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OPENSEQ.org
2F9Y(AC)
Genes: A B A+B
Length: 100 567 666
Sequences: 1169 1212 921
Seq/Len: 11.69 2.14 1.38
MirrorTree (Pazo et al. 2001) 0.79
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 0.31
2 0.00 0.00 1.18
5 0.00 0.00 1.35
10 0.00 0.00 1.38
20 0.00 0.00 1.38
100 0.00 0.00 1.39
∞ 0.01 0.01 1.42
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
9_D 472_H 2.07 0.98 0.93
52_S 306_L 1.91 0.97 0.88
87_P 562_Q 1.65 0.91 0.76
54_A 310_D 1.65 0.91 0.75
70_M 562_Q 1.64 0.90 0.74
8_K 472_H 1.33 0.73 0.47
7_E 443_K 1.31 0.72 0.46
9_D 326_I 1.30 0.71 0.44
76_M 563_R 1.14 0.56 0.28
2_E 469_Q 1.13 0.55 0.28
7_E 565_F 1.11 0.53 0.27
32_Y 439_F 1.04 0.46 0.21
43_I 288_C 0.99 0.41 0.17
91_K 305_T 0.97 0.39 0.16
19_V 124_K 0.94 0.36 0.14
12_L 351_L 0.94 0.36 0.14
71_E 563_R 0.93 0.35 0.13
63_V 30_I 0.93 0.35 0.13
51_K 34_D 0.92 0.34 0.13
33_P 561_A 0.91 0.33 0.12
6_R 145_E 0.89 0.31 0.11
36_V 224_A 0.87 0.30 0.10
84_A 453_I 0.86 0.29 0.10
91_K 328_E 0.85 0.28 0.10
25_A 498_A 0.85 0.28 0.09
73_V 107_N 0.85 0.28 0.09
73_V 347_V 0.84 0.27 0.09
2_E 436_S 0.83 0.27 0.09
42_F 334_E 0.83 0.27 0.09
5_P 148_V 0.83 0.27 0.09
6_R 473_Y 0.83 0.27 0.09
43_I 525_M 0.83 0.26 0.08
71_E 521_Q 0.82 0.26 0.08
78_P 438_A 0.82 0.26 0.08
65_T 108_V 0.82 0.26 0.08
81_Q 319_C 0.82 0.26 0.08
19_V 66_V 0.81 0.25 0.08
49_D 390_E 0.81 0.25 0.08
18_L 66_V 0.80 0.25 0.07
96_H 318_V 0.80 0.24 0.07
47_A 259_T 0.80 0.24 0.07
24_L 414_T 0.79 0.23 0.07
65_T 224_A 0.79 0.23 0.07
79_D 469_Q 0.79 0.23 0.07
13_L 565_F 0.79 0.23 0.07
40_S 424_I 0.78 0.23 0.07
10_K 418_A 0.77 0.22 0.06
81_Q 318_V 0.76 0.21 0.06
96_H 319_C 0.76 0.21 0.06
22_R 110_I 0.75 0.21 0.06
44_M 105_Q 0.75 0.21 0.06
13_L 258_D 0.75 0.20 0.06
9_D 64_D 0.74 0.20 0.05
56_L 312_H 0.74 0.20 0.05
85_T 465_I 0.74 0.20 0.05
44_M 166_H 0.73 0.20 0.05
19_V 310_D 0.73 0.19 0.05
84_A 405_A 0.73 0.19 0.05
69_V 215_G 0.73 0.19 0.05
13_L 174_P 0.73 0.19 0.05
39_I 489_L 0.72 0.19 0.05
25_A 151_V 0.72 0.19 0.05
75_E 264_G 0.72 0.19 0.05
66_R 92_R 0.72 0.19 0.05
80_I 465_I 0.72 0.19 0.05
51_K 486_H 0.72 0.19 0.05
82_V 475_P 0.72 0.19 0.05
95_V 371_I 0.71 0.18 0.05
9_D 231_C 0.71 0.18 0.05
52_S 477_F 0.71 0.18 0.05
28_L 181_L 0.71 0.18 0.05
13_L 457_P 0.71 0.18 0.05
78_P 271_F 0.70 0.18 0.04
14_F 110_I 0.70 0.18 0.04
9_D 534_I 0.70 0.18 0.04
10_K 490_T 0.70 0.18 0.04
67_E 121_A 0.70 0.18 0.04
54_A 183_A 0.70 0.18 0.04
85_T 117_E 0.69 0.17 0.04
77_I 260_L 0.69 0.17 0.04
49_D 24_A 0.69 0.17 0.04
6_R 54_G 0.69 0.17 0.04
87_P 305_T 0.69 0.17 0.04
44_M 131_I 0.69 0.17 0.04
38_L 37_T 0.69 0.17 0.04
70_M 563_R 0.69 0.17 0.04
61_R 539_Q 0.69 0.17 0.04
17_A 114_A 0.69 0.17 0.04
61_R 509_S 0.69 0.17 0.04
84_A 259_T 0.69 0.17 0.04
55_S 291_P 0.68 0.17 0.04
2_E 445_A 0.68 0.17 0.04
97_N 32_V 0.68 0.16 0.04
80_I 356_L 0.68 0.16 0.04
56_L 370_V 0.68 0.16 0.04
17_A 255_F 0.68 0.16 0.04
95_V 293_I 0.68 0.16 0.04
9_D 94_F 0.67 0.16 0.04
4_T 293_I 0.67 0.16 0.04
51_K 75_I 0.67 0.16 0.04
79_D 560_M 0.67 0.16 0.04
85_T 567_F 0.67 0.16 0.04
28_L 103_D 0.67 0.16 0.04
5_P 475_P 0.67 0.16 0.04
36_V 243_V 0.67 0.16 0.04
9_D 545_V 0.67 0.16 0.04
21_E 109_T 0.66 0.15 0.04
32_Y 334_E 0.66 0.15 0.04
10_K 363_A 0.66 0.15 0.04
7_E 140_P 0.66 0.15 0.04
9_D 105_Q 0.66 0.15 0.04
96_H 342_I 0.66 0.15 0.04
13_L 33_E 0.66 0.15 0.04
17_A 537_D 0.65 0.15 0.03
68_Q 194_L 0.65 0.15 0.03
56_L 337_I 0.65 0.15 0.03
11_L 268_I 0.65 0.15 0.03
29_K 258_D 0.65 0.15 0.03
71_E 557_V 0.65 0.15 0.03
29_K 209_V 0.65 0.15 0.03
91_K 321_H 0.65 0.15 0.03
7_E 182_Q 0.65 0.15 0.03
9_D 476_M 0.64 0.14 0.03
13_L 95_A 0.64 0.14 0.03
76_M 442_V 0.64 0.14 0.03
68_Q 204_A 0.64 0.14 0.03
28_L 194_L 0.64 0.14 0.03
32_Y 323_D 0.64 0.14 0.03
84_A 302_L 0.64 0.14 0.03
71_E 438_A 0.64 0.14 0.03
68_Q 450_G 0.64 0.14 0.03
17_A 415_H 0.64 0.14 0.03
46_G 56_G 0.64 0.14 0.03
43_I 546_D 0.64 0.14 0.03
16_A 167_A 0.64 0.14 0.03
6_R 253_S 0.63 0.14 0.03
96_H 467_T 0.63 0.14 0.03
52_S 413_L 0.63 0.14 0.03
82_V 448_I 0.63 0.14 0.03
43_I 176_Y 0.63 0.14 0.03
8_K 59_Q 0.63 0.14 0.03
40_S 560_M 0.63 0.14 0.03
76_M 562_Q 0.63 0.14 0.03
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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