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OPENSEQ.org
XcpQ-nter vs XcpZ
Genes: A B A+B
Length: 323 122 430
Sequences: 757 266 168
Seq/Len: 2.34 2.18 0.39
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 0.01 0.00
2 0.00 0.01 0.01
5 0.01 0.01 0.02
10 0.01 0.01 0.36
20 0.01 0.01 0.38
100 0.01 0.01 0.38
∞ 0.05 0.02 0.41
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
259_T 115_A 1.68 0.62 0.00
45_V 116_R 1.50 0.49 0.00
79_F 94_N 1.37 0.39 0.00
188_A 118_S 1.35 0.38 0.00
96_A 65_R 1.31 0.35 0.00
318_R 60_G 1.29 0.34 0.00
223_P 77_A 1.28 0.34 0.00
231_V 74_V 1.27 0.33 0.00
104_Q 20_L 1.26 0.32 0.00
92_P 55_S 1.25 0.31 0.00
301_L 119_L 1.22 0.30 0.00
71_L 93_L 1.21 0.29 0.00
268_S 78_L 1.21 0.29 0.00
169_Q 106_D 1.20 0.29 0.00
215_T 83_F 1.20 0.29 0.00
52_Q 77_A 1.20 0.29 0.00
95_E 66_L 1.20 0.29 0.00
291_L 18_R 1.20 0.28 0.00
245_A 90_L 1.18 0.28 0.00
295_D 24_I 1.18 0.27 0.00
192_L 72_G 1.18 0.27 0.00
76_T 68_N 1.18 0.27 0.00
88_A 113_V 1.17 0.27 0.00
300_A 122_E 1.17 0.27 0.00
157_I 55_S 1.17 0.27 0.00
53_V 74_V 1.16 0.26 0.00
157_I 116_R 1.15 0.26 0.00
79_F 37_A 1.13 0.25 0.00
213_A 86_L 1.12 0.24 0.00
182_Y 106_D 1.10 0.23 0.00
303_L 61_L 1.09 0.23 0.00
150_I 120_R 1.08 0.22 0.00
259_T 108_Q 1.07 0.22 0.00
45_V 1_R 1.06 0.21 0.00
41_E 19_A 1.06 0.21 0.00
121_P 16_E 1.06 0.21 0.00
228_A 90_L 1.06 0.21 0.00
40_G 62_S 1.06 0.21 0.00
284_G 103_A 1.05 0.21 0.00
206_G 56_A 1.05 0.21 0.00
159_R 89_W 1.05 0.21 0.00
135_Q 118_S 1.04 0.20 0.00
61_L 75_Q 1.04 0.20 0.00
248_R 1_R 1.04 0.20 0.00
284_G 8_Q 1.03 0.20 0.00
220_I 95_G 1.03 0.20 0.00
181_R 87_L 1.03 0.20 0.00
314_E 69_E 1.03 0.20 0.00
322_V 20_L 1.03 0.20 0.00
178_I 10_A 1.03 0.20 0.00
232_Q 100_V 1.02 0.20 0.00
185_V 2_P 1.02 0.19 0.00
255_N 87_L 1.02 0.19 0.00
41_E 55_S 1.02 0.19 0.00
302_V 98_V 1.02 0.19 0.00
80_T 65_R 1.02 0.19 0.00
316_I 7_L 1.01 0.19 0.00
295_D 65_R 1.01 0.19 0.00
25_D 30_N 1.01 0.19 0.00
115_I 119_L 1.01 0.19 0.00
203_G 45_P 1.00 0.18 0.00
97_K 93_L 1.00 0.18 0.00
127_P 83_F 1.00 0.18 0.00
218_L 25_Q 0.99 0.18 0.00
254_H 111_G 0.99 0.18 0.00
319_Q 53_T 0.99 0.18 0.00
182_Y 55_S 0.99 0.18 0.00
255_N 20_L 0.98 0.18 0.00
90_I 100_V 0.98 0.18 0.00
163_V 76_V 0.98 0.18 0.00
60_Q 119_L 0.98 0.18 0.00
213_A 14_F 0.98 0.17 0.00
178_I 66_L 0.98 0.17 0.00
91_V 9_S 0.98 0.17 0.00
188_A 77_A 0.98 0.17 0.00
223_P 29_P 0.98 0.17 0.00
27_D 8_Q 0.97 0.17 0.00
39_T 115_A 0.97 0.17 0.00
302_V 121_V 0.97 0.17 0.00
82_V 90_L 0.97 0.17 0.00
72_S 119_L 0.97 0.17 0.00
237_L 86_L 0.97 0.17 0.00
297_S 81_A 0.97 0.17 0.00
160_I 32_R 0.97 0.17 0.00
50_K 68_N 0.96 0.17 0.00
86_D 115_A 0.96 0.17 0.00
231_V 99_Q 0.96 0.17 0.00
176_S 63_V 0.96 0.17 0.00
163_V 68_N 0.96 0.17 0.00
149_I 66_L 0.96 0.17 0.00
300_A 14_F 0.96 0.17 0.00
152_D 115_A 0.95 0.17 0.00
317_V 23_Y 0.95 0.16 0.00
296_E 94_N 0.95 0.16 0.00
254_H 66_L 0.95 0.16 0.00
292_I 100_V 0.94 0.16 0.00
164_I 50_G 0.94 0.16 0.00
115_I 18_R 0.94 0.16 0.00
126_I 30_N 0.94 0.16 0.00
81_V 29_P 0.94 0.16 0.00
164_I 33_Q 0.94 0.16 0.00
209_V 1_R 0.93 0.16 0.00
184_W 65_R 0.93 0.16 0.00
311_N 103_A 0.93 0.15 0.00
234_A 72_G 0.93 0.15 0.00
164_I 61_L 0.93 0.15 0.00
68_Q 69_E 0.93 0.15 0.00
310_V 73_A 0.92 0.15 0.00
117_V 61_L 0.92 0.15 0.00
114_V 113_V 0.92 0.15 0.00
110_L 80_P 0.92 0.15 0.00
228_A 74_V 0.92 0.15 0.00
101_G 56_A 0.92 0.15 0.00
160_I 36_A 0.92 0.15 0.00
111_E 61_L 0.92 0.15 0.00
317_V 62_S 0.92 0.15 0.00
192_L 31_V 0.91 0.15 0.00
219_I 24_I 0.91 0.15 0.00
169_Q 66_L 0.91 0.15 0.00
36_S 75_Q 0.91 0.15 0.00
54_S 94_N 0.91 0.15 0.00
284_G 4_E 0.91 0.15 0.00
282_T 52_V 0.91 0.15 0.00
125_L 93_L 0.90 0.14 0.00
266_Q 21_H 0.90 0.14 0.00
78_G 93_L 0.90 0.14 0.00
271_M 103_A 0.90 0.14 0.00
224_P 33_Q 0.90 0.14 0.00
190_E 75_Q 0.89 0.14 0.00
191_V 24_I 0.89 0.14 0.00
187_D 65_R 0.89 0.14 0.00
87_Q 5_R 0.89 0.14 0.00
308_D 83_F 0.89 0.14 0.00
12_G 52_V 0.89 0.14 0.00
272_K 55_S 0.89 0.14 0.00
14_Q 112_R 0.89 0.14 0.00
290_I 6_H 0.89 0.14 0.00
308_D 67_D 0.88 0.14 0.00
125_L 23_Y 0.88 0.14 0.00
81_V 59_A 0.88 0.14 0.00
195_A 98_V 0.88 0.14 0.00
208_Q 31_V 0.88 0.14 0.00
229_K 90_L 0.88 0.14 0.00
31_F 53_T 0.88 0.14 0.00
182_Y 12_Q 0.88 0.14 0.00
40_G 47_A 0.87 0.13 0.00
98_T 5_R 0.87 0.13 0.00
11_A 85_K 0.87 0.13 0.00
169_Q 56_A 0.87 0.13 0.00
167_L 67_D 0.87 0.13 0.00
190_E 16_E 0.87 0.13 0.00
189_A 63_V 0.87 0.13 0.00
300_A 41_A 0.86 0.13 0.00
269_E 86_L 0.86 0.13 0.00
75_S 105_L 0.86 0.13 0.00
311_N 8_Q 0.86 0.13 0.00
260_L 55_S 0.86 0.13 0.00
315_D 26_Q 0.86 0.13 0.00
309_T 37_A 0.86 0.13 0.00
296_E 54_A 0.86 0.13 0.00
37_E 54_A 0.86 0.13 0.00
16_E 23_Y 0.85 0.13 0.00
189_A 68_N 0.85 0.13 0.00
272_K 15_T 0.85 0.13 0.00
317_V 98_V 0.85 0.13 0.00
150_I 3_A 0.85 0.13 0.00
53_V 106_D 0.85 0.13 0.00
322_V 17_Q 0.85 0.13 0.00
145_A 64_E 0.85 0.13 0.00
41_E 59_A 0.85 0.13 0.00
16_E 16_E 0.85 0.13 0.00
253_R 56_A 0.84 0.13 0.00
258_K 103_A 0.84 0.13 0.00
308_D 85_K 0.84 0.13 0.00
305_A 7_L 0.84 0.12 0.00
53_V 12_Q 0.84 0.12 0.00
78_G 10_A 0.84 0.12 0.00
215_T 53_T 0.84 0.12 0.00
220_I 64_E 0.84 0.12 0.00
242_A 80_P 0.84 0.12 0.00
185_V 116_R 0.84 0.12 0.00
131_P 115_A 0.84 0.12 0.00
55_V 74_V 0.84 0.12 0.00
296_E 74_V 0.84 0.12 0.00
54_S 31_V 0.84 0.12 0.00
110_L 46_A 0.83 0.12 0.00
40_G 56_A 0.83 0.12 0.00
317_V 17_Q 0.83 0.12 0.00
105_S 54_A 0.83 0.12 0.00
296_E 70_G 0.83 0.12 0.00
260_L 9_S 0.83 0.12 0.00
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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