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OPENSEQ.org
iscaiscu
Genes: A B A+B
Length: 107 128 233
Sequences: 2597 1994 233
Seq/Len: 24.27 15.58 1
MirrorTree (Pazo et al. 2001) 0.61
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 0.99
2 0.00 0.00 1.09
5 0.00 0.00 1.14
10 0.00 0.00 1.16
20 0.01 0.00 1.29
100 0.02 0.00 1.74
∞ 0.10 0.03 3.34
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
24_F 118_I 1.42 0.71 0.01
77_L 73_V 1.28 0.60 0.00
13_V 42_K 1.26 0.57 0.00
83_G 61_Y 1.24 0.56 0.00
29_G 89_K 1.22 0.54 0.00
51_E 82_L 1.16 0.48 0.00
23_G 61_Y 1.14 0.46 0.00
56_E 20_F 1.12 0.45 0.00
64_V 116_A 1.12 0.44 0.00
62_V 122_K 1.10 0.43 0.00
89_K 46_K 1.10 0.43 0.00
43_E 94_A 1.10 0.43 0.00
26_L 45_I 1.10 0.42 0.00
12_R 122_K 1.08 0.41 0.00
53_I 122_K 1.07 0.41 0.00
10_A 73_V 1.06 0.40 0.00
83_G 31_M 1.06 0.39 0.00
36_S 82_L 1.05 0.39 0.00
55_F 49_D 1.04 0.37 0.00
22_K 61_Y 1.03 0.36 0.00
88_F 113_A 1.02 0.36 0.00
4_T 121_Y 1.01 0.35 0.00
42_L 42_K 1.01 0.35 0.00
17_L 20_F 1.00 0.34 0.00
19_N 122_K 1.00 0.34 0.00
47_E 84_E 0.99 0.33 0.00
4_T 123_S 0.98 0.32 0.00
43_E 78_K 0.96 0.31 0.00
41_V 8_I 0.96 0.31 0.00
47_E 50_E 0.96 0.31 0.00
18_A 8_I 0.95 0.30 0.00
62_V 20_F 0.95 0.30 0.00
62_V 116_A 0.95 0.30 0.00
19_N 123_S 0.94 0.29 0.00
33_S 98_E 0.94 0.29 0.00
3_I 26_N 0.94 0.29 0.00
30_V 83_D 0.93 0.28 0.00
50_P 93_I 0.93 0.28 0.00
56_E 5_E 0.93 0.28 0.00
95_V 47_V 0.92 0.28 0.00
106_H 20_F 0.91 0.27 0.00
28_L 77_V 0.91 0.27 0.00
28_L 118_I 0.91 0.27 0.00
100_G 35_P 0.89 0.26 0.00
6_S 9_D 0.89 0.26 0.00
45_V 22_N 0.89 0.25 0.00
103_E 2_A 0.89 0.25 0.00
2_S 77_V 0.88 0.25 0.00
91_T 104_I 0.88 0.24 0.00
39_A 82_L 0.87 0.24 0.00
31_R 83_D 0.86 0.24 0.00
62_V 26_N 0.86 0.23 0.00
7_D 49_D 0.85 0.23 0.00
33_S 61_Y 0.85 0.23 0.00
27_R 79_G 0.85 0.23 0.00
13_V 73_V 0.85 0.23 0.00
39_A 88_I 0.85 0.23 0.00
66_G 28_G 0.85 0.23 0.00
100_G 96_E 0.84 0.22 0.00
3_I 95_E 0.84 0.22 0.00
64_V 92_D 0.84 0.22 0.00
8_S 119_A 0.84 0.22 0.00
30_V 118_I 0.83 0.22 0.00
8_S 92_D 0.83 0.21 0.00
44_F 8_I 0.82 0.21 0.00
4_T 125_R 0.82 0.21 0.00
26_L 108_I 0.82 0.21 0.00
71_F 69_S 0.82 0.21 0.00
15_T 125_R 0.81 0.20 0.00
32_T 31_M 0.81 0.20 0.00
86_E 77_V 0.81 0.20 0.00
31_R 15_R 0.81 0.20 0.00
34_G 18_G 0.81 0.20 0.00
26_L 28_G 0.81 0.20 0.00
62_V 124_K 0.80 0.20 0.00
88_F 74_T 0.80 0.20 0.00
12_R 25_E 0.80 0.20 0.00
105_F 79_G 0.80 0.20 0.00
64_V 121_Y 0.80 0.19 0.00
103_E 104_I 0.80 0.19 0.00
49_T 52_I 0.79 0.19 0.00
5_L 61_Y 0.79 0.19 0.00
58_K 83_D 0.79 0.19 0.00
7_D 82_L 0.79 0.19 0.00
6_S 88_I 0.79 0.19 0.00
28_L 15_R 0.79 0.19 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
1472 1.15 iscaiscu Δgene:(0, 5) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.44 Done - Shared
1471 1 iscaiscu Δgene:(0, 1) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.01 Done - Shared
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