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OPENSEQ.org
RUVX - YQGE
Genes: A B A+B
Length: 138 187 320
Sequences: 2626 1343 517
Seq/Len: 19.03 7.18 1.62
MirrorTree (Pazo et al. 2001) 0.50
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 0.00 1.56
2 0.00 0.00 1.57
5 0.00 0.00 1.58
10 0.00 0.00 1.58
20 0.00 0.00 1.59
100 0.00 0.00 1.66
∞ 0.00 0.00 2.69
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
70_Q 4_Q 1.47 0.86 0.17
33_I 175_V 1.42 0.84 0.15
100_T 11_M 1.30 0.75 0.11
10_F 38_I 1.27 0.73 0.10
94_H 23_V 1.23 0.70 0.09
29_P 39_V 1.23 0.69 0.09
118_K 116_G 1.23 0.69 0.09
131_E 105_M 1.20 0.66 0.08
99_S 47_K 1.15 0.62 0.07
48_L 109_R 1.08 0.55 0.05
76_A 81_D 1.06 0.53 0.05
44_I 156_I 1.06 0.52 0.05
116_L 166_W 1.05 0.52 0.05
49_L 172_L 1.04 0.50 0.05
125_S 22_S 1.03 0.50 0.05
7_A 150_A 1.02 0.49 0.04
53_Q 48_I 1.02 0.48 0.04
42_W 166_W 1.02 0.48 0.04
53_Q 26_I 1.00 0.46 0.04
89_V 9_I 0.99 0.46 0.04
88_G 72_V 0.99 0.45 0.04
131_E 74_L 0.98 0.44 0.04
15_I 157_L 0.98 0.44 0.04
47_R 101_D 0.98 0.44 0.04
80_A 20_R 0.97 0.43 0.04
100_T 53_E 0.97 0.43 0.04
27_A 22_S 0.96 0.42 0.04
41_D 114_T 0.95 0.41 0.03
137_G 184_A 0.94 0.40 0.03
5_L 81_D 0.93 0.39 0.03
130_L 156_I 0.93 0.39 0.03
121_V 35_M 0.93 0.39 0.03
66_D 9_I 0.92 0.38 0.03
19_V 128_L 0.92 0.38 0.03
105_S 81_D 0.91 0.37 0.03
5_L 124_V 0.91 0.37 0.03
105_S 115_L 0.91 0.36 0.03
133_Y 170_A 0.90 0.36 0.03
80_A 124_V 0.90 0.36 0.03
51_E 101_D 0.90 0.36 0.03
70_Q 179_T 0.90 0.36 0.03
76_A 160_T 0.90 0.35 0.03
125_S 168_E 0.89 0.35 0.03
17_V 17_P 0.89 0.35 0.03
94_H 93_F 0.88 0.34 0.03
45_I 101_D 0.88 0.34 0.03
63_L 96_S 0.86 0.32 0.02
102_E 51_I 0.85 0.32 0.02
31_P 5_H 0.85 0.31 0.02
133_Y 18_I 0.84 0.30 0.02
59_V 71_P 0.84 0.30 0.02
70_Q 104_V 0.84 0.30 0.02
30_L 9_I 0.83 0.30 0.02
47_R 142_I 0.82 0.29 0.02
68_T 93_F 0.82 0.29 0.02
8_F 3_L 0.81 0.28 0.02
93_L 95_S 0.81 0.28 0.02
124_A 172_L 0.81 0.28 0.02
128_I 41_K 0.81 0.28 0.02
74_A 38_I 0.81 0.28 0.02
29_P 81_D 0.81 0.28 0.02
107_L 28_E 0.81 0.27 0.02
93_L 80_E 0.80 0.27 0.02
133_Y 179_T 0.80 0.27 0.02
128_I 51_I 0.80 0.27 0.02
19_V 162_I 0.80 0.27 0.02
105_S 85_I 0.80 0.27 0.02
100_T 117_T 0.79 0.26 0.02
133_Y 175_V 0.79 0.26 0.02
26_T 14_L 0.79 0.26 0.02
129_I 150_A 0.79 0.26 0.02
95_D 29_H 0.79 0.26 0.02
41_D 166_W 0.79 0.26 0.02
69_E 48_I 0.79 0.26 0.02
97_R 152_A 0.79 0.26 0.02
53_Q 72_V 0.79 0.26 0.02
61_L 32_N 0.78 0.26 0.02
42_W 170_A 0.78 0.26 0.02
4_T 26_I 0.78 0.26 0.02
43_N 134_E 0.78 0.25 0.02
41_D 184_A 0.78 0.25 0.02
76_A 21_R 0.78 0.25 0.02
106_G 166_W 0.77 0.25 0.02
10_F 66_I 0.77 0.25 0.02
71_P 47_K 0.77 0.25 0.02
124_A 26_I 0.77 0.24 0.02
134_F 118_D 0.77 0.24 0.02
41_D 170_A 0.77 0.24 0.02
66_D 99_I 0.77 0.24 0.02
53_Q 140_Q 0.77 0.24 0.02
55_D 57_I 0.76 0.24 0.02
10_F 102_N 0.76 0.24 0.02
130_L 175_V 0.76 0.24 0.02
38_G 37_I 0.76 0.24 0.02
43_N 135_K 0.76 0.24 0.02
128_I 48_I 0.76 0.24 0.02
92_K 144_D 0.76 0.24 0.02
109_E 6_H 0.76 0.24 0.02
131_E 115_L 0.76 0.24 0.02
12_T 35_M 0.76 0.24 0.02
124_A 157_L 0.76 0.24 0.02
78_K 146_A 0.76 0.23 0.02
113_Y 104_V 0.76 0.23 0.02
39_T 55_L 0.76 0.23 0.02
51_E 60_E 0.76 0.23 0.02
68_T 143_L 0.75 0.23 0.01
87_F 28_E 0.75 0.23 0.01
70_Q 166_W 0.75 0.23 0.01
67_G 136_G 0.75 0.23 0.01
85_G 30_N 0.75 0.23 0.01
45_I 28_E 0.75 0.23 0.01
7_A 180_M 0.75 0.23 0.01
50_K 182_G 0.74 0.23 0.01
125_S 117_T 0.74 0.23 0.01
67_G 60_E 0.74 0.22 0.01
30_L 6_H 0.74 0.22 0.01
7_A 54_K 0.74 0.22 0.01
101_V 51_I 0.74 0.22 0.01
81_N 85_I 0.74 0.22 0.01
69_E 28_E 0.74 0.22 0.01
112_G 52_L 0.74 0.22 0.01
6_L 159_K 0.74 0.22 0.01
22_R 115_L 0.74 0.22 0.01
58_I 56_K 0.74 0.22 0.01
49_L 181_P 0.74 0.22 0.01
70_Q 52_L 0.74 0.22 0.01
71_P 78_L 0.73 0.22 0.01
88_G 11_M 0.73 0.22 0.01
28_R 173_I 0.73 0.22 0.01
130_L 7_F 0.73 0.21 0.01
133_Y 51_I 0.73 0.21 0.01
106_G 55_L 0.73 0.21 0.01
72_L 79_A 0.73 0.21 0.01
75_R 105_M 0.73 0.21 0.01
100_T 126_V 0.73 0.21 0.01
127_V 97_I 0.72 0.21 0.01
37_D 69_D 0.72 0.21 0.01
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
2568 2.78 RUVX_YQGE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.28 Done - Shared
2567 1.84 RUVX_YQGE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.06 Done - Shared
2485 1.62 RUVX - YQGE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.17 Done - Shared
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