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OPENSEQ.org
cI_I_60_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 163 190 345
Sequences: 329 1539 245
Seq/Len: 2.02 8.1 0.71
MirrorTree (Pazo et al. 2001) 0.60
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 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.00 0.01 0.07
∞ 0.01 0.04 0.69
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
27_Y 34_A 1.62 0.75 0.01
108_F 188_K 1.38 0.57 0.01
12_F 131_V 1.34 0.54 0.01
26_R 23_T 1.25 0.46 0.01
155_N 72_L 1.23 0.45 0.01
156_L 47_D 1.22 0.44 0.01
17_F 23_T 1.19 0.41 0.00
122_P 168_G 1.15 0.39 0.00
20_G 41_Q 1.14 0.38 0.00
139_Q 78_I 1.13 0.37 0.00
10_K 131_V 1.12 0.36 0.00
23_L 88_A 1.12 0.36 0.00
160_A 29_V 1.09 0.33 0.00
26_R 19_L 1.09 0.33 0.00
117_A 176_I 1.06 0.31 0.00
12_F 25_G 1.06 0.31 0.00
13_L 13_A 1.05 0.31 0.00
131_R 23_T 1.03 0.29 0.00
26_R 11_H 1.00 0.27 0.00
136_Y 168_G 1.00 0.27 0.00
46_P 29_V 1.00 0.27 0.00
33_P 162_S 1.00 0.27 0.00
161_P 61_V 1.00 0.27 0.00
17_F 38_L 0.99 0.27 0.00
9_T 60_G 0.99 0.26 0.00
85_R 187_I 0.98 0.26 0.00
90_S 167_R 0.98 0.26 0.00
18_I 183_D 0.98 0.26 0.00
59_N 37_T 0.96 0.25 0.00
156_L 45_S 0.96 0.25 0.00
108_F 162_S 0.95 0.24 0.00
158_L 27_G 0.94 0.24 0.00
134_L 42_M 0.94 0.23 0.00
143_A 184_D 0.94 0.23 0.00
17_F 182_L 0.94 0.23 0.00
33_P 68_T 0.94 0.23 0.00
44_L 80_R 0.93 0.23 0.00
83_A 26_A 0.93 0.23 0.00
124_F 68_T 0.93 0.23 0.00
154_R 27_G 0.93 0.23 0.00
90_S 47_D 0.93 0.23 0.00
135_F 33_A 0.92 0.22 0.00
100_M 66_Q 0.91 0.22 0.00
147_R 175_H 0.91 0.22 0.00
144_N 147_F 0.91 0.21 0.00
108_F 119_M 0.91 0.21 0.00
94_T 59_S 0.90 0.21 0.00
16_D 146_D 0.90 0.21 0.00
39_H 182_L 0.90 0.21 0.00
125_E 15_R 0.90 0.21 0.00
90_S 100_R 0.90 0.21 0.00
12_F 66_Q 0.90 0.21 0.00
94_T 130_G 0.89 0.21 0.00
5_F 31_A 0.89 0.20 0.00
126_Y 36_W 0.88 0.20 0.00
24_G 41_Q 0.88 0.20 0.00
147_R 23_T 0.87 0.20 0.00
101_T 25_G 0.87 0.20 0.00
160_A 22_A 0.87 0.19 0.00
13_L 59_S 0.87 0.19 0.00
33_P 41_Q 0.86 0.19 0.00
90_S 87_Q 0.86 0.19 0.00
18_I 18_F 0.86 0.19 0.00
16_D 129_I 0.86 0.19 0.00
100_M 140_I 0.86 0.19 0.00
146_E 48_V 0.86 0.19 0.00
8_A 28_T 0.85 0.19 0.00
87_E 45_S 0.85 0.18 0.00
100_M 150_W 0.85 0.18 0.00
13_L 55_Q 0.84 0.18 0.00
59_N 162_S 0.84 0.18 0.00
43_P 148_G 0.84 0.18 0.00
126_Y 45_S 0.84 0.18 0.00
136_Y 18_F 0.83 0.18 0.00
157_Q 19_L 0.83 0.17 0.00
152_I 30_A 0.83 0.17 0.00
131_R 19_L 0.83 0.17 0.00
32_K 41_Q 0.83 0.17 0.00
160_A 174_L 0.83 0.17 0.00
90_S 45_S 0.82 0.17 0.00
82_D 158_H 0.82 0.17 0.00
24_G 111_P 0.82 0.17 0.00
24_G 119_M 0.82 0.17 0.00
151_E 185_T 0.81 0.17 0.00
89_G 124_E 0.81 0.17 0.00
23_L 39_V 0.81 0.17 0.00
39_H 150_W 0.81 0.17 0.00
23_L 151_F 0.81 0.17 0.00
94_T 56_V 0.81 0.17 0.00
12_F 19_L 0.81 0.17 0.00
162_Y 82_T 0.81 0.16 0.00
140_K 98_I 0.80 0.16 0.00
17_F 41_Q 0.80 0.16 0.00
144_N 117_R 0.80 0.16 0.00
44_L 176_I 0.80 0.16 0.00
13_L 123_G 0.80 0.16 0.00
101_T 42_M 0.80 0.16 0.00
11_Y 35_A 0.80 0.16 0.00
84_E 45_S 0.79 0.15 0.00
29_V 176_I 0.79 0.15 0.00
11_Y 178_V 0.79 0.15 0.00
100_M 98_I 0.78 0.15 0.00
140_K 33_A 0.78 0.15 0.00
18_I 69_V 0.78 0.15 0.00
37_Y 74_K 0.78 0.15 0.00
37_Y 28_T 0.78 0.15 0.00
54_L 163_G 0.78 0.15 0.00
58_P 18_F 0.77 0.15 0.00
73_V 67_L 0.77 0.14 0.00
80_T 72_L 0.77 0.14 0.00
112_A 8_A 0.76 0.14 0.00
143_A 120_D 0.76 0.14 0.00
117_A 144_A 0.76 0.14 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
3050 1.29 cI_I_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3049 0.71 cI_I_60_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3048 0.78 cI_I_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3047 1.09 cI_I_40_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
3046 1.11 cI_I_40_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3044 1.11 cI_I_40_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3043 1.84 cI_I_4_cIII_isp_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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