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OPENSEQ.org
cI_K_20_cIII_isp_20_Pdenitr
Genes: A B A+B
Length: 101 190 285
Sequences: 1319 1043 289
Seq/Len: 13.06 5.49 1.01
MirrorTree (Pazo et al. 2001) 0.45
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 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.08
∞ 0.03 0.02 0.99
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
57_L 93_D 1.39 0.69 0.01
81_L 98_I 1.38 0.68 0.00
81_L 62_E 1.29 0.61 0.00
1_M 25_G 1.23 0.55 0.00
31_V 187_I 1.19 0.51 0.00
11_G 131_V 1.14 0.47 0.00
24_V 176_I 1.13 0.46 0.00
10_V 66_Q 1.11 0.44 0.00
99_M 175_H 1.10 0.43 0.00
99_M 153_P 1.08 0.41 0.00
63_T 24_A 1.08 0.41 0.00
96_V 159_Y 1.07 0.40 0.00
17_T 70_K 1.06 0.40 0.00
2_I 48_V 1.05 0.39 0.00
61_V 176_I 1.05 0.38 0.00
39_M 23_T 1.02 0.36 0.00
20_F 79_R 1.02 0.36 0.00
96_V 77_F 1.01 0.35 0.00
42_A 113_T 1.01 0.35 0.00
32_I 115_E 1.00 0.35 0.00
3_G 127_V 1.00 0.34 0.00
74_A 117_R 1.00 0.34 0.00
39_M 20_Y 1.00 0.34 0.00
2_I 103_Q 0.99 0.33 0.00
89_G 168_G 0.98 0.33 0.00
61_V 91_E 0.97 0.32 0.00
66_V 115_E 0.96 0.31 0.00
66_V 41_Q 0.96 0.31 0.00
9_V 28_T 0.96 0.31 0.00
31_V 184_D 0.95 0.30 0.00
90_T 30_A 0.95 0.30 0.00
39_M 73_G 0.93 0.29 0.00
42_A 51_L 0.93 0.29 0.00
2_I 34_A 0.93 0.28 0.00
19_I 122_A 0.92 0.28 0.00
17_T 186_T 0.91 0.27 0.00
27_K 109_D 0.91 0.27 0.00
72_A 73_G 0.90 0.26 0.00
79_A 173_N 0.90 0.26 0.00
17_T 96_Q 0.90 0.26 0.00
97_N 97_L 0.89 0.26 0.00
17_T 114_D 0.89 0.26 0.00
52_T 150_W 0.89 0.26 0.00
20_F 65_T 0.89 0.26 0.00
4_L 26_A 0.88 0.25 0.00
47_F 22_A 0.88 0.25 0.00
27_K 19_L 0.88 0.25 0.00
99_M 9_G 0.88 0.25 0.00
47_F 41_Q 0.88 0.25 0.00
11_G 96_Q 0.88 0.25 0.00
64_M 148_G 0.87 0.25 0.00
76_I 131_V 0.87 0.25 0.00
55_G 42_M 0.87 0.24 0.00
61_V 19_L 0.87 0.24 0.00
47_F 39_V 0.86 0.24 0.00
20_F 158_H 0.86 0.24 0.00
31_V 88_A 0.86 0.24 0.00
79_A 164_R 0.86 0.23 0.00
83_V 38_L 0.86 0.23 0.00
65_F 129_I 0.86 0.23 0.00
29_V 159_Y 0.85 0.23 0.00
27_K 107_K 0.84 0.22 0.00
49_A 159_Y 0.84 0.22 0.00
5_T 88_A 0.84 0.22 0.00
76_I 68_T 0.84 0.22 0.00
96_V 140_I 0.84 0.22 0.00
39_M 143_G 0.84 0.22 0.00
72_A 81_R 0.83 0.22 0.00
74_A 78_I 0.83 0.22 0.00
32_I 84_D 0.83 0.22 0.00
97_N 90_R 0.83 0.21 0.00
34_M 35_A 0.82 0.21 0.00
85_F 47_D 0.82 0.21 0.00
57_L 141_G 0.82 0.21 0.00
12_A 24_A 0.81 0.21 0.00
7_Y 129_I 0.81 0.21 0.00
33_L 127_V 0.81 0.20 0.00
63_T 119_M 0.81 0.20 0.00
88_R 97_L 0.81 0.20 0.00
56_D 95_G 0.81 0.20 0.00
42_A 54_I 0.80 0.20 0.00
45_I 76_V 0.80 0.20 0.00
84_F 100_R 0.80 0.20 0.00
2_I 106_N 0.80 0.20 0.00
47_F 31_A 0.80 0.20 0.00
2_I 24_A 0.80 0.20 0.00
48_V 181_F 0.80 0.20 0.00
79_A 170_A 0.80 0.20 0.00
61_V 69_V 0.79 0.19 0.00
53_H 189_L 0.79 0.19 0.00
18_G 68_T 0.79 0.19 0.00
30_I 42_M 0.79 0.19 0.00
89_G 36_W 0.79 0.19 0.00
43_V 78_I 0.79 0.19 0.00
61_V 40_N 0.78 0.19 0.00
83_V 30_A 0.78 0.19 0.00
16_V 187_I 0.78 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
2936 1.01 cI_K_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2935 2 cI_K_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2925 1.52 cI_K_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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