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OPENSEQ.org
cI_6_20_cI_9_10_tt
Genes: A B A+B
Length: 181 182 328
Sequences: 1141 961 607
Seq/Len: 6.3 5.28 1.85
MirrorTree (Pazo et al. 2001) 0.73
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 0.01 0.05
2 0.01 0.05 0.09
5 0.01 0.05 0.53
10 0.02 0.06 1.42
20 0.02 0.06 1.47
100 0.03 0.07 1.52
∞ 0.08 0.11 1.67
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
57_R 24_V 1.50 0.90 0.35
149_Y 120_E 1.48 0.89 0.34
135_V 124_Y 1.48 0.89 0.33
149_Y 122_A 1.43 0.87 0.30
125_Q 97_R 1.28 0.77 0.20
141_P 64_P 1.24 0.74 0.18
58_N 31_V 1.23 0.73 0.18
63_F 28_D 1.23 0.73 0.17
81_A 153_T 1.23 0.73 0.17
117_M 99_I 1.17 0.67 0.14
150_A 123_D 1.15 0.65 0.14
113_S 35_P 1.10 0.60 0.11
86_K 70_V 1.09 0.60 0.11
51_M 9_S 1.07 0.58 0.10
143_R 46_H 1.06 0.57 0.10
137_V 16_Y 1.06 0.57 0.10
113_S 96_L 1.05 0.55 0.10
129_S 67_A 1.03 0.54 0.09
23_T 113_I 1.01 0.51 0.09
88_M 64_P 1.01 0.51 0.09
152_M 30_P 1.01 0.51 0.08
77_V 62_A 0.99 0.49 0.08
143_R 37_F 0.98 0.48 0.08
71_S 128_D 0.96 0.46 0.07
123_I 116_G 0.96 0.46 0.07
119_N 97_R 0.95 0.45 0.07
19_I 134_E 0.94 0.43 0.07
93_R 17_L 0.93 0.43 0.06
145_E 124_Y 0.93 0.42 0.06
88_M 129_L 0.93 0.42 0.06
122_A 49_G 0.92 0.41 0.06
57_R 60_A 0.92 0.41 0.06
41_F 68_I 0.92 0.41 0.06
30_W 93_I 0.92 0.41 0.06
118_F 44_T 0.92 0.41 0.06
151_V 114_V 0.91 0.40 0.06
27_L 117_Y 0.91 0.40 0.06
61_A 5_A 0.91 0.40 0.06
32_R 112_A 0.91 0.40 0.06
70_A 120_E 0.91 0.40 0.06
156_K 125_E 0.89 0.39 0.05
85_S 10_L 0.89 0.38 0.05
12_Q 7_A 0.88 0.37 0.05
98_Q 113_I 0.88 0.37 0.05
36_L 12_I 0.87 0.36 0.05
18_G 71_E 0.87 0.36 0.05
118_F 37_F 0.87 0.36 0.05
117_M 65_A 0.86 0.35 0.05
122_A 133_K 0.86 0.35 0.05
97_E 5_A 0.86 0.35 0.05
120_N 41_H 0.86 0.35 0.05
153_Q 124_Y 0.86 0.35 0.05
122_A 41_H 0.85 0.34 0.04
13_E 18_F 0.85 0.34 0.04
117_M 97_R 0.85 0.34 0.04
93_R 49_G 0.84 0.33 0.04
70_A 2_T 0.84 0.33 0.04
132_P 109_P 0.83 0.33 0.04
156_K 128_D 0.83 0.32 0.04
155_Q 91_Y 0.83 0.32 0.04
93_R 60_A 0.83 0.32 0.04
54_T 12_I 0.83 0.32 0.04
150_A 50_L 0.82 0.31 0.04
128_D 126_Y 0.82 0.31 0.04
118_F 47_P 0.81 0.31 0.04
77_V 34_K 0.81 0.31 0.04
158_V 134_E 0.81 0.30 0.04
131_V 71_E 0.81 0.30 0.04
66_E 28_D 0.81 0.30 0.04
60_L 12_I 0.81 0.30 0.04
34_N 94_N 0.81 0.30 0.04
103_K 12_I 0.81 0.30 0.04
107_S 45_R 0.81 0.30 0.04
107_S 18_F 0.80 0.30 0.04
53_S 33_L 0.80 0.29 0.04
143_R 33_L 0.80 0.29 0.04
27_L 17_L 0.80 0.29 0.04
146_A 37_F 0.80 0.29 0.04
97_E 132_G 0.80 0.29 0.04
151_V 52_K 0.80 0.29 0.04
61_A 28_D 0.80 0.29 0.04
75_A 19_S 0.79 0.29 0.04
95_V 91_Y 0.79 0.29 0.04
126_N 106_E 0.79 0.29 0.04
113_S 85_E 0.79 0.29 0.04
27_L 125_E 0.79 0.29 0.04
130_V 103_L 0.79 0.28 0.04
119_N 55_G 0.79 0.28 0.03
117_M 85_E 0.78 0.28 0.03
95_V 119_F 0.78 0.28 0.03
154_L 120_E 0.78 0.28 0.03
110_A 6_L 0.78 0.28 0.03
20_L 7_A 0.78 0.28 0.03
148_I 112_A 0.78 0.28 0.03
141_P 92_E 0.78 0.27 0.03
47_A 86_R 0.78 0.27 0.03
70_A 4_K 0.77 0.27 0.03
60_L 15_K 0.77 0.27 0.03
39_A 91_Y 0.77 0.27 0.03
150_A 31_V 0.77 0.27 0.03
93_R 51_E 0.77 0.27 0.03
117_M 111_G 0.77 0.27 0.03
120_N 85_E 0.77 0.27 0.03
18_G 67_A 0.77 0.26 0.03
147_L 120_E 0.77 0.26 0.03
57_R 6_L 0.76 0.26 0.03
110_A 121_M 0.76 0.26 0.03
125_Q 49_G 0.76 0.26 0.03
107_S 113_I 0.76 0.26 0.03
60_L 25_P 0.75 0.25 0.03
66_E 5_A 0.75 0.25 0.03
123_I 105_E 0.75 0.25 0.03
131_V 40_R 0.75 0.25 0.03
44_A 9_S 0.75 0.25 0.03
92_M 113_I 0.75 0.25 0.03
137_V 20_K 0.75 0.25 0.03
86_K 54_I 0.75 0.25 0.03
118_F 65_A 0.74 0.25 0.03
20_L 48_N 0.74 0.24 0.03
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
4979 0.57 cI_6_20_cI_9_60_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
4978 0.56 cI_6_60_cI_9_60_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4977 0.56 cI_6_40_cI_9_60_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.90 Done - Shared
4976 2.08 cI_6_40_cI_9_20_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.45 Done - Shared
4975 1.47 cI_6_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.64 Done - Shared
4974 1.46 cI_6_20_cI_9_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.63 Done - Shared
4972 1.85 cI_6_20_cI_9_10_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
4971 2.05 cI_6_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
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