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OPENSEQ.org
cI_J_20_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 200 190 383
Sequences: 2148 1539 483
Seq/Len: 10.74 8.1 1.26
MirrorTree (Pazo et al. 2001) 0.70
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 0.08
∞ 0.03 0.04 1.24
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
14_C 61_V 1.54 0.85 0.11
53_A 12_G 1.18 0.57 0.04
193_D 131_V 1.18 0.57 0.04
107_A 28_T 1.18 0.57 0.04
102_A 31_A 1.16 0.56 0.04
153_V 186_T 1.15 0.54 0.04
103_Q 184_D 1.13 0.53 0.03
179_E 183_D 1.13 0.52 0.03
162_I 59_S 1.12 0.51 0.03
185_P 24_A 1.10 0.49 0.03
12_S 31_A 1.08 0.47 0.03
104_L 31_A 1.07 0.46 0.03
152_L 159_Y 1.04 0.43 0.03
161_A 27_G 1.03 0.42 0.02
171_D 127_V 1.00 0.39 0.02
105_G 53_S 0.99 0.39 0.02
96_I 33_A 0.98 0.38 0.02
138_V 35_A 0.97 0.37 0.02
99_V 31_A 0.97 0.37 0.02
29_S 83_E 0.97 0.36 0.02
74_M 177_P 0.96 0.36 0.02
132_T 68_T 0.96 0.36 0.02
144_V 172_Q 0.96 0.36 0.02
146_M 188_K 0.96 0.35 0.02
17_G 91_E 0.95 0.35 0.02
135_L 159_Y 0.94 0.34 0.02
195_K 144_A 0.94 0.34 0.02
151_G 47_D 0.94 0.34 0.02
47_Q 42_M 0.93 0.34 0.02
58_V 78_I 0.93 0.33 0.02
31_L 48_V 0.93 0.33 0.02
25_N 30_A 0.93 0.33 0.02
34_I 150_W 0.92 0.33 0.02
147_F 18_F 0.92 0.32 0.02
181_M 72_L 0.92 0.32 0.02
20_V 19_L 0.92 0.32 0.02
187_K 32_G 0.92 0.32 0.02
156_V 144_A 0.92 0.32 0.02
184_D 87_Q 0.91 0.32 0.02
105_G 131_V 0.91 0.31 0.02
160_G 165_I 0.91 0.31 0.02
22_I 98_I 0.91 0.31 0.02
126_D 84_D 0.91 0.31 0.01
33_L 160_D 0.91 0.31 0.01
80_A 28_T 0.90 0.31 0.01
90_L 26_A 0.90 0.31 0.01
150_A 139_P 0.90 0.31 0.01
134_G 39_V 0.90 0.30 0.01
145_L 76_V 0.90 0.30 0.01
67_L 160_D 0.90 0.30 0.01
97_G 131_V 0.89 0.30 0.01
142_R 60_G 0.89 0.30 0.01
16_A 157_S 0.89 0.30 0.01
134_G 145_G 0.89 0.30 0.01
38_L 148_G 0.89 0.29 0.01
130_E 189_L 0.89 0.29 0.01
153_V 166_R 0.88 0.29 0.01
197_G 159_Y 0.88 0.29 0.01
18_F 60_G 0.88 0.29 0.01
96_I 14_T 0.87 0.28 0.01
196_P 176_I 0.87 0.28 0.01
99_V 187_I 0.87 0.28 0.01
106_I 187_I 0.87 0.28 0.01
55_L 58_V 0.87 0.28 0.01
190_E 141_G 0.87 0.28 0.01
146_M 98_I 0.87 0.28 0.01
190_E 28_T 0.86 0.27 0.01
65_A 17_D 0.86 0.27 0.01
147_F 168_G 0.86 0.27 0.01
149_L 60_G 0.86 0.27 0.01
57_V 55_Q 0.85 0.27 0.01
39_S 15_R 0.85 0.27 0.01
58_V 77_F 0.84 0.26 0.01
193_D 30_A 0.84 0.26 0.01
98_V 12_G 0.84 0.26 0.01
74_M 99_D 0.84 0.26 0.01
37_F 135_L 0.84 0.26 0.01
27_V 153_P 0.84 0.26 0.01
193_D 189_L 0.84 0.26 0.01
188_T 119_M 0.84 0.26 0.01
179_E 32_G 0.84 0.26 0.01
46_L 29_V 0.83 0.25 0.01
53_A 186_T 0.83 0.25 0.01
9_F 133_T 0.83 0.25 0.01
42_G 168_G 0.82 0.24 0.01
22_I 32_G 0.82 0.24 0.01
172_V 189_L 0.81 0.24 0.01
153_V 115_E 0.81 0.24 0.01
105_G 80_R 0.81 0.24 0.01
193_D 151_F 0.81 0.24 0.01
51_F 166_R 0.81 0.23 0.01
36_A 58_V 0.81 0.23 0.01
4_F 105_S 0.81 0.23 0.01
195_K 66_Q 0.80 0.23 0.01
54_M 27_G 0.80 0.23 0.01
104_L 56_V 0.80 0.23 0.01
173_K 35_A 0.80 0.23 0.01
57_V 178_V 0.80 0.23 0.01
107_A 124_E 0.80 0.23 0.01
53_A 117_R 0.80 0.23 0.01
53_A 42_M 0.80 0.23 0.01
44_F 114_D 0.79 0.22 0.01
97_G 78_I 0.79 0.22 0.01
47_Q 74_K 0.79 0.22 0.01
38_L 28_T 0.79 0.22 0.01
192_K 33_A 0.79 0.22 0.01
182_W 144_A 0.79 0.22 0.01
99_V 12_G 0.79 0.22 0.01
37_F 164_R 0.79 0.22 0.01
27_V 18_F 0.79 0.22 0.01
106_I 63_T 0.79 0.22 0.01
61_V 26_A 0.79 0.22 0.01
102_A 38_L 0.79 0.22 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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