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OPENSEQ.org
2F9Y(BC)
Genes: A B A+B
Length: 106 567 670
Sequences: 1844 1212 1026
Seq/Len: 17.4 2.14 1.53
MirrorTree (Pazo et al. 2001) 0.75
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 1.39
2 0.00 0.00 1.46
5 0.00 0.00 1.52
10 0.00 0.00 1.52
20 0.00 0.00 1.52
100 0.00 0.00 1.52
∞ 0.01 0.01 1.55
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
7_H 29_W 3.06 1.00 1.00
65_A 50_V 2.12 0.99 0.97
47_P 258_D 1.76 0.95 0.90
84_F 104_I 1.67 0.93 0.86
12_Q 3_N 1.63 0.92 0.85
85_A 106_P 1.57 0.90 0.81
13_I 39_Y 1.48 0.85 0.75
7_H 20_K 1.44 0.83 0.72
34_I 75_I 1.20 0.65 0.48
14_A 3_N 1.09 0.54 0.37
87_H 103_D 1.08 0.53 0.36
40_Y 253_S 1.07 0.52 0.34
75_Q 59_Q 1.05 0.50 0.33
77_R 289_A 0.97 0.42 0.25
94_R 258_D 0.97 0.42 0.24
82_V 41_E 0.97 0.41 0.24
60_R 41_E 0.95 0.39 0.23
9_K 394_D 0.94 0.39 0.22
40_Y 145_E 0.93 0.38 0.21
6_Y 21_V 0.93 0.37 0.21
63_I 89_K 0.93 0.37 0.21
48_A 438_A 0.93 0.37 0.20
93_F 472_H 0.88 0.33 0.17
67_T 284_I 0.88 0.33 0.17
90_V 104_I 0.87 0.32 0.16
90_V 204_A 0.85 0.30 0.15
19_R 41_E 0.85 0.30 0.15
98_M 106_P 0.85 0.30 0.15
93_F 105_Q 0.83 0.28 0.14
59_Y 424_I 0.83 0.28 0.14
29_H 327_A 0.83 0.28 0.13
34_I 90_D 0.82 0.28 0.13
11_G 10_A 0.82 0.27 0.13
83_A 104_I 0.82 0.27 0.13
56_A 89_K 0.80 0.26 0.12
24_V 356_L 0.80 0.26 0.12
34_I 3_N 0.80 0.26 0.12
65_A 68_L 0.80 0.26 0.12
78_E 400_V 0.80 0.26 0.12
36_V 151_V 0.80 0.26 0.12
102_E 118_V 0.79 0.25 0.11
75_Q 457_P 0.77 0.24 0.10
68_A 261_A 0.77 0.23 0.10
93_F 304_Y 0.77 0.23 0.10
88_R 20_K 0.76 0.23 0.10
62_N 400_V 0.76 0.23 0.10
21_T 82_V 0.76 0.23 0.10
98_M 59_Q 0.76 0.23 0.10
48_A 255_F 0.75 0.22 0.09
15_L 4_I 0.74 0.22 0.09
34_I 544_R 0.74 0.21 0.09
63_I 271_F 0.74 0.21 0.09
7_H 394_D 0.73 0.21 0.09
56_A 546_D 0.73 0.21 0.08
75_Q 103_D 0.73 0.21 0.08
45_V 253_S 0.73 0.20 0.08
95_G 509_S 0.73 0.20 0.08
7_H 28_L 0.72 0.20 0.08
6_Y 65_C 0.72 0.20 0.08
94_R 145_E 0.72 0.20 0.08
65_A 99_A 0.72 0.20 0.08
78_E 30_I 0.72 0.20 0.08
78_E 372_L 0.72 0.20 0.08
3_P 563_R 0.71 0.20 0.08
62_N 241_I 0.71 0.19 0.07
62_N 548_E 0.71 0.19 0.07
75_Q 253_S 0.70 0.19 0.07
64_P 4_I 0.70 0.19 0.07
64_P 13_F 0.70 0.19 0.07
19_R 192_G 0.70 0.19 0.07
6_Y 446_T 0.70 0.19 0.07
64_P 287_A 0.69 0.18 0.07
68_A 32_V 0.69 0.18 0.07
64_P 12_M 0.69 0.18 0.07
67_T 12_M 0.69 0.18 0.07
96_E 339_R 0.69 0.18 0.07
57_A 203_D 0.69 0.18 0.07
98_M 227_A 0.69 0.18 0.07
97_V 523_A 0.68 0.18 0.07
77_R 445_A 0.68 0.18 0.06
82_V 271_F 0.68 0.17 0.06
83_A 517_C 0.68 0.17 0.06
75_Q 339_R 0.67 0.17 0.06
65_A 288_C 0.67 0.17 0.06
15_L 379_H 0.67 0.17 0.06
44_E 481_G 0.67 0.17 0.06
67_T 450_G 0.67 0.17 0.06
33_P 299_N 0.66 0.17 0.06
30_G 540_T 0.66 0.17 0.06
97_V 304_Y 0.66 0.17 0.06
15_L 5_S 0.66 0.17 0.06
37_G 157_G 0.66 0.16 0.06
28_N 112_I 0.66 0.16 0.06
68_A 249_T 0.66 0.16 0.06
64_P 327_A 0.66 0.16 0.06
75_Q 270_T 0.66 0.16 0.06
15_L 10_A 0.66 0.16 0.06
36_V 56_G 0.66 0.16 0.06
5_E 328_E 0.65 0.16 0.05
64_P 154_M 0.65 0.16 0.05
98_M 231_C 0.65 0.16 0.05
5_E 305_T 0.65 0.16 0.05
62_N 30_I 0.65 0.16 0.05
59_Y 66_V 0.65 0.16 0.05
19_R 98_K 0.65 0.16 0.05
30_G 268_I 0.65 0.16 0.05
68_A 385_R 0.65 0.16 0.05
98_M 253_S 0.65 0.15 0.05
60_R 293_I 0.65 0.15 0.05
54_Q 498_A 0.65 0.15 0.05
34_I 255_F 0.64 0.15 0.05
44_E 304_Y 0.64 0.15 0.05
96_E 258_D 0.64 0.15 0.05
95_G 82_V 0.64 0.15 0.05
67_T 319_C 0.64 0.15 0.05
62_N 213_V 0.63 0.15 0.05
98_M 472_H 0.63 0.15 0.05
9_K 30_I 0.63 0.15 0.05
2_I 557_V 0.63 0.15 0.05
23_R 271_F 0.62 0.14 0.05
94_R 514_V 0.62 0.14 0.05
10_P 520_V 0.62 0.14 0.05
63_I 326_I 0.62 0.14 0.05
33_P 308_T 0.62 0.14 0.04
93_F 54_G 0.62 0.14 0.04
98_M 99_A 0.62 0.14 0.04
73_P 299_N 0.62 0.14 0.04
88_R 565_F 0.62 0.14 0.04
93_F 461_I 0.62 0.14 0.04
77_R 472_H 0.62 0.14 0.04
82_V 99_A 0.62 0.14 0.04
11_G 92_R 0.62 0.14 0.04
6_Y 34_D 0.62 0.14 0.04
18_G 520_V 0.61 0.14 0.04
24_V 526_V 0.61 0.14 0.04
78_E 554_P 0.61 0.14 0.04
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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