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OPENSEQ.org
cI_J_20_cIII_cytb_20_Pdenitr
Genes: A B A+B
Length: 200 440 612
Sequences: 2148 3290 709
Seq/Len: 10.74 7.48 1.16
MirrorTree (Pazo et al. 2001) 0.64
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 0.45
∞ 0.03 0.01 1.11
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 1.48 0.79 0.04
14_C 204_V 1.42 0.76 0.03
176_N 383_M 1.36 0.70 0.03
38_L 42_N 1.29 0.64 0.02
64_V 331_F 1.25 0.61 0.02
97_G 186_V 1.21 0.58 0.02
136_G 121_Y 1.20 0.56 0.02
100_L 269_F 1.18 0.55 0.02
41_A 39_K 1.14 0.51 0.01
192_K 93_L 1.12 0.49 0.01
72_V 113_F 1.12 0.48 0.01
159_I 60_A 1.11 0.48 0.01
104_L 364_K 1.09 0.46 0.01
21_V 29_V 1.08 0.45 0.01
74_M 356_S 1.06 0.43 0.01
51_F 372_V 1.04 0.42 0.01
135_L 56_V 1.04 0.41 0.01
103_Q 80_V 1.03 0.40 0.01
4_F 267_V 1.03 0.40 0.01
23_G 284_N 1.02 0.40 0.01
32_W 286_L 1.01 0.39 0.01
140_Y 216_F 1.01 0.39 0.01
99_V 264_F 1.00 0.38 0.01
173_K 277_P 1.00 0.38 0.01
107_A 242_L 1.00 0.38 0.01
147_F 251_K 1.00 0.38 0.01
132_T 115_G 1.00 0.37 0.01
41_A 122_K 1.00 0.37 0.01
45_V 414_I 0.98 0.36 0.01
149_L 63_I 0.98 0.36 0.01
92_L 138_M 0.98 0.36 0.01
54_M 374_F 0.98 0.35 0.01
73_M 150_P 0.98 0.35 0.01
22_I 176_I 0.98 0.35 0.01
160_G 200_L 0.97 0.35 0.01
57_V 143_A 0.97 0.35 0.01
52_V 207_A 0.96 0.34 0.01
96_I 29_V 0.96 0.34 0.01
40_A 369_L 0.95 0.34 0.01
59_V 402_A 0.95 0.33 0.01
66_V 72_H 0.95 0.33 0.01
29_S 56_V 0.94 0.33 0.01
21_V 200_L 0.94 0.32 0.01
139_L 213_I 0.94 0.32 0.01
157_A 361_P 0.94 0.32 0.01
191_L 57_L 0.91 0.30 0.01
14_C 179_W 0.91 0.30 0.01
17_G 59_I 0.90 0.29 0.01
176_N 169_I 0.90 0.29 0.01
37_F 224_P 0.89 0.28 0.01
64_V 75_L 0.89 0.28 0.01
147_F 399_Y 0.89 0.28 0.01
167_R 122_K 0.88 0.27 0.01
10_A 33_L 0.88 0.27 0.01
37_F 271_P 0.88 0.27 0.01
159_I 258_V 0.88 0.27 0.01
189_M 136_Y 0.88 0.27 0.01
56_L 367_F 0.88 0.27 0.01
26_P 396_G 0.88 0.27 0.01
103_Q 197_L 0.87 0.27 0.01
15_V 131_V 0.87 0.26 0.01
45_V 214_W 0.86 0.26 0.01
17_G 237_A 0.86 0.26 0.01
52_V 376_V 0.86 0.26 0.01
31_L 266_I 0.86 0.26 0.01
36_A 394_L 0.85 0.26 0.01
69_L 114_R 0.85 0.26 0.01
57_V 392_I 0.85 0.26 0.01
24_R 392_I 0.85 0.25 0.01
126_D 372_V 0.85 0.25 0.01
172_V 134_L 0.85 0.25 0.01
84_G 282_E 0.85 0.25 0.01
153_V 189_P 0.85 0.25 0.01
66_V 284_N 0.85 0.25 0.01
135_L 388_I 0.85 0.25 0.01
17_G 63_I 0.85 0.25 0.01
80_A 243_P 0.85 0.25 0.01
30_V 380_V 0.84 0.24 0.01
32_W 32_T 0.84 0.24 0.01
153_V 307_A 0.84 0.24 0.01
76_D 80_V 0.84 0.24 0.01
66_V 171_G 0.83 0.24 0.01
108_F 259_V 0.83 0.24 0.01
40_A 392_I 0.83 0.24 0.01
130_E 371_A 0.83 0.24 0.01
165_T 56_V 0.83 0.23 0.01
191_L 339_A 0.82 0.23 0.01
50_E 151_W 0.82 0.23 0.01
173_K 380_V 0.82 0.23 0.01
57_V 56_V 0.82 0.23 0.01
68_F 217_H 0.82 0.23 0.01
8_L 392_I 0.82 0.23 0.01
141_D 28_L 0.82 0.23 0.01
112_T 334_I 0.82 0.23 0.01
124_P 206_A 0.81 0.22 0.01
32_W 300_P 0.81 0.22 0.01
10_A 204_V 0.80 0.22 0.01
55_L 175_A 0.80 0.22 0.01
10_A 176_I 0.80 0.22 0.01
81_E 138_M 0.80 0.21 0.01
149_L 426_E 0.80 0.21 0.01
100_L 19_L 0.80 0.21 0.01
8_L 14_G 0.80 0.21 0.01
32_W 259_V 0.79 0.21 0.00
176_N 204_V 0.79 0.21 0.00
99_V 176_I 0.79 0.21 0.00
46_L 344_A 0.79 0.21 0.00
183_R 415_E 0.79 0.21 0.00
32_W 35_I 0.79 0.21 0.00
27_V 123_A 0.79 0.21 0.00
51_F 189_P 0.79 0.21 0.00
65_A 275_G 0.79 0.21 0.00
146_M 46_I 0.79 0.21 0.00
5_A 64_V 0.79 0.21 0.00
141_D 261_V 0.78 0.21 0.00
30_V 373_D 0.78 0.20 0.00
143_Y 121_Y 0.78 0.20 0.00
135_L 61_T 0.78 0.20 0.00
21_V 96_L 0.78 0.20 0.00
151_G 73_V 0.78 0.20 0.00
52_V 343_M 0.78 0.20 0.00
5_A 167_G 0.78 0.20 0.00
136_G 80_V 0.78 0.20 0.00
64_V 215_A 0.77 0.20 0.00
173_K 341_L 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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