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OPENSEQ.org
AtmxQ
Genes: A B A+B
Length: 339 89 404
Sequences: 1350 1330 940
Seq/Len: 3.98 14.94 2.33
MirrorTree (Pazo et al. 2001) 0.61
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 0.10
2 0.01 0.00 0.26
5 0.01 0.00 1.62
10 0.01 0.01 1.79
20 0.02 0.01 1.94
100 0.03 0.02 2.20
∞ 0.07 0.05 2.53
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
122_F 54_K 1.49 0.93 0.55
133_I 35_I 1.31 0.85 0.39
258_S 45_N 1.25 0.81 0.34
23_K 34_V 1.16 0.73 0.26
123_V 77_T 1.15 0.73 0.26
59_L 60_V 1.10 0.68 0.22
270_A 36_S 1.07 0.65 0.20
105_G 38_F 1.04 0.62 0.18
299_L 38_F 1.03 0.60 0.18
75_D 43_Q 1.03 0.60 0.18
122_F 23_P 1.02 0.59 0.17
320_G 58_V 1.02 0.59 0.17
165_M 6_L 1.01 0.58 0.17
252_I 75_D 0.98 0.55 0.15
305_L 19_L 0.98 0.55 0.15
138_L 29_L 0.96 0.52 0.14
296_R 30_I 0.96 0.52 0.14
56_S 66_M 0.96 0.52 0.14
178_A 19_L 0.95 0.52 0.13
146_V 14_F 0.95 0.52 0.13
82_L 56_I 0.95 0.51 0.13
122_F 25_L 0.94 0.51 0.13
264_I 47_M 0.94 0.50 0.13
309_A 85_P 0.94 0.50 0.13
137_I 43_Q 0.93 0.49 0.12
150_S 11_V 0.93 0.49 0.12
70_I 33_L 0.93 0.48 0.12
215_V 43_Q 0.93 0.48 0.12
129_V 30_I 0.92 0.47 0.12
247_Y 44_I 0.92 0.47 0.12
262_G 17_T 0.91 0.47 0.12
244_A 14_F 0.91 0.46 0.11
81_T 35_I 0.91 0.46 0.11
146_V 55_I 0.91 0.46 0.11
185_T 62_L 0.90 0.46 0.11
97_T 50_S 0.90 0.46 0.11
235_Q 85_P 0.90 0.45 0.11
307_I 7_V 0.90 0.45 0.11
116_I 26_L 0.90 0.45 0.11
120_G 68_W 0.89 0.44 0.10
211_K 43_Q 0.89 0.44 0.10
287_T 73_M 0.88 0.43 0.10
202_A 75_D 0.88 0.43 0.10
321_F 80_I 0.88 0.43 0.10
58_A 7_V 0.88 0.43 0.10
99_R 6_L 0.87 0.42 0.10
134_V 25_L 0.87 0.42 0.10
180_L 43_Q 0.87 0.42 0.10
107_N 45_N 0.86 0.41 0.09
29_I 36_S 0.86 0.41 0.09
141_I 58_V 0.86 0.41 0.09
185_T 26_L 0.86 0.40 0.09
119_F 40_A 0.85 0.40 0.09
70_I 14_F 0.85 0.40 0.09
267_T 67_P 0.84 0.39 0.09
182_D 60_V 0.84 0.38 0.09
153_V 58_V 0.83 0.38 0.08
275_R 81_L 0.83 0.38 0.08
101_I 54_K 0.83 0.37 0.08
199_F 53_P 0.83 0.37 0.08
230_L 73_M 0.83 0.37 0.08
324_L 79_N 0.82 0.37 0.08
240_L 20_L 0.82 0.36 0.08
92_S 8_A 0.81 0.36 0.08
96_A 3_E 0.81 0.35 0.08
130_I 55_I 0.81 0.35 0.07
164_A 13_T 0.81 0.35 0.07
124_V 47_M 0.81 0.35 0.07
215_V 40_A 0.81 0.35 0.07
53_L 55_I 0.80 0.35 0.07
151_T 66_M 0.80 0.34 0.07
37_L 38_F 0.80 0.34 0.07
76_L 81_L 0.79 0.33 0.07
67_S 61_I 0.79 0.33 0.07
32_F 75_D 0.79 0.33 0.07
38_A 76_F 0.78 0.33 0.07
141_I 10_G 0.78 0.33 0.07
143_F 67_P 0.78 0.32 0.07
174_A 46_E 0.77 0.31 0.06
313_G 85_P 0.77 0.31 0.06
274_T 47_M 0.77 0.31 0.06
64_I 74_I 0.77 0.31 0.06
240_L 73_M 0.76 0.30 0.06
115_I 4_S 0.76 0.30 0.06
128_M 84_I 0.76 0.30 0.06
287_T 17_T 0.76 0.30 0.06
314_L 41_T 0.76 0.30 0.06
326_F 80_I 0.75 0.30 0.06
68_I 6_L 0.75 0.30 0.06
285_E 57_L 0.75 0.29 0.06
147_T 84_I 0.75 0.29 0.06
55_L 65_L 0.75 0.29 0.06
137_I 67_P 0.75 0.29 0.06
182_D 47_M 0.75 0.29 0.06
86_I 36_S 0.75 0.29 0.06
320_G 61_I 0.74 0.29 0.06
251_T 74_I 0.74 0.29 0.06
127_N 55_I 0.74 0.29 0.06
28_T 8_A 0.74 0.28 0.06
187_R 88_I 0.74 0.28 0.06
94_N 53_P 0.74 0.28 0.06
178_A 40_A 0.74 0.28 0.06
86_I 21_S 0.74 0.28 0.05
223_I 9_L 0.74 0.28 0.05
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)
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