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OPENSEQ.org
cI_5_10_cI_9_10_tt
Genes: A B A+B
Length: 207 182 344
Sequences: 1025 961 585
Seq/Len: 4.95 5.28 1.7
MirrorTree (Pazo et al. 2001) 0.93
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 0.03
2 0.00 0.05 0.06
5 0.01 0.05 0.40
10 0.01 0.06 1.28
20 0.01 0.06 1.38
100 0.02 0.07 1.40
∞ 0.06 0.11 1.50
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
154_E 85_E 1.45 0.86 0.18
109_G 22_V 1.44 0.85 0.17
144_H 47_P 1.41 0.84 0.16
31_R 7_A 1.40 0.83 0.15
103_T 19_S 1.25 0.72 0.10
154_E 96_L 1.23 0.70 0.09
124_I 134_E 1.20 0.68 0.09
36_E 8_Q 1.19 0.67 0.08
49_L 43_L 1.16 0.65 0.08
102_P 30_P 1.15 0.63 0.07
174_L 5_A 1.14 0.62 0.07
94_V 74_E 1.09 0.57 0.06
77_L 85_E 1.07 0.55 0.06
161_E 74_E 1.05 0.53 0.05
48_F 130_V 1.04 0.52 0.05
92_V 149_E 1.04 0.52 0.05
42_K 7_A 1.03 0.51 0.05
108_W 31_V 1.03 0.51 0.05
171_R 48_N 1.00 0.48 0.04
84_D 126_Y 1.00 0.47 0.04
49_L 22_V 0.99 0.46 0.04
72_Y 150_A 0.98 0.46 0.04
168_A 48_N 0.97 0.45 0.04
138_P 97_R 0.96 0.43 0.04
171_R 124_Y 0.95 0.43 0.04
73_E 6_L 0.95 0.42 0.04
27_V 15_K 0.95 0.42 0.04
15_Y 119_F 0.95 0.42 0.04
106_D 19_S 0.95 0.42 0.04
38_M 152_R 0.95 0.42 0.04
109_G 7_A 0.94 0.41 0.04
146_L 122_A 0.93 0.40 0.03
103_T 24_V 0.92 0.40 0.03
45_G 19_S 0.92 0.39 0.03
78_P 71_E 0.92 0.39 0.03
108_W 13_T 0.91 0.38 0.03
94_V 22_V 0.91 0.38 0.03
106_D 20_K 0.90 0.37 0.03
59_T 19_S 0.90 0.37 0.03
49_L 33_L 0.90 0.37 0.03
68_F 29_A 0.90 0.37 0.03
118_V 33_L 0.89 0.36 0.03
150_Y 111_G 0.89 0.36 0.03
122_F 145_P 0.89 0.36 0.03
37_E 74_E 0.88 0.35 0.03
21_G 2_T 0.88 0.35 0.03
47_N 13_T 0.88 0.35 0.03
39_A 11_G 0.87 0.34 0.03
8_E 11_G 0.87 0.34 0.03
65_P 19_S 0.87 0.34 0.03
91_R 17_L 0.87 0.34 0.03
33_R 4_K 0.86 0.33 0.03
78_P 134_E 0.85 0.33 0.03
47_N 10_L 0.85 0.33 0.03
108_W 105_E 0.85 0.32 0.03
36_E 16_Y 0.85 0.32 0.03
141_L 92_E 0.85 0.32 0.03
38_M 107_A 0.85 0.32 0.03
26_W 103_L 0.84 0.31 0.02
110_S 145_P 0.84 0.31 0.02
58_L 129_L 0.84 0.31 0.02
30_P 15_K 0.83 0.31 0.02
109_G 8_Q 0.83 0.31 0.02
84_D 138_V 0.83 0.31 0.02
108_W 25_P 0.83 0.30 0.02
51_D 39_G 0.82 0.30 0.02
121_L 148_R 0.82 0.30 0.02
11_R 10_L 0.82 0.30 0.02
8_E 142_G 0.82 0.30 0.02
86_S 7_A 0.82 0.29 0.02
62_D 131_Y 0.82 0.29 0.02
101_L 6_L 0.82 0.29 0.02
16_P 15_K 0.81 0.29 0.02
101_L 142_G 0.81 0.29 0.02
22_L 30_P 0.81 0.29 0.02
110_S 143_T 0.81 0.29 0.02
110_S 73_A 0.81 0.29 0.02
14_G 134_E 0.81 0.29 0.02
37_E 72_P 0.81 0.29 0.02
10_A 4_K 0.81 0.28 0.02
101_L 74_E 0.81 0.28 0.02
186_G 6_L 0.81 0.28 0.02
43_A 24_V 0.81 0.28 0.02
64_R 25_P 0.81 0.28 0.02
143_G 133_K 0.81 0.28 0.02
11_R 4_K 0.80 0.28 0.02
113_F 52_K 0.80 0.28 0.02
58_L 131_Y 0.80 0.28 0.02
65_P 16_Y 0.79 0.27 0.02
125_V 103_L 0.79 0.27 0.02
158_L 57_S 0.79 0.27 0.02
5_R 82_S 0.79 0.27 0.02
124_I 7_A 0.78 0.27 0.02
34_F 119_F 0.78 0.26 0.02
118_V 145_P 0.78 0.26 0.02
72_Y 135_D 0.78 0.26 0.02
39_A 2_T 0.78 0.26 0.02
90_V 10_L 0.78 0.26 0.02
34_F 31_V 0.78 0.26 0.02
140_D 75_N 0.77 0.26 0.02
119_Y 24_V 0.77 0.26 0.02
125_V 25_P 0.77 0.25 0.02
129_H 38_H 0.77 0.25 0.02
30_P 103_L 0.77 0.25 0.02
37_E 4_K 0.77 0.25 0.02
173_A 17_L 0.77 0.25 0.02
65_P 33_L 0.77 0.25 0.02
168_A 21_P 0.77 0.25 0.02
15_Y 17_L 0.77 0.25 0.02
40_H 134_E 0.76 0.25 0.02
29_L 11_G 0.76 0.24 0.02
98_D 72_P 0.76 0.24 0.02
138_P 94_N 0.76 0.24 0.02
186_G 13_T 0.76 0.24 0.02
27_V 134_E 0.76 0.24 0.02
97_E 15_K 0.75 0.24 0.02
103_T 119_F 0.75 0.24 0.02
141_L 97_R 0.75 0.24 0.02
103_T 9_S 0.75 0.24 0.02
23_G 153_T 0.75 0.24 0.02
132_L 102_G 0.75 0.24 0.02
88_F 22_V 0.75 0.24 0.02
38_M 150_A 0.75 0.24 0.02
135_I 133_K 0.75 0.24 0.02
8_E 103_L 0.75 0.24 0.02
129_H 102_G 0.75 0.24 0.02
119_Y 147_R 0.75 0.23 0.02
71_V 100_F 0.75 0.23 0.02
48_F 126_Y 0.74 0.23 0.02
72_Y 117_Y 0.74 0.23 0.02
63_P 19_S 0.74 0.23 0.02
78_P 33_L 0.74 0.23 0.02
157_T 21_P 0.74 0.23 0.02
3_L 10_L 0.74 0.23 0.02
123_G 53_C 0.74 0.23 0.02
123_G 56_C 0.74 0.23 0.02
123_G 59_C 0.74 0.23 0.02
123_G 63_C 0.74 0.23 0.02
123_G 98_C 0.74 0.23 0.02
123_G 101_C 0.74 0.23 0.02
123_G 104_C 0.74 0.23 0.02
123_G 108_C 0.74 0.23 0.02
123_G 109_P 0.74 0.23 0.02
131_D 12_I 0.74 0.23 0.02
127_E 107_A 0.74 0.23 0.02
135_I 15_K 0.74 0.23 0.02
93_Y 15_K 0.74 0.23 0.02
37_E 134_E 0.73 0.23 0.02
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
4911 1.52 cI_5_10_cI_9_4_tt2 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4910 1.59 cI_5_6_cI_2_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4909 1.52 cI_5_10_cI_9_4_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4908 1.56 cI_5_6_cI_9_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4907 1.7 cI_5_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4906 1.69 cI_5_6_cI_9_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4905 1.52 cI_5_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4904 0.04 cI_5_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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