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OPENSEQ.org
cI_6_20_cI_9_40_tt
Genes: A B A+B
Length: 181 182 328
Sequences: 1141 683 479
Seq/Len: 6.3 3.75 1.46
MirrorTree (Pazo et al. 2001) 0.83
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 1.21
100 0.03 0.00 1.23
∞ 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
135_V 124_Y 1.73 0.94 0.63
18_G 67_A 1.72 0.94 0.62
47_A 86_R 1.60 0.90 0.52
70_A 55_G 1.46 0.83 0.41
110_A 100_F 1.43 0.81 0.38
149_Y 122_A 1.39 0.79 0.34
80_V 71_E 1.37 0.78 0.33
34_N 74_E 1.30 0.72 0.27
63_F 28_D 1.30 0.72 0.27
12_Q 7_A 1.29 0.72 0.27
77_V 62_A 1.23 0.66 0.22
78_M 121_M 1.22 0.66 0.22
146_A 37_F 1.18 0.62 0.19
40_T 91_Y 1.17 0.60 0.18
158_V 106_E 1.16 0.59 0.18
118_F 37_F 1.16 0.59 0.18
71_S 128_D 1.15 0.59 0.18
144_P 97_R 1.15 0.58 0.17
128_D 126_Y 1.09 0.53 0.14
101_D 31_V 1.09 0.53 0.14
42_G 86_R 1.09 0.52 0.14
120_N 46_H 1.08 0.51 0.14
143_R 97_R 1.08 0.51 0.13
110_A 73_A 1.06 0.50 0.13
118_F 140_V 1.06 0.49 0.12
130_V 10_L 1.05 0.48 0.12
107_S 18_F 1.04 0.47 0.12
138_P 137_L 1.03 0.46 0.11
40_T 86_R 1.02 0.46 0.11
152_M 129_L 1.02 0.46 0.11
156_K 125_E 1.01 0.45 0.11
101_D 77_P 1.01 0.44 0.10
67_V 54_I 1.01 0.44 0.10
104_W 58_L 1.01 0.44 0.10
24_L 7_A 1.00 0.43 0.10
148_I 20_K 1.00 0.43 0.10
70_A 86_R 1.00 0.43 0.10
130_V 67_A 0.99 0.42 0.10
83_R 75_N 0.99 0.42 0.10
157_K 100_F 0.98 0.42 0.10
95_V 76_D 0.98 0.42 0.10
110_A 103_L 0.98 0.41 0.09
103_K 122_A 0.97 0.41 0.09
125_Q 97_R 0.97 0.41 0.09
84_L 12_I 0.96 0.40 0.09
68_F 86_R 0.96 0.39 0.09
95_V 91_Y 0.96 0.39 0.09
31_G 72_P 0.96 0.39 0.09
78_M 11_G 0.95 0.39 0.08
26_K 131_Y 0.93 0.37 0.08
103_K 106_E 0.93 0.36 0.07
120_N 85_E 0.93 0.36 0.07
71_S 122_A 0.92 0.36 0.07
93_R 15_K 0.91 0.35 0.07
83_R 82_S 0.91 0.34 0.07
131_V 85_E 0.91 0.34 0.07
145_E 22_V 0.90 0.34 0.07
125_Q 147_R 0.90 0.34 0.07
155_Q 19_S 0.90 0.34 0.07
145_E 151_K 0.90 0.34 0.07
107_S 51_E 0.90 0.34 0.07
35_S 106_E 0.90 0.34 0.07
61_A 99_I 0.90 0.33 0.07
114_S 97_R 0.90 0.33 0.07
50_M 86_R 0.89 0.33 0.06
52_A 47_P 0.89 0.33 0.06
112_A 29_A 0.89 0.32 0.06
71_S 62_A 0.89 0.32 0.06
36_L 35_P 0.88 0.32 0.06
23_T 17_L 0.88 0.32 0.06
56_A 153_T 0.88 0.32 0.06
113_S 96_L 0.88 0.32 0.06
34_N 94_N 0.88 0.32 0.06
43_L 86_R 0.88 0.32 0.06
51_M 9_S 0.88 0.32 0.06
58_N 30_P 0.88 0.31 0.06
44_A 94_N 0.87 0.31 0.06
107_S 128_D 0.87 0.31 0.06
43_L 55_G 0.87 0.31 0.06
151_V 132_G 0.87 0.31 0.06
85_S 60_A 0.86 0.30 0.06
85_S 41_H 0.86 0.30 0.06
44_A 69_Y 0.86 0.30 0.06
42_G 36_R 0.86 0.30 0.06
27_L 3_L 0.85 0.29 0.06
61_A 5_A 0.85 0.29 0.05
101_D 47_P 0.84 0.29 0.05
58_N 37_F 0.84 0.28 0.05
157_K 163_V 0.84 0.28 0.05
147_L 2_T 0.83 0.28 0.05
103_K 45_R 0.83 0.28 0.05
84_L 86_R 0.83 0.28 0.05
135_V 158_K 0.83 0.27 0.05
65_S 115_L 0.83 0.27 0.05
104_W 151_K 0.83 0.27 0.05
94_R 9_S 0.82 0.27 0.05
159_R 73_A 0.82 0.27 0.05
58_N 31_V 0.82 0.27 0.05
67_V 130_V 0.82 0.27 0.05
107_S 154_G 0.82 0.27 0.05
108_M 54_I 0.82 0.27 0.05
123_I 55_G 0.82 0.27 0.05
130_V 15_K 0.82 0.27 0.05
70_A 70_V 0.82 0.26 0.05
91_V 134_E 0.82 0.26 0.05
159_R 103_L 0.81 0.26 0.05
60_L 25_P 0.81 0.26 0.05
27_L 73_A 0.81 0.26 0.05
22_T 130_V 0.81 0.26 0.04
107_S 130_V 0.81 0.26 0.04
78_M 55_G 0.80 0.25 0.04
94_R 79_N 0.80 0.25 0.04
160_G 20_K 0.80 0.25 0.04
130_V 54_I 0.80 0.25 0.04
26_K 7_A 0.80 0.25 0.04
80_V 96_L 0.80 0.25 0.04
84_L 54_I 0.80 0.25 0.04
116_G 93_I 0.80 0.25 0.04
19_I 12_I 0.80 0.25 0.04
93_R 45_R 0.79 0.25 0.04
56_A 15_K 0.79 0.25 0.04
86_K 70_V 0.79 0.24 0.04
129_S 113_I 0.79 0.24 0.04
70_A 111_G 0.79 0.24 0.04
161_Q 127_S 0.79 0.24 0.04
118_F 41_H 0.78 0.24 0.04
15_E 103_L 0.78 0.24 0.04
91_V 147_R 0.78 0.24 0.04
120_N 60_A 0.78 0.24 0.04
113_S 35_P 0.78 0.23 0.04
101_D 151_K 0.78 0.23 0.04
53_S 6_L 0.78 0.23 0.04
79_I 17_L 0.77 0.23 0.04
34_N 134_E 0.77 0.23 0.04
44_A 52_K 0.77 0.23 0.04
40_T 70_V 0.76 0.23 0.04
153_Q 113_I 0.76 0.23 0.04
107_S 117_Y 0.76 0.22 0.04
123_I 75_N 0.76 0.22 0.04
85_S 147_R 0.76 0.22 0.04
152_M 24_V 0.76 0.22 0.04
77_V 76_D 0.76 0.22 0.04
32_R 77_P 0.76 0.22 0.04
71_S 24_V 0.75 0.22 0.04
103_K 152_R 0.75 0.22 0.04
58_N 100_F 0.75 0.22 0.04
118_F 44_T 0.75 0.22 0.04
68_F 122_A 0.75 0.22 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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