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OPENSEQ.org
iscxiscs
Genes: A B A+B
Length: 66 404 470
Sequences: 255 8787 119
Seq/Len: 3.86 21.75 0.25
MirrorTree (Pazo et al. 2001) 0.18
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.02 0.03
10 0.00 0.03 0.24
20 0.00 0.04 0.25
100 0.00 0.09 0.27
∞ 0.00 0.18 0.37
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
10_E 307_Y 1.56 0.41 0.00
62_L 63_G 1.43 0.33 0.00
50_N 383_L 1.35 0.29 0.00
63_D 377_I 1.26 0.24 0.00
52_K 377_I 1.26 0.24 0.00
58_L 256_Y 1.26 0.24 0.00
30_T 71_F 1.24 0.23 0.00
62_L 258_I 1.20 0.21 0.00
35_W 370_I 1.20 0.21 0.00
22_L 373_V 1.19 0.21 0.00
63_D 170_C 1.17 0.20 0.00
27_V 43_F 1.14 0.19 0.00
6_T 52_D 1.12 0.18 0.00
28_R 71_F 1.10 0.17 0.00
13_E 366_I 1.07 0.16 0.00
40_E 126_P 1.06 0.16 0.00
63_D 383_L 1.04 0.15 0.00
52_K 169_M 1.04 0.15 0.00
50_N 284_I 1.00 0.14 0.00
19_Y 126_P 1.00 0.14 0.00
19_Y 169_M 0.99 0.14 0.00
21_D 377_I 0.99 0.14 0.00
49_S 348_L 0.99 0.14 0.00
27_V 194_Q 0.98 0.14 0.00
24_P 94_G 0.98 0.14 0.00
36_I 5_I 0.98 0.13 0.00
3_L 368_Y 0.97 0.13 0.00
48_A 390_Y 0.97 0.13 0.00
1_M 1_M 0.97 0.13 0.00
35_W 307_Y 0.96 0.13 0.00
32_M 182_T 0.96 0.13 0.00
4_K 370_I 0.96 0.13 0.00
12_G 213_I 0.96 0.13 0.00
50_N 403_H 0.95 0.12 0.00
4_K 176_I 0.93 0.12 0.00
37_C 67_R 0.92 0.12 0.00
24_P 235_H 0.91 0.12 0.00
10_E 284_I 0.91 0.11 0.00
48_A 287_V 0.91 0.11 0.00
30_T 125_A 0.90 0.11 0.00
63_D 394_V 0.90 0.11 0.00
12_G 270_L 0.89 0.11 0.00
49_S 284_I 0.89 0.11 0.00
25_K 179_V 0.89 0.11 0.00
53_I 161_Q 0.89 0.11 0.00
48_A 284_I 0.87 0.10 0.00
38_D 86_A 0.87 0.10 0.00
62_L 182_T 0.87 0.10 0.00
50_N 366_I 0.87 0.10 0.00
17_D 176_I 0.86 0.10 0.00
62_L 306_N 0.86 0.10 0.00
3_L 143_D 0.86 0.10 0.00
21_D 383_L 0.86 0.10 0.00
8_S 52_D 0.86 0.10 0.00
19_Y 150_I 0.85 0.10 0.00
36_I 402_A 0.85 0.10 0.00
3_L 204_G 0.85 0.10 0.00
65_A 306_N 0.84 0.10 0.00
52_K 159_V 0.84 0.10 0.00
14_A 382_D 0.83 0.10 0.00
52_K 388_E 0.83 0.10 0.00
27_V 21_E 0.83 0.10 0.00
24_P 61_L 0.83 0.10 0.00
14_A 98_I 0.83 0.10 0.00
41_D 281_I 0.83 0.10 0.00
23_D 17_P 0.83 0.10 0.00
14_A 265_T 0.83 0.10 0.00
34_Q 383_L 0.82 0.09 0.00
36_I 58_I 0.82 0.09 0.00
21_D 265_T 0.82 0.09 0.00
28_R 374_R 0.82 0.09 0.00
63_D 261_E 0.82 0.09 0.00
30_T 383_L 0.82 0.09 0.00
22_L 58_I 0.81 0.09 0.00
62_L 254_E 0.81 0.09 0.00
56_A 115_E 0.81 0.09 0.00
8_S 306_N 0.81 0.09 0.00
52_K 137_L 0.81 0.09 0.00
33_H 284_I 0.81 0.09 0.00
28_R 26_F 0.80 0.09 0.00
26_T 79_D 0.80 0.09 0.00
28_R 383_L 0.80 0.09 0.00
40_E 132_I 0.79 0.09 0.00
30_T 58_I 0.79 0.09 0.00
63_D 371_E 0.79 0.09 0.00
63_D 219_R 0.79 0.09 0.00
27_V 373_V 0.79 0.09 0.00
35_W 141_M 0.79 0.09 0.00
27_V 30_D 0.78 0.09 0.00
21_D 392_Q 0.78 0.09 0.00
33_H 275_N 0.78 0.09 0.00
56_A 171_R 0.78 0.09 0.00
27_V 184_S 0.78 0.08 0.00
19_Y 132_I 0.78 0.08 0.00
58_L 58_I 0.78 0.08 0.00
48_A 46_Q 0.77 0.08 0.00
18_A 200_M 0.77 0.08 0.00
53_I 62_V 0.76 0.08 0.00
53_I 399_I 0.76 0.08 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)
ID Seq/Len Name Options I_Prob Status
1461 0.27 iscxiscs Δgene:(1, 10) A:(1E-02, 4) B:(1E-06, 4) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1459 0.25 iscxiscs Δgene:(1, 20) A:(1E-06, 2) B:(1E-06, 2) msa: Jackhmmer (2014_03) 0.00 Done - Shared
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