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OPENSEQ.org
cI_E_cIII_isp_Pdenitr
Genes: A B A+B
Length: 239 190 420
Sequences: 755 1692 236
Seq/Len: 3.16 8.91 0.56
MirrorTree (Pazo et al. 2001) 0.43
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 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.00
100 0.01 0.01 0.04
∞ 0.04 0.05 0.55
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
62_A 174_L 1.56 0.64 0.00
17_P 67_L 1.51 0.60 0.00
53_L 35_A 1.37 0.50 0.00
29_K 56_V 1.27 0.42 0.00
20_L 34_A 1.16 0.34 0.00
68_P 52_A 1.15 0.33 0.00
68_P 187_I 1.14 0.32 0.00
53_L 39_V 1.12 0.30 0.00
24_R 9_G 1.09 0.29 0.00
163_A 51_L 1.07 0.27 0.00
93_I 12_G 1.07 0.27 0.00
125_S 66_Q 1.05 0.26 0.00
66_G 131_V 1.01 0.24 0.00
34_R 23_T 1.00 0.23 0.00
35_Q 62_E 0.99 0.23 0.00
158_T 87_Q 0.99 0.22 0.00
137_C 157_S 0.98 0.22 0.00
110_I 183_D 0.97 0.22 0.00
24_R 26_A 0.97 0.21 0.00
117_I 22_A 0.97 0.21 0.00
35_Q 65_T 0.96 0.21 0.00
167_D 129_I 0.95 0.20 0.00
158_T 33_A 0.94 0.20 0.00
66_G 51_L 0.94 0.20 0.00
150_G 183_D 0.94 0.20 0.00
93_I 102_A 0.94 0.20 0.00
196_A 67_L 0.94 0.20 0.00
58_I 32_G 0.93 0.19 0.00
66_G 186_T 0.93 0.19 0.00
3_R 183_D 0.92 0.19 0.00
72_A 187_I 0.92 0.19 0.00
11_D 124_E 0.92 0.19 0.00
107_E 54_I 0.92 0.19 0.00
149_I 38_L 0.92 0.19 0.00
164_A 31_A 0.91 0.19 0.00
108_D 78_I 0.91 0.19 0.00
129_R 98_I 0.90 0.18 0.00
37_S 44_P 0.89 0.18 0.00
56_P 19_L 0.89 0.18 0.00
109_L 60_G 0.88 0.17 0.00
47_Q 64_G 0.88 0.17 0.00
135_V 23_T 0.88 0.17 0.00
68_P 122_A 0.88 0.17 0.00
161_K 162_S 0.88 0.17 0.00
116_K 176_I 0.87 0.17 0.00
72_A 89_G 0.87 0.17 0.00
177_P 180_E 0.87 0.17 0.00
63_D 51_L 0.87 0.17 0.00
25_A 33_A 0.87 0.17 0.00
103_I 80_R 0.86 0.16 0.00
178_G 133_T 0.86 0.16 0.00
69_Y 38_L 0.86 0.16 0.00
9_Q 23_T 0.85 0.16 0.00
103_I 38_L 0.85 0.16 0.00
66_G 88_A 0.85 0.16 0.00
166_I 67_L 0.84 0.16 0.00
165_L 98_I 0.84 0.15 0.00
142_T 186_T 0.84 0.15 0.00
165_L 131_V 0.84 0.15 0.00
58_I 182_L 0.83 0.15 0.00
77_T 41_Q 0.83 0.15 0.00
111_R 151_F 0.83 0.15 0.00
42_V 35_A 0.83 0.15 0.00
160_E 103_Q 0.83 0.15 0.00
61_C 9_G 0.83 0.15 0.00
125_S 116_N 0.82 0.15 0.00
28_T 6_E 0.82 0.15 0.00
23_A 35_A 0.82 0.15 0.00
137_C 170_A 0.82 0.15 0.00
32_E 80_R 0.82 0.15 0.00
24_R 176_I 0.82 0.14 0.00
189_L 182_L 0.81 0.14 0.00
215_G 31_A 0.81 0.14 0.00
73_L 48_V 0.81 0.14 0.00
160_E 28_T 0.81 0.14 0.00
28_T 92_V 0.81 0.14 0.00
36_Q 128_M 0.81 0.14 0.00
125_S 58_V 0.81 0.14 0.00
147_A 72_L 0.81 0.14 0.00
34_R 15_R 0.80 0.14 0.00
121_P 87_Q 0.80 0.14 0.00
41_P 51_L 0.80 0.14 0.00
55_R 131_V 0.80 0.14 0.00
24_R 115_E 0.80 0.14 0.00
185_S 28_T 0.80 0.14 0.00
93_I 113_T 0.79 0.14 0.00
197_D 88_A 0.79 0.14 0.00
130_F 124_E 0.79 0.14 0.00
53_L 94_L 0.79 0.13 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
3023 0.57 cI_E_4_cIII_isp_2_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3022 0.58 cI_E_2_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2799 0.56 cI_E_cIII_isp_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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