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OPENSEQ.org
iscxiscs
Genes: A B A+B
Length: 59 380 439
Sequences: 264 37240 129
Seq/Len: 4.47 98 0.29
MirrorTree (Pazo et al. 2001) 0.14
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 0.03 0.02
2 0.00 0.03 0.02
5 0.00 0.05 0.06
10 0.00 0.07 0.29
20 0.00 0.11 0.31
100 0.00 0.22 0.38
∞ 0.00 0.28 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
11_E 363_I 1.59 0.47 0.00
56_L 253_Y 1.49 0.40 0.00
8_E 304_Y 1.47 0.39 0.00
34_I 317_L 1.36 0.32 0.00
25_V 40_F 1.32 0.30 0.00
50_K 374_I 1.27 0.27 0.00
10_G 267_L 1.26 0.27 0.00
30_M 179_T 1.22 0.25 0.00
34_I 161_A 1.18 0.22 0.00
48_N 281_I 1.14 0.21 0.00
20_L 370_V 1.13 0.20 0.00
21_D 14_P 1.13 0.20 0.00
28_T 68_F 1.13 0.20 0.00
36_D 83_A 1.12 0.20 0.00
1_L 365_Y 1.10 0.19 0.00
47_S 345_L 1.09 0.19 0.00
12_A 95_I 1.09 0.19 0.00
4_T 49_D 1.09 0.19 0.00
55_I 216_R 1.08 0.18 0.00
56_L 55_I 1.04 0.17 0.00
22_P 58_L 1.04 0.17 0.00
5_D 118_V 1.03 0.17 0.00
27_F 91_G 1.02 0.16 0.00
33_W 367_I 1.02 0.16 0.00
26_R 68_F 1.01 0.16 0.00
48_N 68_F 1.01 0.16 0.00
46_A 370_V 0.99 0.15 0.00
42_D 177_D 0.99 0.15 0.00
42_D 203_K 0.99 0.15 0.00
22_P 91_G 0.98 0.15 0.00
25_V 18_E 0.96 0.14 0.00
2_K 173_I 0.96 0.14 0.00
2_K 300_V 0.95 0.14 0.00
50_K 166_M 0.95 0.14 0.00
8_E 281_I 0.95 0.14 0.00
25_V 191_Q 0.95 0.14 0.00
25_V 370_V 0.94 0.13 0.00
47_S 281_I 0.93 0.13 0.00
51_I 136_A 0.93 0.13 0.00
26_R 371_R 0.93 0.13 0.00
28_T 122_A 0.93 0.13 0.00
25_V 27_D 0.92 0.13 0.00
56_L 179_T 0.91 0.13 0.00
22_P 232_H 0.91 0.12 0.00
11_E 64_R 0.91 0.12 0.00
17_Y 129_I 0.90 0.12 0.00
50_K 156_V 0.89 0.12 0.00
36_D 165_E 0.89 0.12 0.00
12_A 262_T 0.88 0.12 0.00
26_R 23_F 0.88 0.12 0.00
31_H 272_N 0.86 0.11 0.00
15_D 172_I 0.86 0.11 0.00
17_Y 147_I 0.86 0.11 0.00
10_G 294_A 0.85 0.11 0.00
1_L 201_G 0.85 0.11 0.00
19_D 374_I 0.85 0.11 0.00
36_D 23_F 0.85 0.11 0.00
38_E 255_I 0.84 0.10 0.00
46_A 281_I 0.83 0.10 0.00
38_E 129_I 0.83 0.10 0.00
51_I 158_Q 0.82 0.10 0.00
15_D 173_I 0.82 0.10 0.00
30_M 253_Y 0.82 0.10 0.00
34_I 265_E 0.82 0.10 0.00
58_V 210_I 0.82 0.10 0.00
1_L 140_D 0.81 0.10 0.00
51_I 353_S 0.80 0.10 0.00
39_D 278_I 0.80 0.10 0.00
4_T 172_I 0.80 0.10 0.00
34_I 2_I 0.79 0.09 0.00
8_E 18_E 0.79 0.09 0.00
42_D 8_A 0.78 0.09 0.00
42_D 167_C 0.78 0.09 0.00
23_K 22_Q 0.78 0.09 0.00
12_A 369_L 0.78 0.09 0.00
48_N 311_I 0.78 0.09 0.00
15_D 60_G 0.78 0.09 0.00
57_L 169_A 0.78 0.09 0.00
25_V 110_Q 0.78 0.09 0.00
31_H 281_I 0.77 0.09 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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