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OPENSEQ.org
cI_2_40_cI_6_40_tt
Genes: A B A+B
Length: 181 181 331
Sequences: 1903 1163 849
Seq/Len: 10.51 6.43 2.56
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 0.01 0.05
2 0.00 0.01 0.35
5 0.01 0.01 1.89
10 0.01 0.02 1.93
20 0.01 0.02 1.92
100 0.02 0.03 1.98
∞ 0.04 0.08 2.35
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_L 158_V 1.03 0.63 0.01
131_A 147_L 1.01 0.61 0.01
143_E 18_G 0.95 0.54 0.01
77_K 71_S 0.92 0.50 0.01
64_A 107_S 0.88 0.46 0.00
154_L 94_R 0.88 0.45 0.00
59_E 85_S 0.85 0.42 0.00
47_E 26_K 0.85 0.42 0.00
133_V 33_S 0.84 0.41 0.00
87_S 137_V 0.84 0.41 0.00
120_Q 85_S 0.83 0.40 0.00
64_A 146_A 0.83 0.40 0.00
119_V 37_W 0.83 0.40 0.00
58_T 158_V 0.83 0.40 0.00
40_W 119_N 0.82 0.39 0.00
25_A 47_A 0.81 0.38 0.00
11_L 88_M 0.81 0.37 0.00
62_G 118_F 0.80 0.37 0.00
61_M 120_N 0.79 0.36 0.00
77_K 56_A 0.79 0.35 0.00
69_Y 92_M 0.77 0.33 0.00
17_K 131_V 0.77 0.33 0.00
61_M 32_R 0.76 0.32 0.00
16_A 148_I 0.76 0.32 0.00
36_Q 28_V 0.75 0.31 0.00
158_R 23_T 0.75 0.31 0.00
30_L 129_S 0.75 0.31 0.00
126_G 17_E 0.74 0.30 0.00
27_I 28_V 0.74 0.30 0.00
32_R 37_W 0.74 0.30 0.00
53_V 52_A 0.73 0.30 0.00
14_T 61_A 0.73 0.30 0.00
62_G 145_E 0.73 0.29 0.00
137_N 92_M 0.73 0.29 0.00
29_P 44_A 0.72 0.29 0.00
69_Y 137_V 0.72 0.28 0.00
89_K 48_I 0.71 0.28 0.00
40_W 127_V 0.71 0.27 0.00
41_I 32_R 0.71 0.27 0.00
11_L 75_A 0.71 0.27 0.00
86_L 85_S 0.71 0.27 0.00
104_L 38_P 0.71 0.27 0.00
4_F 107_S 0.71 0.27 0.00
49_I 150_A 0.71 0.27 0.00
26_A 137_V 0.70 0.27 0.00
80_L 104_W 0.70 0.27 0.00
65_S 151_V 0.70 0.27 0.00
29_P 48_I 0.70 0.26 0.00
65_S 123_I 0.70 0.26 0.00
70_Y 26_K 0.69 0.26 0.00
19_P 92_M 0.69 0.25 0.00
131_A 108_M 0.69 0.25 0.00
16_A 97_E 0.69 0.25 0.00
86_L 65_S 0.69 0.25 0.00
86_L 138_P 0.68 0.25 0.00
112_T 148_I 0.68 0.25 0.00
130_T 118_F 0.68 0.24 0.00
96_L 26_K 0.68 0.24 0.00
44_E 114_S 0.67 0.23 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
4936 2.84 cI_2_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4934 2.73 cI_2_10_cI_6_20_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4933 2.82 cI_2_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4932 2.56 cI_2_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
4931 2.74 cI_2_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
4930 2.9 cI_2_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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