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OPENSEQ.org
fdxHscA
Genes: A B A+B
Length: 111 616 725
Sequences: 5163 5144 404
Seq/Len: 46.51 8.35 0.56
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 0.02 0.02 0.52
2 0.04 0.02 0.53
5 0.05 0.03 0.56
10 0.05 0.03 0.59
20 0.06 0.03 0.65
100 0.08 0.05 0.99
∞ 0.13 0.09 2.20
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
86_S 509_I 1.60 0.67 0.00
31_A 341_V 1.51 0.60 0.00
28_L 589_D 1.39 0.51 0.00
31_A 304_I 1.34 0.47 0.00
107_H 408_V 1.34 0.47 0.00
98_V 300_F 1.34 0.47 0.00
66_S 507_S 1.23 0.39 0.00
64_E 268_L 1.19 0.36 0.00
91_V 522_Q 1.18 0.35 0.00
31_A 386_M 1.17 0.34 0.00
6_I 381_K 1.16 0.33 0.00
72_M 488_K 1.12 0.31 0.00
75_K 601_D 1.11 0.30 0.00
28_L 304_I 1.09 0.29 0.00
98_V 323_G 1.08 0.28 0.00
19_L 334_M 1.07 0.27 0.00
20_E 229_A 1.06 0.27 0.00
55_V 271_A 1.05 0.26 0.00
25_E 601_D 1.04 0.26 0.00
54_I 540_L 1.04 0.26 0.00
66_S 496_I 1.04 0.26 0.00
17_A 584_A 1.02 0.24 0.00
43_E 311_T 1.02 0.24 0.00
6_I 338_S 1.00 0.23 0.00
3_K 89_M 1.00 0.23 0.00
9_H 494_A 1.00 0.23 0.00
35_G 117_I 1.00 0.23 0.00
98_V 548_A 0.99 0.23 0.00
107_H 295_I 0.99 0.23 0.00
55_V 52_L 0.99 0.23 0.00
95_D 228_L 0.98 0.22 0.00
102_R 354_R 0.98 0.22 0.00
107_H 310_R 0.97 0.22 0.00
36_I 62_Q 0.97 0.22 0.00
67_E 484_T 0.96 0.21 0.00
37_E 516_S 0.95 0.21 0.00
31_A 203_I 0.95 0.20 0.00
107_H 18_R 0.95 0.20 0.00
43_E 49_G 0.94 0.20 0.00
67_E 545_G 0.94 0.20 0.00
2_P 345_R 0.94 0.20 0.00
98_V 516_S 0.93 0.20 0.00
70_D 152_V 0.93 0.20 0.00
1_M 417_V 0.92 0.19 0.00
31_A 589_D 0.92 0.19 0.00
86_S 588_V 0.92 0.19 0.00
26_T 489_S 0.91 0.19 0.00
66_S 52_L 0.91 0.19 0.00
31_A 315_C 0.91 0.18 0.00
53_C 378_V 0.91 0.18 0.00
92_T 283_S 0.91 0.18 0.00
28_L 341_V 0.90 0.18 0.00
102_R 297_R 0.90 0.18 0.00
109_R 410_P 0.90 0.18 0.00
3_K 297_R 0.90 0.18 0.00
18_V 413_T 0.90 0.18 0.00
19_L 565_A 0.90 0.18 0.00
20_E 132_D 0.90 0.18 0.00
25_E 413_T 0.89 0.18 0.00
25_E 355_P 0.89 0.18 0.00
31_A 343_L 0.89 0.18 0.00
54_I 435_I 0.89 0.17 0.00
98_V 17_Q 0.89 0.17 0.00
107_H 91_R 0.89 0.17 0.00
40_H 164_Q 0.88 0.17 0.00
89_A 385_E 0.88 0.17 0.00
64_E 231_G 0.88 0.17 0.00
54_I 162_D 0.88 0.17 0.00
105_I 199_Q 0.88 0.17 0.00
66_S 326_A 0.88 0.17 0.00
3_K 276_I 0.88 0.17 0.00
66_S 173_R 0.88 0.17 0.00
6_I 386_M 0.87 0.17 0.00
81_P 592_T 0.87 0.17 0.00
105_I 58_H 0.87 0.17 0.00
27_I 231_G 0.87 0.17 0.00
43_E 41_A 0.87 0.17 0.00
70_D 42_E 0.87 0.17 0.00
91_V 261_N 0.87 0.17 0.00
3_K 270_A 0.86 0.16 0.00
35_G 538_R 0.86 0.16 0.00
98_V 199_Q 0.86 0.16 0.00
81_P 569_L 0.86 0.16 0.00
54_I 284_V 0.86 0.16 0.00
21_A 586_K 0.86 0.16 0.00
37_E 260_D 0.85 0.16 0.00
102_R 205_V 0.85 0.16 0.00
58_G 164_Q 0.85 0.16 0.00
6_I 203_I 0.85 0.16 0.00
31_A 263_V 0.85 0.16 0.00
54_I 250_R 0.84 0.16 0.00
35_G 75_A 0.84 0.16 0.00
28_L 114_L 0.84 0.15 0.00
11_D 437_V 0.84 0.15 0.00
15_D 590_K 0.84 0.15 0.00
27_I 222_R 0.83 0.15 0.00
5_V 233_D 0.83 0.15 0.00
2_P 519_Y 0.83 0.15 0.00
55_V 563_D 0.83 0.15 0.00
109_R 19_R 0.82 0.15 0.00
22_N 42_E 0.82 0.15 0.00
21_A 72_T 0.82 0.15 0.00
11_D 581_I 0.82 0.15 0.00
54_I 484_T 0.82 0.15 0.00
105_I 191_I 0.82 0.15 0.00
94_E 383_D 0.82 0.14 0.00
59_F 557_A 0.82 0.14 0.00
36_I 569_L 0.81 0.14 0.00
104_T 417_V 0.81 0.14 0.00
36_I 608_L 0.81 0.14 0.00
35_G 94_A 0.81 0.14 0.00
19_L 324_V 0.81 0.14 0.00
53_C 320_K 0.81 0.14 0.00
3_K 113_G 0.81 0.14 0.00
67_E 549_A 0.81 0.14 0.00
31_A 331_E 0.81 0.14 0.00
3_K 283_S 0.81 0.14 0.00
98_V 251_E 0.80 0.14 0.00
63_P 612_S 0.80 0.14 0.00
75_K 361_D 0.80 0.14 0.00
26_T 539_V 0.80 0.14 0.00
64_E 234_S 0.80 0.14 0.00
72_M 608_L 0.80 0.14 0.00
57_E 495_S 0.80 0.14 0.00
21_A 358_T 0.80 0.14 0.00
108_A 446_Q 0.80 0.14 0.00
66_S 11_L 0.80 0.14 0.00
28_L 74_A 0.80 0.14 0.00
94_E 525_K 0.80 0.14 0.00
59_F 577_D 0.80 0.14 0.00
31_A 543_L 0.80 0.14 0.00
21_A 579_D 0.80 0.14 0.00
19_L 308_V 0.80 0.14 0.00
31_A 539_V 0.79 0.14 0.00
2_P 229_A 0.79 0.14 0.00
3_K 264_Q 0.79 0.14 0.00
99_E 80_N 0.79 0.14 0.00
104_T 422_D 0.79 0.14 0.00
104_T 489_S 0.79 0.14 0.00
30_V 125_N 0.79 0.14 0.00
29_D 284_V 0.79 0.13 0.00
29_D 533_K 0.79 0.13 0.00
98_V 524_V 0.79 0.13 0.00
30_V 169_K 0.79 0.13 0.00
15_D 88_L 0.79 0.13 0.00
33_R 592_T 0.78 0.13 0.00
55_V 100_Y 0.78 0.13 0.00
37_E 409_I 0.78 0.13 0.00
63_P 573_A 0.78 0.13 0.00
5_V 66_V 0.78 0.13 0.00
93_D 613_V 0.78 0.13 0.00
66_S 509_I 0.78 0.13 0.00
98_V 535_E 0.78 0.13 0.00
64_E 590_K 0.78 0.13 0.00
67_E 324_V 0.78 0.13 0.00
37_E 435_I 0.78 0.13 0.00
86_S 177_L 0.77 0.13 0.00
3_K 88_L 0.77 0.13 0.00
65_S 106_Q 0.77 0.13 0.00
31_A 291_W 0.77 0.13 0.00
81_P 543_L 0.77 0.13 0.00
64_E 508_E 0.77 0.13 0.00
28_L 360_I 0.77 0.13 0.00
37_E 7_S 0.77 0.13 0.00
46_C 444_L 0.77 0.13 0.00
45_S 41_A 0.77 0.13 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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