0.83 0.12 0.00
132_S 79_A 0.83 0.12 0.00
65_I 29_N 0.83 0.12 0.00
136_F 45_S 0.83 0.12 0.00
145_V 46_L 0.83 0.12 0.00
161_V 34_T 0.82 0.12 0.00
118_S 26_S 0.82 0.12 0.00
83_A 124_A 0.82 0.12 0.00
134_Q 136_I 0.82 0.12 0.00
90_I 8_P 0.81 0.12 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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