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OPENSEQ.org
iscxiscs
Genes: A B A+B
Length: 66 404 469
Sequences: 256 32154 126
Seq/Len: 3.88 79.59 0.27
MirrorTree (Pazo et al. 2001) 0.16
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 0.01
2 0.00 0.03 0.01
5 0.00 0.05 0.05
10 0.00 0.06 0.27
20 0.00 0.10 0.27
100 0.00 0.20 0.35
∞ 0.00 0.25 0.45
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 1.49 0.39 0.00
22_L 373_V 1.43 0.35 0.00
58_L 256_Y 1.30 0.27 0.00
62_L 63_G 1.29 0.27 0.00
63_D 377_I 1.28 0.26 0.00
53_I 399_I 1.26 0.26 0.00
13_E 366_I 1.24 0.24 0.00
50_N 284_I 1.22 0.23 0.00
52_K 169_M 1.20 0.23 0.00
27_V 43_F 1.20 0.22 0.00
62_L 258_I 1.15 0.20 0.00
30_T 71_F 1.13 0.20 0.00
52_K 377_I 1.12 0.19 0.00
32_M 182_T 1.12 0.19 0.00
50_N 383_L 1.12 0.19 0.00
27_V 21_E 1.08 0.17 0.00
48_A 390_Y 1.07 0.17 0.00
53_I 7_L 1.06 0.17 0.00
57_I 219_R 1.06 0.17 0.00
49_S 348_L 1.06 0.17 0.00
24_P 94_G 1.06 0.17 0.00
27_V 391_K 1.04 0.16 0.00
23_D 17_P 1.04 0.16 0.00
24_P 61_L 1.03 0.16 0.00
21_D 377_I 1.03 0.16 0.00
28_R 71_F 1.03 0.16 0.00
27_V 194_Q 1.02 0.15 0.00
10_E 284_I 1.02 0.15 0.00
38_D 86_A 1.01 0.15 0.00
21_D 392_Q 1.01 0.15 0.00
6_T 52_D 1.00 0.15 0.00
27_V 373_V 1.00 0.15 0.00
12_G 270_L 0.99 0.14 0.00
63_D 170_C 0.98 0.14 0.00
58_L 58_I 0.96 0.13 0.00
50_N 71_F 0.96 0.13 0.00
3_L 143_D 0.95 0.13 0.00
63_D 383_L 0.95 0.13 0.00
14_A 98_I 0.94 0.13 0.00
30_T 383_L 0.94 0.13 0.00
13_E 67_R 0.93 0.13 0.00
38_D 26_F 0.93 0.13 0.00
21_D 383_L 0.93 0.12 0.00
36_I 5_I 0.93 0.12 0.00
40_E 132_I 0.92 0.12 0.00
4_K 370_I 0.92 0.12 0.00
4_K 176_I 0.92 0.12 0.00
28_R 383_L 0.92 0.12 0.00
52_K 388_E 0.91 0.12 0.00
12_G 213_I 0.91 0.12 0.00
34_Q 383_L 0.90 0.12 0.00
3_L 368_Y 0.89 0.12 0.00
14_A 265_T 0.89 0.11 0.00
62_L 182_T 0.89 0.11 0.00
17_D 63_G 0.89 0.11 0.00
24_P 235_H 0.88 0.11 0.00
28_R 26_F 0.88 0.11 0.00
44_D 180_D 0.87 0.11 0.00
44_D 206_K 0.87 0.11 0.00
33_H 275_N 0.87 0.11 0.00
36_I 46_Q 0.87 0.11 0.00
29_F 94_G 0.87 0.11 0.00
49_S 284_I 0.86 0.11 0.00
36_I 320_L 0.86 0.11 0.00
25_K 25_Q 0.86 0.11 0.00
40_E 375_K 0.85 0.10 0.00
48_A 284_I 0.85 0.10 0.00
19_Y 132_I 0.85 0.10 0.00
17_D 176_I 0.85 0.10 0.00
3_L 43_F 0.84 0.10 0.00
17_D 143_D 0.84 0.10 0.00
17_D 175_I 0.84 0.10 0.00
40_E 258_I 0.83 0.10 0.00
65_A 306_N 0.83 0.10 0.00
30_T 125_A 0.83 0.10 0.00
63_D 261_E 0.83 0.10 0.00
59_L 46_Q 0.82 0.10 0.00
52_K 159_V 0.82 0.10 0.00
14_A 377_I 0.81 0.10 0.00
37_C 67_R 0.81 0.09 0.00
36_I 402_A 0.80 0.09 0.00
3_L 398_S 0.80 0.09 0.00
35_W 307_Y 0.80 0.09 0.00
63_D 372_L 0.79 0.09 0.00
62_L 267_M 0.79 0.09 0.00
6_T 391_K 0.79 0.09 0.00
7_D 121_V 0.79 0.09 0.00
41_D 281_I 0.79 0.09 0.00
43_D 394_V 0.79 0.09 0.00
1_M 368_Y 0.78 0.09 0.00
36_I 267_M 0.78 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)
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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