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OPENSEQ.org
cI_J_20_cIII_cytb_20_Pdenitr
Genes: A B A+B
Length: 200 440 612
Sequences: 2148 3303 706
Seq/Len: 10.74 7.51 1.15
MirrorTree (Pazo et al. 2001) 0.63
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 0.05
2 0.00 0.00 0.09
5 0.01 0.00 0.22
10 0.01 0.00 0.31
20 0.01 0.00 0.36
100 0.02 0.00 0.44
∞ 0.03 0.01 1.10
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
41_A 414_I 1.41 0.74 0.01
14_C 204_V 1.34 0.69 0.01
97_G 186_V 1.31 0.66 0.01
176_N 383_M 1.28 0.64 0.01
64_V 331_F 1.23 0.59 0.01
159_I 60_A 1.22 0.58 0.01
38_L 42_N 1.21 0.57 0.01
136_G 121_Y 1.15 0.52 0.01
135_L 56_V 1.13 0.49 0.01
74_M 356_S 1.12 0.49 0.01
41_A 39_K 1.12 0.48 0.01
72_V 113_F 1.08 0.45 0.01
192_K 93_L 1.08 0.45 0.01
104_L 364_K 1.08 0.45 0.01
21_V 29_V 1.07 0.44 0.01
92_L 138_M 1.07 0.44 0.01
140_Y 216_F 1.06 0.43 0.01
100_L 269_F 1.06 0.42 0.01
32_W 286_L 1.05 0.42 0.01
52_V 207_A 1.05 0.41 0.01
4_F 267_V 1.04 0.41 0.01
107_A 242_L 1.04 0.41 0.01
57_V 392_I 1.04 0.41 0.01
100_L 19_L 1.03 0.40 0.01
99_V 264_F 1.02 0.39 0.01
173_K 277_P 1.02 0.39 0.01
23_G 284_N 1.01 0.38 0.00
139_L 213_I 1.00 0.38 0.00
41_A 122_K 1.00 0.37 0.00
57_V 143_A 0.99 0.36 0.00
160_G 200_L 0.99 0.36 0.00
103_Q 80_V 0.99 0.36 0.00
45_V 414_I 0.98 0.36 0.00
51_F 372_V 0.98 0.36 0.00
40_A 369_L 0.98 0.35 0.00
149_L 63_I 0.97 0.35 0.00
66_V 72_H 0.97 0.34 0.00
73_M 150_P 0.96 0.34 0.00
147_F 251_K 0.96 0.34 0.00
132_T 115_G 0.96 0.34 0.00
54_M 374_F 0.95 0.33 0.00
21_V 200_L 0.95 0.33 0.00
149_L 426_E 0.93 0.31 0.00
96_I 29_V 0.92 0.31 0.00
14_C 179_W 0.92 0.30 0.00
76_D 80_V 0.91 0.30 0.00
27_V 123_A 0.91 0.29 0.00
37_F 224_P 0.91 0.29 0.00
31_L 266_I 0.91 0.29 0.00
17_G 63_I 0.90 0.29 0.00
147_F 399_Y 0.90 0.29 0.00
189_M 136_Y 0.90 0.29 0.00
29_S 56_V 0.90 0.29 0.00
10_A 33_L 0.89 0.28 0.00
167_R 122_K 0.89 0.28 0.00
17_G 59_I 0.89 0.28 0.00
103_Q 197_L 0.89 0.28 0.00
191_L 57_L 0.88 0.27 0.00
59_V 402_A 0.88 0.27 0.00
17_G 237_A 0.88 0.27 0.00
45_V 214_W 0.87 0.27 0.00
126_D 372_V 0.87 0.27 0.00
157_A 361_P 0.87 0.26 0.00
37_F 271_P 0.87 0.26 0.00
64_V 215_A 0.86 0.26 0.00
30_V 380_V 0.86 0.26 0.00
26_P 396_G 0.86 0.26 0.00
165_T 56_V 0.86 0.26 0.00
141_D 28_L 0.85 0.25 0.00
56_L 367_F 0.85 0.25 0.00
36_A 394_L 0.85 0.25 0.00
22_I 176_I 0.85 0.25 0.00
153_V 189_P 0.85 0.25 0.00
66_V 171_G 0.85 0.25 0.00
104_L 422_Q 0.84 0.24 0.00
135_L 284_N 0.84 0.24 0.00
5_A 64_V 0.84 0.24 0.00
176_N 169_I 0.84 0.24 0.00
104_L 250_I 0.84 0.24 0.00
153_V 307_A 0.84 0.24 0.00
57_V 56_V 0.83 0.24 0.00
40_A 392_I 0.83 0.24 0.00
32_W 32_T 0.83 0.24 0.00
172_V 134_L 0.83 0.24 0.00
15_V 131_V 0.83 0.23 0.00
108_F 259_V 0.83 0.23 0.00
135_L 238_K 0.82 0.23 0.00
69_L 114_R 0.82 0.23 0.00
32_W 259_V 0.82 0.23 0.00
30_V 373_D 0.81 0.22 0.00
57_V 133_M 0.81 0.22 0.00
55_L 175_A 0.81 0.22 0.00
68_F 217_H 0.81 0.22 0.00
5_A 167_G 0.80 0.22 0.00
140_Y 359_Y 0.80 0.22 0.00
183_R 415_E 0.80 0.22 0.00
142_R 164_G 0.80 0.21 0.00
159_I 258_V 0.80 0.21 0.00
72_V 396_G 0.80 0.21 0.00
164_L 294_P 0.79 0.21 0.00
50_E 151_W 0.79 0.21 0.00
111_W 60_A 0.79 0.21 0.00
112_T 334_I 0.79 0.21 0.00
181_M 254_F 0.79 0.21 0.00
106_I 78_A 0.79 0.21 0.00
30_V 139_M 0.79 0.21 0.00
139_L 180_L 0.79 0.21 0.00
143_Y 121_Y 0.79 0.21 0.00
64_V 270_M 0.79 0.21 0.00
100_L 209_V 0.79 0.21 0.00
118_E 172_V 0.79 0.21 0.00
66_V 284_N 0.79 0.21 0.00
155_L 206_A 0.78 0.20 0.00
142_R 136_Y 0.78 0.20 0.00
99_V 186_V 0.78 0.20 0.00
47_Q 282_E 0.78 0.20 0.00
74_M 140_M 0.78 0.20 0.00
136_G 80_V 0.78 0.20 0.00
64_V 133_M 0.78 0.20 0.00
20_V 59_I 0.78 0.20 0.00
96_I 134_L 0.78 0.20 0.00
84_G 282_E 0.78 0.20 0.00
173_K 380_V 0.78 0.20 0.00
86_L 158_G 0.78 0.20 0.00
38_L 286_L 0.78 0.20 0.00
19_M 395_A 0.77 0.20 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
2980 1.15 cI_J_20_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2979 1.16 cI_J_20_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
2939 1.18 cI_J_10_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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