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OPENSEQ.org
clpV_vipB
Genes: A B A+B
Length: 159 492 641
Sequences: 732 558 442
Seq/Len: 4.6 1.13 0.69
MirrorTree (Pazo et al. 2001) 0.68
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 0.07 0.00
2 0.01 0.08 0.03
5 0.02 0.08 0.47
10 0.03 0.09 0.68
20 0.03 0.10 0.73
100 0.05 0.11 0.73
∞ 0.10 0.16 0.74
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
119_A 279_F 1.53 0.68 0.00
65_D 457_V 1.42 0.60 0.00
28_C 344_F 1.39 0.57 0.00
116_I 440_D 1.36 0.55 0.00
98_A 236_L 1.33 0.53 0.00
135_L 81_D 1.31 0.51 0.00
10_I 76_I 1.25 0.46 0.00
126_R 212_L 1.23 0.44 0.00
21_L 19_L 1.22 0.43 0.00
136_F 315_F 1.20 0.41 0.00
45_L 234_R 1.14 0.37 0.00
141_R 94_S 1.14 0.36 0.00
111_L 410_I 1.14 0.36 0.00
139_I 308_E 1.13 0.36 0.00
113_S 420_E 1.13 0.36 0.00
143_N 329_V 1.11 0.34 0.00
130_F 72_L 1.10 0.34 0.00
120_A 33_E 1.10 0.34 0.00
143_N 74_K 1.10 0.33 0.00
58_K 410_I 1.08 0.33 0.00
125_D 225_R 1.06 0.31 0.00
95_L 185_A 1.06 0.30 0.00
110_E 190_I 1.06 0.30 0.00
102_S 317_S 1.05 0.30 0.00
85_P 199_G 1.05 0.30 0.00
103_S 258_S 1.04 0.29 0.00
91_L 219_P 1.03 0.29 0.00
91_L 410_I 1.03 0.29 0.00
91_L 273_L 1.03 0.29 0.00
62_L 91_A 1.02 0.28 0.00
62_L 401_Y 1.02 0.28 0.00
142_E 185_A 1.02 0.28 0.00
75_Y 179_G 1.02 0.28 0.00
39_E 227_L 1.02 0.28 0.00
124_A 94_S 1.01 0.27 0.00
129_S 452_I 1.01 0.27 0.00
60_A 81_D 1.00 0.27 0.00
8_T 126_E 1.00 0.27 0.00
15_A 277_T 1.00 0.27 0.00
115_A 139_L 0.99 0.26 0.00
60_A 72_L 0.99 0.26 0.00
86_A 281_F 0.99 0.26 0.00
62_L 347_L 0.98 0.25 0.00
15_A 48_E 0.98 0.25 0.00
6_L 199_G 0.97 0.25 0.00
8_T 52_G 0.97 0.25 0.00
139_I 221_Y 0.97 0.25 0.00
113_S 118_H 0.97 0.25 0.00
102_S 10_E 0.97 0.25 0.00
111_L 240_A 0.97 0.24 0.00
17_S 218_S 0.96 0.24 0.00
29_I 176_Q 0.96 0.24 0.00
119_A 131_A 0.96 0.24 0.00
75_Y 160_I 0.96 0.24 0.00
142_E 160_I 0.96 0.24 0.00
36_V 276_N 0.95 0.24 0.00
103_S 25_A 0.95 0.24 0.00
119_A 163_Y 0.95 0.24 0.00
58_K 233_A 0.95 0.24 0.00
13_L 237_G 0.95 0.24 0.00
110_E 456_D 0.95 0.23 0.00
67_V 212_L 0.95 0.23 0.00
87_F 158_A 0.95 0.23 0.00
100_L 39_A 0.94 0.23 0.00
136_F 404_V 0.94 0.23 0.00
66_Q 340_A 0.94 0.23 0.00
153_S 77_S 0.94 0.23 0.00
41_Y 157_G 0.93 0.23 0.00
56_V 292_Y 0.93 0.22 0.00
139_I 81_D 0.93 0.22 0.00
20_A 71_E 0.93 0.22 0.00
151_I 317_S 0.93 0.22 0.00
125_D 179_G 0.93 0.22 0.00
136_F 280_A 0.93 0.22 0.00
111_L 128_F 0.92 0.22 0.00
85_P 127_D 0.92 0.22 0.00
12_K 226_S 0.92 0.21 0.00
32_Q 352_G 0.91 0.21 0.00
34_P 303_S 0.91 0.21 0.00
22_E 69_L 0.91 0.21 0.00
10_I 143_V 0.91 0.21 0.00
35_E 128_F 0.91 0.21 0.00
56_V 139_L 0.90 0.21 0.00
20_A 340_A 0.90 0.21 0.00
103_S 365_Q 0.90 0.21 0.00
45_L 117_L 0.90 0.21 0.00
75_Y 69_L 0.90 0.20 0.00
66_Q 185_A 0.90 0.20 0.00
152_L 233_A 0.90 0.20 0.00
63_E 116_I 0.90 0.20 0.00
28_C 50_L 0.90 0.20 0.00
139_I 146_A 0.89 0.20 0.00
14_N 282_A 0.89 0.20 0.00
80_V 131_A 0.89 0.20 0.00
132_L 179_G 0.89 0.20 0.00
42_L 16_Q 0.88 0.20 0.00
53_V 178_M 0.88 0.20 0.00
42_L 216_F 0.88 0.20 0.00
87_F 189_F 0.88 0.20 0.00
130_F 438_P 0.88 0.19 0.00
37_T 61_N 0.88 0.19 0.00
88_S 369_V 0.87 0.19 0.00
137_E 65_V 0.87 0.19 0.00
139_I 384_K 0.87 0.19 0.00
102_S 349_M 0.87 0.19 0.00
147_H 236_L 0.87 0.19 0.00
117_F 72_L 0.86 0.19 0.00
52_D 336_E 0.86 0.19 0.00
24_A 161_G 0.86 0.19 0.00
18_K 39_A 0.86 0.18 0.00
18_K 218_S 0.86 0.18 0.00
151_I 111_N 0.86 0.18 0.00
60_A 456_D 0.86 0.18 0.00
47_D 84_L 0.86 0.18 0.00
115_A 221_Y 0.86 0.18 0.00
94_L 200_I 0.86 0.18 0.00
75_Y 147_G 0.86 0.18 0.00
17_S 297_N 0.85 0.18 0.00
116_I 205_E 0.85 0.18 0.00
15_A 185_A 0.85 0.18 0.00
88_S 204_E 0.85 0.18 0.00
151_I 44_A 0.85 0.18 0.00
102_S 185_A 0.85 0.18 0.00
45_L 21_D 0.85 0.18 0.00
19_L 156_V 0.85 0.18 0.00
23_Q 282_A 0.85 0.18 0.00
73_S 185_A 0.85 0.18 0.00
107_E 309_D 0.84 0.18 0.00
154_D 191_S 0.84 0.18 0.00
116_I 201_D 0.84 0.18 0.00
15_A 282_A 0.84 0.18 0.00
153_S 74_K 0.84 0.17 0.00
41_Y 240_A 0.84 0.17 0.00
119_A 399_A 0.84 0.17 0.00
63_E 353_S 0.84 0.17 0.00
25_A 133_E 0.83 0.17 0.00
62_L 396_N 0.83 0.17 0.00
4_I 333_D 0.83 0.17 0.00
113_S 288_S 0.83 0.17 0.00
11_A 349_M 0.83 0.17 0.00
39_E 117_L 0.83 0.17 0.00
117_F 160_I 0.83 0.17 0.00
108_Q 139_L 0.83 0.17 0.00
113_S 233_A 0.83 0.17 0.00
153_S 48_E 0.83 0.17 0.00
81_L 415_E 0.83 0.17 0.00
39_E 280_A 0.82 0.17 0.00
77_R 185_A 0.82 0.17 0.00
93_E 225_R 0.82 0.17 0.00
114_G 332_T 0.82 0.17 0.00
40_H 431_V 0.82 0.17 0.00
84_Y 419_L 0.82 0.17 0.00
125_D 198_F 0.82 0.17 0.00
135_L 384_K 0.82 0.17 0.00
7_P 25_A 0.82 0.16 0.00
63_E 163_Y 0.82 0.16 0.00
114_G 174_L 0.82 0.16 0.00
136_F 481_F 0.82 0.16 0.00
12_K 491_Q 0.81 0.16 0.00
24_A 449_A 0.81 0.16 0.00
36_V 261_Y 0.81 0.16 0.00
79_Q 116_I 0.81 0.16 0.00
10_I 27_T 0.81 0.16 0.00
143_N 123_E 0.81 0.16 0.00
136_F 448_R 0.81 0.16 0.00
98_A 296_P 0.81 0.16 0.00
41_Y 212_L 0.81 0.16 0.00
115_A 288_S 0.81 0.16 0.00
80_V 484_S 0.81 0.16 0.00
120_A 89_F 0.81 0.16 0.00
37_T 135_A 0.81 0.16 0.00
92_V 439_A 0.81 0.16 0.00
12_K 41_K 0.80 0.16 0.00
121_L 230_S 0.80 0.16 0.00
14_N 119_V 0.80 0.16 0.00
20_A 236_L 0.80 0.16 0.00
150_M 247_V 0.80 0.16 0.00
98_A 119_V 0.80 0.16 0.00
53_V 399_A 0.80 0.16 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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