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OPENSEQ.org
RUVX_YQGE
Genes: A B A+B
Length: 138 187 293
Sequences: 2702 1466 538
Seq/Len: 19.58 7.84 1.84
MirrorTree (Pazo et al. 2001) 0.50
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.08 1.63
2 0.07 0.08 1.66
5 0.07 0.08 1.65
10 0.07 0.08 1.64
20 0.07 0.08 1.66
100 0.07 0.08 1.74
∞ 0.07 0.08 2.66
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 1.32 0.80 0.06
100_T 11_M 1.30 0.79 0.06
134_F 1_M 1.27 0.76 0.05
29_P 39_V 1.27 0.76 0.05
48_L 109_R 1.25 0.75 0.05
45_I 101_D 1.25 0.74 0.05
118_K 116_G 1.20 0.71 0.04
66_D 9_I 1.18 0.69 0.04
124_A 26_I 1.10 0.61 0.03
94_H 23_V 1.09 0.60 0.03
10_F 38_I 1.08 0.59 0.03
105_S 81_D 1.07 0.58 0.03
70_Q 176_D 1.07 0.57 0.03
53_Q 72_V 1.05 0.56 0.03
5_L 81_D 1.05 0.55 0.03
42_W 166_W 1.04 0.54 0.03
41_D 114_T 1.02 0.52 0.03
76_A 81_D 1.02 0.52 0.02
85_G 176_D 1.02 0.52 0.02
44_I 156_I 1.02 0.52 0.02
131_E 105_M 1.00 0.50 0.02
49_L 172_L 0.98 0.48 0.02
80_A 20_R 0.97 0.46 0.02
53_Q 48_I 0.96 0.46 0.02
6_L 159_K 0.95 0.45 0.02
106_G 166_W 0.95 0.44 0.02
7_A 54_K 0.95 0.44 0.02
15_I 157_L 0.95 0.44 0.02
26_T 14_L 0.94 0.43 0.02
133_Y 170_A 0.93 0.43 0.02
125_S 22_S 0.92 0.41 0.02
80_A 124_V 0.92 0.41 0.02
5_L 124_V 0.91 0.40 0.02
136_Q 126_V 0.91 0.40 0.02
43_N 135_K 0.91 0.40 0.02
121_V 35_M 0.91 0.40 0.02
99_S 47_K 0.91 0.40 0.02
17_V 17_P 0.90 0.39 0.02
89_V 9_I 0.90 0.39 0.02
7_A 177_I 0.90 0.39 0.02
51_E 101_D 0.89 0.38 0.02
19_V 128_L 0.88 0.36 0.01
42_W 170_A 0.88 0.36 0.01
41_D 166_W 0.87 0.36 0.01
88_G 72_V 0.86 0.35 0.01
100_T 53_E 0.86 0.35 0.01
53_Q 26_I 0.86 0.35 0.01
125_S 168_E 0.86 0.35 0.01
7_A 150_A 0.85 0.34 0.01
133_Y 175_V 0.85 0.34 0.01
95_D 29_H 0.85 0.34 0.01
108_F 20_R 0.85 0.34 0.01
41_D 170_A 0.85 0.34 0.01
69_E 172_L 0.85 0.34 0.01
102_E 51_I 0.84 0.33 0.01
70_Q 52_L 0.84 0.33 0.01
131_E 74_L 0.83 0.32 0.01
31_P 5_H 0.83 0.32 0.01
125_S 1_M 0.83 0.32 0.01
61_L 37_I 0.83 0.32 0.01
118_K 173_I 0.83 0.32 0.01
19_V 107_T 0.82 0.32 0.01
6_L 105_M 0.82 0.31 0.01
83_I 67_R 0.81 0.30 0.01
58_I 73_M 0.81 0.30 0.01
7_A 1_M 0.81 0.30 0.01
71_P 6_H 0.81 0.30 0.01
105_S 85_I 0.81 0.30 0.01
71_P 78_L 0.81 0.30 0.01
93_L 80_E 0.81 0.30 0.01
12_T 35_M 0.80 0.29 0.01
44_I 49_E 0.80 0.29 0.01
56_E 157_L 0.80 0.29 0.01
59_V 71_P 0.79 0.29 0.01
76_A 160_T 0.79 0.28 0.01
76_A 21_R 0.79 0.28 0.01
70_Q 104_V 0.79 0.28 0.01
10_F 4_Q 0.79 0.28 0.01
33_I 175_V 0.78 0.28 0.01
136_Q 146_A 0.78 0.27 0.01
5_L 5_H 0.77 0.27 0.01
4_T 184_A 0.77 0.27 0.01
48_L 149_T 0.77 0.27 0.01
81_N 85_I 0.77 0.27 0.01
108_F 166_W 0.77 0.27 0.01
30_L 9_I 0.77 0.26 0.01
3_G 131_A 0.76 0.26 0.01
47_R 142_I 0.76 0.26 0.01
72_L 146_A 0.76 0.26 0.01
85_G 89_P 0.76 0.26 0.01
100_T 117_T 0.76 0.26 0.01
100_T 126_V 0.76 0.25 0.01
32_A 52_L 0.75 0.25 0.01
27_A 148_L 0.75 0.25 0.01
67_G 136_G 0.75 0.25 0.01
88_G 11_M 0.75 0.25 0.01
47_R 31_T 0.74 0.24 0.01
130_L 156_I 0.74 0.24 0.01
64_N 100_S 0.74 0.24 0.01
33_I 135_K 0.74 0.24 0.01
108_F 28_E 0.74 0.24 0.01
68_T 105_M 0.74 0.24 0.01
53_Q 140_Q 0.74 0.24 0.01
108_F 162_I 0.74 0.24 0.01
24_T 37_I 0.74 0.24 0.01
128_I 48_I 0.73 0.24 0.01
43_N 163_A 0.73 0.24 0.01
129_I 150_A 0.73 0.23 0.01
131_E 115_L 0.73 0.23 0.01
101_V 51_I 0.73 0.23 0.01
29_P 130_Y 0.73 0.23 0.01
29_P 170_A 0.72 0.23 0.01
41_D 184_A 0.72 0.23 0.01
74_A 143_L 0.72 0.23 0.01
51_E 56_K 0.72 0.23 0.01
43_N 134_E 0.72 0.23 0.01
120_K 4_Q 0.72 0.22 0.01
47_R 101_D 0.72 0.22 0.01
128_I 41_K 0.72 0.22 0.01
108_F 88_T 0.71 0.22 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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