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OPENSEQ.org
IscUHscA
Genes: A B A+B
Length: 128 616 741
Sequences: 2384 5112 371
Seq/Len: 18.62 8.3 0.5
MirrorTree (Pazo et al. 2001) 0.55
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 0.02 0.00
2 0.00 0.02 0.03
5 0.00 0.02 0.49
10 0.00 0.03 0.50
20 0.01 0.03 0.52
100 0.01 0.04 0.67
∞ 0.02 0.08 1.69
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
57_R 30_N 1.72 0.71 0.01
108_I 191_I 1.66 0.68 0.01
29_S 276_I 1.61 0.65 0.01
98_E 434_S 1.59 0.63 0.01
98_E 455_A 1.59 0.63 0.01
86_Q 413_T 1.57 0.61 0.01
57_R 601_D 1.53 0.58 0.01
118_I 360_I 1.48 0.54 0.00
47_V 615_E 1.29 0.40 0.00
95_E 288_V 1.27 0.39 0.00
45_I 457_R 1.24 0.37 0.00
8_I 297_R 1.23 0.35 0.00
89_K 275_K 1.21 0.34 0.00
42_K 50_R 1.20 0.34 0.00
45_I 463_P 1.18 0.32 0.00
28_G 528_M 1.18 0.32 0.00
48_N 540_L 1.17 0.32 0.00
42_K 528_M 1.16 0.31 0.00
57_R 234_S 1.16 0.31 0.00
28_G 7_S 1.16 0.31 0.00
52_I 131_A 1.15 0.30 0.00
45_I 341_V 1.15 0.30 0.00
57_R 310_R 1.15 0.30 0.00
73_V 463_P 1.14 0.30 0.00
123_S 585_I 1.14 0.30 0.00
48_N 297_R 1.14 0.29 0.00
5_E 243_H 1.13 0.29 0.00
91_T 296_S 1.13 0.29 0.00
82_L 445_V 1.11 0.28 0.00
45_I 528_M 1.11 0.28 0.00
8_I 71_R 1.10 0.27 0.00
119_A 173_R 1.10 0.27 0.00
61_Y 151_G 1.10 0.27 0.00
28_G 13_A 1.09 0.27 0.00
22_N 415_I 1.08 0.26 0.00
52_I 544_H 1.08 0.26 0.00
122_K 215_I 1.07 0.26 0.00
81_S 519_Y 1.06 0.25 0.00
118_I 482_S 1.04 0.24 0.00
61_Y 191_I 1.04 0.24 0.00
88_I 545_G 1.04 0.24 0.00
19_S 113_G 1.04 0.23 0.00
26_N 385_E 1.03 0.23 0.00
20_F 484_T 1.02 0.23 0.00
45_I 615_E 1.02 0.23 0.00
118_I 318_A 1.01 0.22 0.00
61_Y 404_L 1.00 0.21 0.00
87_A 398_L 1.00 0.21 0.00
83_D 329_V 1.00 0.21 0.00
52_I 332_V 0.99 0.21 0.00
20_F 50_R 0.99 0.21 0.00
61_Y 77_D 0.99 0.21 0.00
92_D 566_A 0.98 0.21 0.00
104_I 473_F 0.98 0.21 0.00
61_Y 122_G 0.98 0.21 0.00
123_S 354_R 0.98 0.20 0.00
108_I 245_L 0.98 0.20 0.00
61_Y 427_K 0.98 0.20 0.00
28_G 615_E 0.97 0.20 0.00
49_D 279_S 0.97 0.20 0.00
87_A 312_L 0.97 0.20 0.00
91_T 496_I 0.96 0.19 0.00
86_Q 338_S 0.96 0.19 0.00
61_Y 80_N 0.95 0.19 0.00
8_I 183_L 0.95 0.19 0.00
88_I 463_P 0.95 0.19 0.00
20_F 191_I 0.94 0.19 0.00
118_I 510_A 0.94 0.19 0.00
52_I 612_S 0.94 0.19 0.00
28_G 586_K 0.94 0.19 0.00
29_S 586_K 0.94 0.19 0.00
49_D 310_R 0.94 0.18 0.00
77_V 524_V 0.94 0.18 0.00
84_E 505_T 0.94 0.18 0.00
49_D 490_T 0.94 0.18 0.00
119_A 13_A 0.93 0.18 0.00
8_I 326_A 0.93 0.18 0.00
50_E 13_A 0.93 0.18 0.00
86_Q 314_A 0.93 0.18 0.00
119_A 606_R 0.92 0.18 0.00
57_R 443_E 0.92 0.18 0.00
123_S 217_I 0.92 0.18 0.00
49_D 85_V 0.92 0.18 0.00
108_I 426_F 0.91 0.17 0.00
84_E 100_Y 0.91 0.17 0.00
122_K 327_D 0.91 0.17 0.00
8_I 413_T 0.91 0.17 0.00
89_K 169_K 0.90 0.17 0.00
47_V 457_R 0.90 0.17 0.00
28_G 533_K 0.90 0.17 0.00
28_G 582_E 0.90 0.17 0.00
108_I 100_Y 0.90 0.17 0.00
87_A 93_L 0.90 0.17 0.00
92_D 296_S 0.90 0.17 0.00
125_R 615_E 0.89 0.17 0.00
26_N 324_V 0.89 0.17 0.00
118_I 117_I 0.89 0.16 0.00
49_D 522_Q 0.89 0.16 0.00
108_I 592_T 0.89 0.16 0.00
61_Y 164_Q 0.89 0.16 0.00
91_T 612_S 0.89 0.16 0.00
83_D 462_L 0.89 0.16 0.00
87_A 559_R 0.89 0.16 0.00
95_E 350_E 0.89 0.16 0.00
26_N 123_L 0.88 0.16 0.00
50_E 111_E 0.88 0.16 0.00
45_I 125_N 0.88 0.16 0.00
52_I 511_S 0.88 0.16 0.00
91_T 271_A 0.88 0.16 0.00
28_G 588_V 0.88 0.16 0.00
57_R 522_Q 0.88 0.16 0.00
77_V 204_A 0.88 0.16 0.00
5_E 488_K 0.88 0.16 0.00
92_D 615_E 0.88 0.16 0.00
20_F 108_Q 0.87 0.16 0.00
87_A 108_Q 0.87 0.16 0.00
48_N 384_S 0.87 0.15 0.00
73_V 587_N 0.87 0.15 0.00
87_A 69_D 0.87 0.15 0.00
8_I 266_E 0.87 0.15 0.00
57_R 524_V 0.86 0.15 0.00
81_S 89_M 0.86 0.15 0.00
123_S 614_D 0.85 0.15 0.00
77_V 2_A 0.85 0.15 0.00
108_I 92_S 0.85 0.15 0.00
91_T 510_A 0.85 0.15 0.00
108_I 517_M 0.85 0.15 0.00
95_E 334_M 0.84 0.14 0.00
98_E 276_I 0.84 0.14 0.00
92_D 572_V 0.84 0.14 0.00
121_Y 245_L 0.84 0.14 0.00
26_N 557_A 0.84 0.14 0.00
31_M 151_G 0.84 0.14 0.00
84_E 93_L 0.84 0.14 0.00
115_K 82_I 0.84 0.14 0.00
28_G 398_L 0.84 0.14 0.00
8_I 290_G 0.84 0.14 0.00
108_I 167_G 0.83 0.14 0.00
22_N 437_V 0.83 0.14 0.00
24_D 219_R 0.83 0.14 0.00
31_M 5_Q 0.83 0.14 0.00
50_E 315_C 0.83 0.14 0.00
61_Y 119_T 0.83 0.14 0.00
31_M 164_Q 0.83 0.14 0.00
31_M 122_G 0.83 0.14 0.00
23_N 66_V 0.83 0.14 0.00
118_I 199_Q 0.83 0.14 0.00
25_E 613_V 0.82 0.14 0.00
45_I 408_V 0.82 0.14 0.00
123_S 17_Q 0.82 0.14 0.00
49_D 145_L 0.82 0.14 0.00
95_E 82_I 0.82 0.14 0.00
52_I 384_S 0.82 0.14 0.00
91_T 83_S 0.82 0.14 0.00
23_N 496_I 0.82 0.14 0.00
118_I 557_A 0.82 0.14 0.00
91_T 48_E 0.81 0.13 0.00
50_E 14_A 0.81 0.13 0.00
73_V 413_T 0.81 0.13 0.00
94_A 421_Q 0.81 0.13 0.00
125_R 173_R 0.81 0.13 0.00
20_F 414_T 0.81 0.13 0.00
61_Y 19_R 0.81 0.13 0.00
123_S 93_L 0.81 0.13 0.00
82_L 568_H 0.81 0.13 0.00
92_D 298_E 0.81 0.13 0.00
45_I 263_V 0.80 0.13 0.00
5_E 495_S 0.80 0.13 0.00
57_R 577_D 0.80 0.13 0.00
19_S 205_V 0.80 0.13 0.00
61_Y 183_L 0.80 0.13 0.00
22_N 19_R 0.80 0.13 0.00
123_S 587_N 0.80 0.13 0.00
20_F 243_H 0.80 0.13 0.00
50_E 92_S 0.80 0.13 0.00
91_T 605_R 0.80 0.13 0.00
124_K 270_A 0.80 0.13 0.00
120_D 169_K 0.79 0.13 0.00
8_I 217_I 0.79 0.13 0.00
19_S 331_E 0.79 0.13 0.00
19_S 592_T 0.79 0.13 0.00
22_N 539_V 0.79 0.13 0.00
87_A 382_P 0.79 0.13 0.00
26_N 74_A 0.79 0.12 0.00
119_A 552_A 0.79 0.12 0.00
125_R 98_Q 0.79 0.12 0.00
42_K 74_A 0.78 0.12 0.00
52_I 378_V 0.78 0.12 0.00
122_K 590_K 0.78 0.12 0.00
42_K 233_D 0.78 0.12 0.00
118_I 257_D 0.78 0.12 0.00
42_K 505_T 0.78 0.12 0.00
7_V 296_S 0.78 0.12 0.00
119_A 537_A 0.77 0.12 0.00
23_N 586_K 0.77 0.12 0.00
81_S 167_G 0.77 0.12 0.00
26_N 575_G 0.77 0.12 0.00
8_I 324_V 0.77 0.12 0.00
118_I 221_S 0.77 0.12 0.00
31_M 404_L 0.77 0.12 0.00
8_I 11_L 0.77 0.12 0.00
123_S 285_T 0.77 0.12 0.00
28_G 52_L 0.77 0.12 0.00
8_I 13_A 0.77 0.12 0.00
57_R 274_A 0.77 0.12 0.00
19_S 515_D 0.76 0.12 0.00
26_N 279_S 0.76 0.12 0.00
123_S 262_R 0.76 0.12 0.00
61_Y 494_A 0.76 0.12 0.00
108_I 604_V 0.76 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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