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OPENSEQ.org
iscuisca
Genes: A B A+B
Length: 128 107 233
Sequences: 2384 2875 298
Seq/Len: 18.62 26.87 1.28
MirrorTree (Pazo et al. 2001) 0.55
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 1.14
2 0.00 0.00 1.27
5 0.00 0.01 1.32
10 0.00 0.01 1.34
20 0.01 0.02 1.53
100 0.01 0.03 2.09
∞ 0.02 0.09 3.80
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
118_I 62_V 1.55 0.86 0.14
46_K 89_K 1.39 0.76 0.09
122_K 62_V 1.30 0.69 0.07
104_I 79_F 1.24 0.63 0.06
26_N 62_V 1.22 0.62 0.05
73_V 77_L 1.20 0.59 0.05
118_I 24_F 1.17 0.57 0.05
88_I 22_K 1.15 0.54 0.04
61_Y 83_G 1.13 0.52 0.04
113_A 88_F 1.09 0.49 0.04
10_H 56_E 1.09 0.48 0.03
74_T 88_F 1.08 0.48 0.03
15_R 28_L 1.07 0.47 0.03
118_I 30_V 1.06 0.46 0.03
122_K 53_I 1.06 0.46 0.03
8_I 18_A 1.05 0.45 0.03
77_V 61_K 1.04 0.44 0.03
122_K 12_R 1.02 0.42 0.03
7_V 45_V 1.02 0.42 0.03
20_F 22_K 1.01 0.41 0.03
35_P 100_G 1.00 0.40 0.03
77_V 28_L 0.98 0.38 0.02
123_S 79_F 0.98 0.38 0.02
73_V 10_A 0.97 0.38 0.02
49_D 6_S 0.96 0.37 0.02
31_M 45_V 0.96 0.36 0.02
15_R 56_E 0.96 0.36 0.02
78_K 43_E 0.95 0.35 0.02
8_I 44_F 0.93 0.34 0.02
26_N 3_I 0.93 0.33 0.02
82_L 81_K 0.92 0.33 0.02
21_D 18_A 0.92 0.33 0.02
98_E 33_S 0.90 0.31 0.02
31_M 76_Q 0.90 0.31 0.02
122_K 63_V 0.90 0.31 0.02
20_F 29_G 0.90 0.31 0.02
108_I 26_L 0.90 0.31 0.02
88_I 14_N 0.90 0.31 0.02
82_L 36_S 0.90 0.30 0.02
125_R 5_L 0.88 0.29 0.02
86_Q 103_E 0.88 0.29 0.02
28_G 26_L 0.87 0.28 0.02
21_D 4_T 0.86 0.28 0.01
61_Y 33_S 0.86 0.28 0.01
61_Y 23_G 0.86 0.27 0.01
94_A 43_E 0.85 0.27 0.01
57_R 47_E 0.85 0.27 0.01
7_V 4_T 0.85 0.27 0.01
89_K 33_S 0.85 0.27 0.01
13_N 38_M 0.85 0.27 0.01
92_D 63_V 0.84 0.26 0.01
42_K 42_L 0.84 0.26 0.01
7_V 78_D 0.83 0.26 0.01
88_I 8_S 0.83 0.26 0.01
86_Q 31_R 0.83 0.25 0.01
48_N 8_S 0.82 0.24 0.01
44_Q 46_D 0.82 0.24 0.01
61_Y 51_E 0.81 0.24 0.01
111_E 100_G 0.81 0.24 0.01
41_M 70_Q 0.81 0.24 0.01
96_E 71_F 0.81 0.24 0.01
14_P 27_R 0.81 0.24 0.01
114_I 44_F 0.80 0.23 0.01
95_E 82_E 0.80 0.23 0.01
47_V 95_V 0.80 0.23 0.01
5_E 62_V 0.79 0.23 0.01
73_V 13_V 0.79 0.23 0.01
13_N 60_V 0.78 0.22 0.01
54_E 82_E 0.78 0.21 0.01
36_A 86_E 0.77 0.21 0.01
122_K 19_N 0.77 0.21 0.01
77_V 82_E 0.77 0.21 0.01
101_P 67_K 0.77 0.21 0.01
14_P 6_S 0.77 0.21 0.01
88_I 39_A 0.76 0.20 0.01
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
2092 1.35 IscUIscA Δgene:(1, 10) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.81 Done - Shared
2008 1.28 iscuisca Δgene:(1, 2) A:(1E-10, 8) B:(1E-10, 4) msa: Jackhmmer (2015_03) 0.14 Done - Shared
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