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OPENSEQ.org
cI_6_40_cI_9_40_tt
Genes: A B A+B
Length: 181 182 327
Sequences: 1163 683 480
Seq/Len: 6.43 3.75 1.47
MirrorTree (Pazo et al. 2001) 0.82
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 0.01
2 0.01 0.00 0.04
5 0.01 0.00 0.15
10 0.02 0.00 1.16
20 0.02 0.00 1.20
100 0.03 0.00 1.22
∞ 0.08 0.01 1.32
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
18_G 67_A 1.73 0.94 0.64
135_V 124_Y 1.65 0.92 0.57
47_A 86_R 1.59 0.90 0.53
80_V 71_E 1.41 0.81 0.37
110_A 100_F 1.40 0.80 0.35
70_A 55_G 1.39 0.79 0.35
63_F 28_D 1.38 0.79 0.35
77_V 62_A 1.34 0.76 0.31
149_Y 122_A 1.33 0.75 0.31
34_N 74_E 1.26 0.69 0.25
78_M 121_M 1.21 0.65 0.22
118_F 37_F 1.20 0.64 0.21
71_S 128_D 1.17 0.61 0.19
158_V 106_E 1.16 0.60 0.19
146_A 37_F 1.15 0.59 0.18
40_T 91_Y 1.13 0.57 0.17
42_G 86_R 1.10 0.54 0.15
130_V 10_L 1.09 0.53 0.15
120_N 46_H 1.09 0.53 0.15
103_K 7_A 1.08 0.52 0.14
107_S 18_F 1.08 0.51 0.14
143_R 97_R 1.08 0.51 0.14
24_L 7_A 1.06 0.49 0.13
144_P 97_R 1.06 0.49 0.13
110_A 73_A 1.06 0.49 0.13
101_D 31_V 1.03 0.47 0.12
118_F 140_V 1.03 0.47 0.12
128_D 126_Y 1.02 0.45 0.11
95_V 76_D 1.02 0.45 0.11
70_A 86_R 1.01 0.45 0.11
40_T 86_R 1.01 0.45 0.11
95_V 91_Y 1.00 0.44 0.10
67_V 54_I 1.00 0.44 0.10
130_V 67_A 1.00 0.43 0.10
35_S 106_E 0.99 0.43 0.10
150_A 52_K 0.99 0.42 0.10
145_E 151_K 0.98 0.41 0.10
83_R 75_N 0.98 0.41 0.10
148_I 20_K 0.98 0.41 0.09
103_K 122_A 0.97 0.40 0.09
68_F 86_R 0.96 0.40 0.09
104_W 58_L 0.96 0.40 0.09
101_D 77_P 0.96 0.39 0.09
152_M 129_L 0.96 0.39 0.09
71_S 122_A 0.96 0.39 0.09
103_K 106_E 0.95 0.39 0.09
22_T 130_V 0.94 0.38 0.08
44_A 69_Y 0.94 0.38 0.08
56_A 153_T 0.94 0.37 0.08
156_K 125_E 0.93 0.37 0.08
157_K 100_F 0.93 0.37 0.08
130_V 15_K 0.93 0.36 0.08
125_Q 97_R 0.93 0.36 0.08
138_P 137_L 0.92 0.35 0.07
61_A 99_I 0.91 0.35 0.07
112_A 29_A 0.91 0.35 0.07
78_M 11_G 0.91 0.34 0.07
120_N 85_E 0.91 0.34 0.07
145_E 22_V 0.91 0.34 0.07
58_N 30_P 0.91 0.34 0.07
113_S 96_L 0.90 0.34 0.07
123_I 55_G 0.90 0.34 0.07
84_L 12_I 0.90 0.34 0.07
83_R 82_S 0.90 0.34 0.07
151_V 132_G 0.90 0.33 0.07
34_N 94_N 0.90 0.33 0.07
107_S 51_E 0.89 0.33 0.07
26_K 131_Y 0.89 0.33 0.07
125_Q 147_R 0.89 0.33 0.07
43_L 55_G 0.88 0.32 0.06
85_S 60_A 0.88 0.32 0.06
31_G 72_P 0.88 0.32 0.06
131_V 85_E 0.88 0.32 0.06
155_Q 19_S 0.87 0.31 0.06
36_L 35_P 0.87 0.31 0.06
60_L 25_P 0.87 0.31 0.06
67_V 130_V 0.87 0.31 0.06
26_K 7_A 0.87 0.31 0.06
101_D 47_P 0.86 0.30 0.06
85_S 41_H 0.86 0.30 0.06
43_L 86_R 0.86 0.30 0.06
52_A 47_P 0.86 0.30 0.06
58_N 31_V 0.86 0.30 0.06
19_I 134_E 0.85 0.30 0.06
94_R 9_S 0.85 0.30 0.06
58_N 100_F 0.85 0.29 0.06
80_V 96_L 0.85 0.29 0.06
104_W 151_K 0.84 0.29 0.05
159_R 73_A 0.84 0.29 0.05
74_Q 116_G 0.84 0.28 0.05
103_K 12_I 0.84 0.28 0.05
70_A 70_V 0.84 0.28 0.05
157_K 163_V 0.84 0.28 0.05
24_L 134_E 0.84 0.28 0.05
27_L 73_A 0.84 0.28 0.05
130_V 54_I 0.84 0.28 0.05
107_S 128_D 0.83 0.28 0.05
110_A 103_L 0.83 0.28 0.05
108_M 54_I 0.83 0.28 0.05
24_L 62_A 0.83 0.28 0.05
61_A 5_A 0.83 0.28 0.05
44_A 52_K 0.83 0.28 0.05
107_S 130_V 0.82 0.27 0.05
114_S 97_R 0.82 0.27 0.05
120_N 60_A 0.82 0.27 0.05
84_L 86_R 0.82 0.27 0.05
93_R 15_K 0.81 0.26 0.05
118_F 41_H 0.81 0.26 0.04
74_Q 73_A 0.81 0.26 0.04
33_S 10_L 0.80 0.26 0.04
160_G 20_K 0.80 0.25 0.04
37_W 14_L 0.80 0.25 0.04
116_G 93_I 0.80 0.25 0.04
147_L 2_T 0.80 0.25 0.04
129_S 113_I 0.80 0.25 0.04
107_S 21_P 0.79 0.25 0.04
113_S 35_P 0.79 0.25 0.04
33_S 121_M 0.79 0.25 0.04
36_L 128_D 0.79 0.24 0.04
23_T 17_L 0.79 0.24 0.04
12_Q 7_A 0.79 0.24 0.04
58_N 37_F 0.79 0.24 0.04
107_S 154_G 0.79 0.24 0.04
93_R 45_R 0.78 0.24 0.04
155_Q 72_P 0.78 0.24 0.04
78_M 55_G 0.78 0.24 0.04
123_I 75_N 0.78 0.24 0.04
65_S 115_L 0.78 0.23 0.04
159_R 103_L 0.78 0.23 0.04
86_K 70_V 0.77 0.23 0.04
101_D 151_K 0.77 0.23 0.04
50_M 86_R 0.77 0.23 0.04
16_R 103_L 0.76 0.23 0.04
107_S 117_Y 0.76 0.23 0.04
79_I 32_A 0.76 0.23 0.04
21_F 62_A 0.76 0.22 0.04
84_L 54_I 0.76 0.22 0.04
118_F 44_T 0.76 0.22 0.04
18_G 71_E 0.76 0.22 0.04
91_V 134_E 0.76 0.22 0.04
91_V 147_R 0.76 0.22 0.04
40_T 70_V 0.75 0.22 0.04
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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