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OPENSEQ.org
cI_J_20_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 200 190 382
Sequences: 2148 1013 304
Seq/Len: 10.74 5.33 0.8
MirrorTree (Pazo et al. 2001) 0.44
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 0.01 0.01 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.01
100 0.02 0.01 0.06
∞ 0.03 0.02 0.78
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
53_A 12_G 1.52 0.72 0.01
99_V 31_A 1.36 0.59 0.01
17_G 91_E 1.35 0.59 0.00
34_I 150_W 1.35 0.58 0.00
162_I 59_S 1.30 0.55 0.00
14_C 61_V 1.30 0.54 0.00
22_I 98_I 1.25 0.50 0.00
14_C 19_L 1.24 0.49 0.00
193_D 131_V 1.21 0.47 0.00
171_D 127_V 1.21 0.46 0.00
179_E 183_D 1.18 0.44 0.00
36_A 58_V 1.18 0.44 0.00
181_M 72_L 1.17 0.43 0.00
58_V 85_E 1.15 0.42 0.00
90_L 124_E 1.15 0.41 0.00
58_V 78_I 1.15 0.41 0.00
132_T 68_T 1.14 0.40 0.00
83_K 55_Q 1.14 0.40 0.00
130_E 189_L 1.14 0.40 0.00
196_P 176_I 1.13 0.40 0.00
135_L 159_Y 1.13 0.39 0.00
122_A 176_I 1.12 0.39 0.00
96_I 14_T 1.11 0.38 0.00
93_A 65_T 1.11 0.38 0.00
155_L 156_G 1.10 0.37 0.00
140_Y 24_A 1.10 0.37 0.00
91_P 52_A 1.10 0.37 0.00
152_L 181_F 1.09 0.37 0.00
169_R 29_V 1.09 0.36 0.00
30_V 22_A 1.07 0.35 0.00
159_I 14_T 1.06 0.34 0.00
105_G 53_S 1.06 0.34 0.00
53_A 15_R 1.05 0.33 0.00
47_Q 42_M 1.05 0.33 0.00
11_I 176_I 1.05 0.33 0.00
52_V 48_V 1.04 0.33 0.00
8_L 184_D 1.04 0.32 0.00
30_V 86_I 1.03 0.32 0.00
153_V 186_T 1.03 0.32 0.00
162_I 188_K 1.03 0.31 0.00
53_A 74_K 1.02 0.31 0.00
82_L 93_D 1.01 0.30 0.00
141_D 179_A 1.00 0.30 0.00
192_K 48_V 1.00 0.30 0.00
90_L 26_A 0.99 0.29 0.00
180_Q 41_Q 0.99 0.29 0.00
16_A 144_A 0.99 0.28 0.00
36_A 84_D 0.98 0.28 0.00
25_N 30_A 0.97 0.28 0.00
126_D 84_D 0.97 0.27 0.00
97_G 68_T 0.97 0.27 0.00
58_V 150_W 0.97 0.27 0.00
152_L 185_T 0.97 0.27 0.00
28_H 162_S 0.96 0.27 0.00
148_Q 86_I 0.96 0.27 0.00
185_P 24_A 0.96 0.27 0.00
187_K 32_G 0.96 0.26 0.00
197_G 159_Y 0.96 0.26 0.00
134_G 145_G 0.95 0.26 0.00
16_A 91_E 0.95 0.26 0.00
142_R 60_G 0.95 0.26 0.00
103_Q 184_D 0.95 0.26 0.00
58_V 77_F 0.95 0.26 0.00
105_G 187_I 0.95 0.26 0.00
20_V 162_S 0.95 0.26 0.00
47_Q 76_V 0.95 0.26 0.00
168_H 41_Q 0.94 0.25 0.00
57_V 55_Q 0.94 0.25 0.00
9_F 66_Q 0.94 0.25 0.00
121_R 51_L 0.94 0.25 0.00
21_V 88_A 0.94 0.25 0.00
53_A 186_T 0.94 0.25 0.00
152_L 77_F 0.93 0.25 0.00
135_L 59_S 0.93 0.25 0.00
144_V 65_T 0.93 0.24 0.00
42_G 168_G 0.93 0.24 0.00
12_S 175_H 0.92 0.24 0.00
144_V 90_R 0.92 0.24 0.00
180_Q 37_T 0.91 0.23 0.00
107_A 124_E 0.90 0.23 0.00
14_C 87_Q 0.90 0.23 0.00
147_F 19_L 0.90 0.23 0.00
160_G 165_I 0.90 0.22 0.00
56_L 174_L 0.89 0.22 0.00
195_K 58_V 0.89 0.22 0.00
97_G 78_I 0.89 0.22 0.00
84_G 141_G 0.89 0.22 0.00
39_S 43_N 0.89 0.22 0.00
102_A 83_E 0.89 0.22 0.00
169_R 47_D 0.88 0.22 0.00
21_V 84_D 0.88 0.22 0.00
188_T 51_L 0.88 0.22 0.00
135_L 26_A 0.88 0.22 0.00
36_A 22_A 0.88 0.21 0.00
138_V 39_V 0.87 0.21 0.00
161_A 27_G 0.87 0.21 0.00
102_A 31_A 0.87 0.21 0.00
45_V 35_A 0.86 0.21 0.00
9_F 63_T 0.86 0.21 0.00
8_L 25_G 0.86 0.20 0.00
147_F 168_G 0.86 0.20 0.00
120_L 78_I 0.86 0.20 0.00
192_K 33_A 0.86 0.20 0.00
83_K 25_G 0.85 0.20 0.00
192_K 38_L 0.85 0.20 0.00
153_V 166_R 0.85 0.20 0.00
8_L 151_F 0.85 0.20 0.00
55_L 129_I 0.85 0.20 0.00
146_M 188_K 0.85 0.20 0.00
41_A 182_L 0.85 0.20 0.00
4_F 70_K 0.85 0.20 0.00
99_V 78_I 0.84 0.20 0.00
33_L 71_W 0.84 0.19 0.00
152_L 159_Y 0.84 0.19 0.00
55_L 58_V 0.83 0.19 0.00
57_V 131_V 0.83 0.19 0.00
20_V 73_G 0.83 0.19 0.00
93_A 52_A 0.83 0.19 0.00
96_I 96_Q 0.83 0.19 0.00
156_V 33_A 0.83 0.19 0.00
32_W 183_D 0.83 0.19 0.00
147_F 18_F 0.83 0.18 0.00
42_G 25_G 0.83 0.18 0.00
152_L 138_V 0.83 0.18 0.00
119_S 147_F 0.83 0.18 0.00
48_G 18_F 0.82 0.18 0.00
193_D 30_A 0.82 0.18 0.00
191_L 39_V 0.82 0.18 0.00
57_V 124_E 0.82 0.18 0.00
149_L 165_I 0.82 0.18 0.00
17_G 84_D 0.82 0.18 0.00
182_W 30_A 0.81 0.18 0.00
153_V 175_H 0.81 0.18 0.00
88_R 97_L 0.81 0.18 0.00
146_M 98_I 0.81 0.18 0.00
147_F 16_R 0.81 0.18 0.00
35_L 22_A 0.81 0.17 0.00
98_V 61_V 0.81 0.17 0.00
134_G 168_G 0.80 0.17 0.00
188_T 41_Q 0.80 0.17 0.00
178_L 34_A 0.80 0.17 0.00
171_D 33_A 0.80 0.17 0.00
157_A 84_D 0.80 0.17 0.00
110_G 33_A 0.80 0.17 0.00
57_V 178_V 0.80 0.17 0.00
81_E 176_I 0.80 0.17 0.00
20_V 129_I 0.79 0.17 0.00
31_L 129_I 0.79 0.17 0.00
195_K 69_V 0.79 0.17 0.00
148_Q 14_T 0.79 0.17 0.00
16_A 25_G 0.79 0.17 0.00
139_L 105_S 0.79 0.17 0.00
65_A 17_D 0.79 0.17 0.00
94_L 50_A 0.78 0.16 0.00
146_M 38_L 0.78 0.16 0.00
162_I 50_A 0.78 0.16 0.00
138_V 88_A 0.78 0.16 0.00
24_R 176_I 0.78 0.16 0.00
134_G 156_G 0.78 0.16 0.00
38_L 28_T 0.78 0.16 0.00
80_A 34_A 0.78 0.16 0.00
8_L 183_D 0.78 0.16 0.00
102_A 185_T 0.78 0.16 0.00
52_V 116_N 0.78 0.16 0.00
196_P 108_P 0.78 0.16 0.00
58_V 48_V 0.78 0.16 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
2989 0.8 cI_J_20_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2978 1.3 cI_J_20_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2977 0.84 cI_J_20_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
2968 1.26 cI_J_20_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
2949 0.84 cI_J_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
2938 1.3 cI_J_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
2937 1.26 cI_J_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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