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OPENSEQ.org
cI_2_4_cI_3_4_ec
Genes: A B A+B
Length: 166 908 1034
Sequences: 2609 706 516
Seq/Len: 15.72 0.78 0.5
MirrorTree (Pazo et al. 2001) 0.71
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 0.07
2 0.01 0.00 0.42
5 0.01 0.00 0.44
10 0.02 0.01 0.44
20 0.02 0.02 0.44
100 0.04 0.03 0.45
∞ 0.10 0.07 0.48
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
65_P 434_V 1.46 0.53 0.00
25_E 676_V 1.36 0.45 0.00
156_E 475_I 1.32 0.43 0.00
65_P 489_A 1.21 0.35 0.00
145_I 9_K 1.20 0.34 0.00
50_V 73_D 1.20 0.34 0.00
89_I 689_A 1.16 0.31 0.00
121_T 296_E 1.11 0.28 0.00
51_P 393_V 1.08 0.26 0.00
50_V 689_A 1.07 0.26 0.00
94_S 7_D 1.06 0.25 0.00
118_G 325_N 1.05 0.24 0.00
43_V 203_T 1.05 0.24 0.00
115_I 27_G 1.04 0.24 0.00
130_P 24_L 1.04 0.24 0.00
49_W 659_L 1.02 0.23 0.00
99_I 569_N 1.01 0.22 0.00
103_Q 453_D 0.99 0.21 0.00
77_S 88_R 0.99 0.21 0.00
140_G 495_K 0.98 0.21 0.00
121_T 244_G 0.98 0.21 0.00
37_I 28_L 0.98 0.21 0.00
136_N 433_N 0.98 0.20 0.00
94_S 20_L 0.97 0.20 0.00
44_Q 103_C 0.97 0.20 0.00
94_S 171_G 0.97 0.20 0.00
102_Y 586_K 0.96 0.20 0.00
67_S 269_G 0.96 0.20 0.00
77_S 156_R 0.96 0.20 0.00
77_S 369_I 0.96 0.19 0.00
49_W 693_A 0.95 0.19 0.00
37_I 306_L 0.95 0.19 0.00
73_A 583_A 0.94 0.19 0.00
109_L 576_S 0.94 0.19 0.00
82_Q 655_L 0.94 0.19 0.00
77_S 30_I 0.94 0.19 0.00
89_I 576_S 0.94 0.19 0.00
145_I 244_G 0.94 0.19 0.00
140_G 648_S 0.93 0.18 0.00
110_E 452_E 0.93 0.18 0.00
140_G 628_Q 0.93 0.18 0.00
55_I 270_Y 0.93 0.18 0.00
68_D 327_A 0.93 0.18 0.00
145_I 653_H 0.92 0.18 0.00
109_L 495_K 0.92 0.18 0.00
74_T 210_T 0.92 0.18 0.00
39_A 28_L 0.92 0.18 0.00
147_E 305_I 0.92 0.18 0.00
99_I 7_D 0.92 0.18 0.00
63_G 646_L 0.91 0.17 0.00
123_D 106_C 0.91 0.17 0.00
128_L 24_L 0.90 0.17 0.00
127_T 663_E 0.90 0.17 0.00
136_N 146_H 0.90 0.17 0.00
58_I 294_N 0.90 0.17 0.00
59_A 634_Y 0.89 0.17 0.00
106_Q 276_K 0.89 0.17 0.00
115_I 284_Q 0.89 0.17 0.00
43_V 370_E 0.89 0.16 0.00
65_P 301_G 0.89 0.16 0.00
26_M 555_E 0.89 0.16 0.00
75_F 383_T 0.89 0.16 0.00
89_I 296_E 0.88 0.16 0.00
99_I 397_V 0.88 0.16 0.00
39_A 141_G 0.88 0.16 0.00
129_L 108_E 0.88 0.16 0.00
123_D 326_F 0.88 0.16 0.00
22_I 560_R 0.88 0.16 0.00
128_L 331_L 0.87 0.16 0.00
146_D 90_S 0.87 0.16 0.00
70_E 496_P 0.87 0.16 0.00
161_L 6_V 0.87 0.16 0.00
143_M 684_A 0.87 0.16 0.00
138_D 153_A 0.87 0.15 0.00
146_D 541_L 0.87 0.15 0.00
42_I 435_D 0.87 0.15 0.00
74_T 633_V 0.86 0.15 0.00
158_I 390_A 0.86 0.15 0.00
102_Y 627_A 0.86 0.15 0.00
22_I 595_H 0.86 0.15 0.00
136_N 648_S 0.86 0.15 0.00
50_V 108_E 0.85 0.15 0.00
57_A 398_K 0.85 0.15 0.00
105_I 366_L 0.85 0.15 0.00
73_A 148_M 0.85 0.15 0.00
47_R 341_I 0.85 0.15 0.00
150_H 299_M 0.85 0.15 0.00
146_D 307_R 0.85 0.15 0.00
127_T 512_A 0.84 0.14 0.00
111_K 186_D 0.84 0.14 0.00
157_A 443_A 0.83 0.14 0.00
115_I 469_A 0.83 0.14 0.00
74_T 142_P 0.83 0.14 0.00
59_A 47_Q 0.83 0.14 0.00
109_L 326_F 0.82 0.14 0.00
149_T 328_L 0.82 0.14 0.00
126_F 82_E 0.82 0.14 0.00
134_L 683_L 0.82 0.14 0.00
60_D 448_R 0.82 0.14 0.00
67_S 569_N 0.82 0.14 0.00
115_I 629_R 0.82 0.14 0.00
148_D 130_F 0.82 0.14 0.00
109_L 553_L 0.81 0.14 0.00
37_I 269_G 0.81 0.14 0.00
76_Y 600_I 0.81 0.13 0.00
54_A 334_E 0.81 0.13 0.00
51_P 633_V 0.81 0.13 0.00
149_T 268_F 0.80 0.13 0.00
150_H 97_T 0.80 0.13 0.00
48_G 649_W 0.80 0.13 0.00
123_D 115_Q 0.80 0.13 0.00
126_F 30_I 0.80 0.13 0.00
130_P 519_A 0.80 0.13 0.00
34_A 41_S 0.80 0.13 0.00
123_D 112_C 0.79 0.13 0.00
49_W 483_I 0.79 0.13 0.00
154_T 473_D 0.79 0.13 0.00
68_D 421_I 0.79 0.13 0.00
73_A 347_E 0.79 0.13 0.00
86_R 585_A 0.79 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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