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OPENSEQ.org
cI_J_20_cIII_cytb_20_Pdenitr
Genes: A B A+B
Length: 200 190 382
Sequences: 2148 1043 319
Seq/Len: 10.74 5.49 0.84
MirrorTree (Pazo et al. 2001) 0.53
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 0.07
∞ 0.03 0.02 0.82
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
53_A 12_G 1.70 0.84 0.09
162_I 59_S 1.53 0.74 0.06
99_V 31_A 1.34 0.59 0.03
171_D 127_V 1.33 0.58 0.03
25_N 30_A 1.27 0.54 0.03
17_G 91_E 1.26 0.52 0.03
14_C 61_V 1.23 0.50 0.02
8_L 184_D 1.23 0.49 0.02
96_I 14_T 1.17 0.45 0.02
58_V 85_E 1.17 0.44 0.02
181_M 72_L 1.16 0.43 0.02
34_I 150_W 1.14 0.42 0.02
52_V 116_N 1.14 0.41 0.02
162_I 156_G 1.12 0.40 0.02
196_P 176_I 1.11 0.40 0.02
135_L 159_Y 1.10 0.38 0.01
152_L 185_T 1.10 0.38 0.01
97_G 78_I 1.10 0.38 0.01
30_V 22_A 1.09 0.38 0.01
57_V 55_Q 1.08 0.36 0.01
58_V 78_I 1.07 0.36 0.01
144_V 65_T 1.06 0.35 0.01
58_V 77_F 1.04 0.34 0.01
47_Q 42_M 1.04 0.34 0.01
130_E 189_L 1.04 0.34 0.01
180_Q 41_Q 1.04 0.34 0.01
160_G 165_I 1.04 0.33 0.01
53_A 74_K 1.04 0.33 0.01
22_I 98_I 1.04 0.33 0.01
14_C 19_L 1.03 0.33 0.01
30_V 86_I 1.03 0.33 0.01
83_K 55_Q 1.03 0.33 0.01
91_P 52_A 1.03 0.33 0.01
134_G 145_G 1.02 0.32 0.01
52_V 48_V 1.02 0.32 0.01
155_L 156_G 1.01 0.31 0.01
16_A 144_A 1.01 0.31 0.01
42_G 25_G 1.01 0.31 0.01
36_A 58_V 1.01 0.31 0.01
9_F 63_T 1.01 0.31 0.01
187_K 32_G 1.01 0.31 0.01
193_D 131_V 0.99 0.30 0.01
90_L 26_A 0.99 0.29 0.01
179_E 183_D 0.99 0.29 0.01
103_Q 184_D 0.99 0.29 0.01
193_D 30_A 0.99 0.29 0.01
11_I 176_I 0.99 0.29 0.01
36_A 84_D 0.98 0.29 0.01
161_A 27_G 0.98 0.29 0.01
32_W 183_D 0.98 0.29 0.01
71_V 37_T 0.98 0.29 0.01
20_V 162_S 0.98 0.29 0.01
147_F 18_F 0.97 0.28 0.01
24_R 176_I 0.96 0.28 0.01
153_V 186_T 0.96 0.28 0.01
68_F 173_N 0.96 0.28 0.01
126_D 84_D 0.96 0.27 0.01
41_A 182_L 0.96 0.27 0.01
142_R 60_G 0.95 0.27 0.01
139_L 105_S 0.95 0.27 0.01
146_M 188_K 0.94 0.26 0.01
168_H 41_Q 0.94 0.26 0.01
12_S 175_H 0.94 0.26 0.01
21_V 88_A 0.94 0.26 0.01
39_S 43_N 0.94 0.26 0.01
55_L 129_I 0.94 0.26 0.01
191_L 58_V 0.93 0.26 0.01
86_L 58_V 0.93 0.25 0.01
169_R 29_V 0.93 0.25 0.01
90_L 124_E 0.92 0.25 0.01
57_V 131_V 0.92 0.25 0.01
147_F 168_G 0.92 0.25 0.01
68_F 164_R 0.92 0.24 0.01
102_A 31_A 0.92 0.24 0.01
53_A 15_R 0.92 0.24 0.01
147_F 19_L 0.92 0.24 0.01
58_V 150_W 0.92 0.24 0.01
141_D 179_A 0.91 0.24 0.01
192_K 48_V 0.91 0.24 0.01
57_V 124_E 0.90 0.23 0.01
192_K 33_A 0.90 0.23 0.01
105_G 53_S 0.90 0.23 0.01
197_G 159_Y 0.89 0.23 0.01
188_T 51_L 0.89 0.23 0.01
17_G 80_R 0.89 0.23 0.01
144_V 90_R 0.89 0.23 0.01
11_I 121_E 0.89 0.23 0.01
21_V 183_D 0.88 0.22 0.01
56_L 174_L 0.88 0.22 0.01
20_V 189_L 0.88 0.22 0.01
185_P 24_A 0.88 0.22 0.01
53_A 186_T 0.88 0.22 0.01
135_L 59_S 0.88 0.22 0.01
162_I 188_K 0.87 0.22 0.01
147_F 15_R 0.87 0.22 0.01
151_G 17_D 0.87 0.22 0.01
152_L 181_F 0.87 0.22 0.01
93_A 65_T 0.87 0.22 0.01
4_F 70_K 0.87 0.21 0.01
146_M 58_V 0.87 0.21 0.01
132_T 68_T 0.86 0.21 0.01
191_L 39_V 0.86 0.21 0.01
124_P 91_E 0.86 0.21 0.01
127_A 189_L 0.85 0.21 0.01
67_L 160_D 0.85 0.21 0.01
68_F 157_S 0.85 0.21 0.01
92_L 124_E 0.85 0.20 0.01
47_Q 74_K 0.85 0.20 0.01
8_L 183_D 0.85 0.20 0.01
107_A 124_E 0.85 0.20 0.01
144_V 172_Q 0.85 0.20 0.01
68_F 160_D 0.85 0.20 0.01
196_P 11_H 0.84 0.20 0.01
41_A 19_L 0.84 0.20 0.01
106_I 176_I 0.84 0.20 0.01
58_V 48_V 0.84 0.20 0.01
197_G 19_L 0.84 0.20 0.01
9_F 66_Q 0.84 0.20 0.01
100_L 186_T 0.83 0.19 0.01
65_A 17_D 0.83 0.19 0.01
119_S 147_F 0.83 0.19 0.01
42_G 168_G 0.83 0.19 0.01
102_A 83_E 0.83 0.19 0.01
29_S 140_I 0.83 0.19 0.01
159_I 14_T 0.82 0.19 0.01
8_L 25_G 0.82 0.19 0.01
53_A 117_R 0.82 0.19 0.01
68_F 170_A 0.82 0.19 0.01
98_V 61_V 0.82 0.19 0.01
121_R 51_L 0.82 0.19 0.01
130_E 127_V 0.81 0.18 0.01
180_Q 37_T 0.81 0.18 0.01
33_L 71_W 0.81 0.18 0.01
96_I 96_Q 0.81 0.18 0.01
83_K 25_G 0.80 0.18 0.01
105_G 80_R 0.80 0.18 0.01
62_G 160_D 0.80 0.18 0.01
81_E 176_I 0.80 0.18 0.01
188_T 119_M 0.80 0.18 0.01
75_L 148_G 0.80 0.18 0.01
8_L 151_F 0.80 0.17 0.01
168_H 63_T 0.80 0.17 0.01
52_V 38_L 0.80 0.17 0.01
184_D 87_Q 0.79 0.17 0.01
98_V 92_V 0.79 0.17 0.01
178_L 48_V 0.79 0.17 0.01
20_V 131_V 0.79 0.17 0.01
132_T 73_G 0.79 0.17 0.01
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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