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OPENSEQ.org
IscUIscA
Genes: A B A+B
Length: 128 107 233
Sequences: 2384 2921 315
Seq/Len: 18.62 27.3 1.35
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 3.82
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 1.89 0.96 0.81
122_K 62_V 1.83 0.95 0.78
118_I 24_F 1.53 0.86 0.55
46_K 89_K 1.45 0.81 0.48
73_V 77_L 1.17 0.58 0.23
15_R 28_L 1.14 0.56 0.21
61_Y 83_G 1.14 0.55 0.21
26_N 3_I 1.14 0.55 0.21
13_N 38_M 1.11 0.52 0.19
88_I 14_N 1.10 0.51 0.18
122_K 63_V 1.08 0.49 0.17
118_I 30_V 1.05 0.46 0.15
88_I 22_K 1.04 0.45 0.15
41_M 70_Q 1.03 0.44 0.14
82_L 81_K 1.02 0.43 0.14
86_Q 103_E 1.02 0.43 0.14
122_K 19_N 1.02 0.43 0.14
74_T 88_F 1.01 0.42 0.13
10_H 56_E 1.00 0.42 0.13
26_N 62_V 1.00 0.41 0.13
119_A 8_S 0.99 0.40 0.12
86_Q 31_R 0.97 0.38 0.11
10_H 38_M 0.97 0.38 0.11
25_E 26_L 0.94 0.36 0.10
122_K 53_I 0.94 0.36 0.10
8_I 18_A 0.93 0.35 0.10
61_Y 33_S 0.91 0.33 0.09
31_M 76_Q 0.91 0.33 0.09
98_E 33_S 0.90 0.32 0.08
4_S 3_I 0.90 0.32 0.08
24_D 56_E 0.90 0.32 0.08
35_P 100_G 0.90 0.32 0.08
108_I 26_L 0.89 0.31 0.08
8_I 44_F 0.89 0.31 0.08
111_E 100_G 0.88 0.30 0.08
73_V 13_V 0.87 0.29 0.07
47_V 95_V 0.87 0.29 0.07
14_P 27_R 0.86 0.29 0.07
23_N 31_R 0.86 0.29 0.07
82_L 26_L 0.86 0.29 0.07
20_F 29_G 0.86 0.29 0.07
113_A 88_F 0.86 0.29 0.07
104_I 79_F 0.86 0.28 0.07
77_V 61_K 0.85 0.28 0.07
51_G 41_V 0.85 0.28 0.07
95_E 62_V 0.85 0.28 0.07
125_R 5_L 0.84 0.27 0.06
47_V 28_L 0.84 0.27 0.06
7_V 4_T 0.84 0.27 0.06
53_I 30_V 0.84 0.27 0.06
92_D 63_V 0.84 0.27 0.06
118_I 49_T 0.83 0.26 0.06
8_I 41_V 0.83 0.26 0.06
7_V 78_D 0.83 0.26 0.06
49_D 55_F 0.83 0.26 0.06
44_Q 46_D 0.82 0.25 0.06
20_F 57_D 0.81 0.25 0.06
104_I 103_E 0.81 0.25 0.06
116_A 64_V 0.81 0.24 0.06
7_V 45_V 0.80 0.24 0.05
89_K 33_S 0.79 0.23 0.05
119_A 7_D 0.79 0.23 0.05
84_E 61_K 0.79 0.23 0.05
57_R 47_E 0.79 0.23 0.05
61_Y 23_G 0.78 0.23 0.05
89_K 26_L 0.78 0.23 0.05
36_A 85_N 0.78 0.23 0.05
61_Y 85_N 0.78 0.23 0.05
15_R 56_E 0.78 0.22 0.05
84_E 4_T 0.77 0.22 0.05
48_N 8_S 0.77 0.22 0.05
95_E 28_L 0.77 0.22 0.04
9_D 4_T 0.77 0.22 0.04
96_E 71_F 0.77 0.21 0.04
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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