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OPENSEQ.org
cI_J_10_cIII_cytb_20_Pdenitr
Genes: A B A+B
Length: 200 440 612
Sequences: 2223 3290 724
Seq/Len: 11.12 7.48 1.18
MirrorTree (Pazo et al. 2001) 0.62
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 0.23
10 0.01 0.00 0.32
20 0.01 0.00 0.37
100 0.02 0.00 0.45
∞ 0.03 0.01 1.13
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 204_V 1.47 0.79 0.04
136_G 121_Y 1.35 0.70 0.03
38_L 42_N 1.33 0.69 0.03
176_N 383_M 1.32 0.68 0.03
107_A 242_L 1.32 0.68 0.02
92_L 138_M 1.24 0.60 0.02
41_A 414_I 1.24 0.60 0.02
192_K 93_L 1.20 0.57 0.02
135_L 56_V 1.16 0.53 0.01
159_I 60_A 1.15 0.52 0.01
72_V 113_F 1.15 0.52 0.01
41_A 39_K 1.06 0.44 0.01
132_T 115_G 1.06 0.43 0.01
73_M 150_P 1.05 0.43 0.01
108_F 56_V 1.05 0.42 0.01
96_I 44_W 1.02 0.40 0.01
64_V 331_F 1.02 0.39 0.01
104_L 364_K 1.00 0.38 0.01
4_F 267_V 0.99 0.37 0.01
23_G 284_N 0.99 0.37 0.01
21_V 29_V 0.99 0.37 0.01
51_F 372_V 0.98 0.36 0.01
41_A 122_K 0.98 0.36 0.01
74_M 356_S 0.98 0.36 0.01
191_L 57_L 0.97 0.36 0.01
66_V 284_N 0.97 0.35 0.01
66_V 72_H 0.97 0.35 0.01
40_A 369_L 0.96 0.35 0.01
29_S 56_V 0.95 0.34 0.01
45_V 414_I 0.95 0.33 0.01
140_Y 216_F 0.93 0.32 0.01
149_L 63_I 0.93 0.32 0.01
106_I 78_A 0.93 0.32 0.01
160_G 200_L 0.93 0.32 0.01
36_A 394_L 0.93 0.32 0.01
107_A 376_V 0.92 0.31 0.01
42_G 249_V 0.92 0.31 0.01
102_A 56_V 0.92 0.31 0.01
159_I 258_V 0.92 0.31 0.01
52_V 207_A 0.92 0.30 0.01
100_L 19_L 0.91 0.30 0.01
17_G 63_I 0.91 0.30 0.01
93_A 262_V 0.91 0.30 0.01
167_R 122_K 0.91 0.30 0.01
173_K 277_P 0.91 0.30 0.01
157_A 361_P 0.91 0.30 0.01
135_L 238_K 0.91 0.30 0.01
17_G 59_I 0.90 0.29 0.01
32_W 286_L 0.90 0.29 0.01
141_D 261_V 0.90 0.29 0.01
38_L 375_V 0.89 0.29 0.01
22_I 176_I 0.89 0.28 0.01
110_G 133_M 0.88 0.28 0.01
21_V 200_L 0.88 0.28 0.01
96_I 412_G 0.88 0.27 0.01
57_V 56_V 0.87 0.27 0.01
56_L 367_F 0.87 0.27 0.01
176_N 169_I 0.87 0.27 0.01
130_E 371_A 0.87 0.27 0.01
14_C 179_W 0.86 0.27 0.01
112_T 411_L 0.86 0.26 0.01
10_A 33_L 0.86 0.26 0.01
124_P 206_A 0.86 0.26 0.01
139_L 213_I 0.85 0.25 0.01
189_M 136_Y 0.85 0.25 0.01
15_V 131_V 0.85 0.25 0.01
157_A 397_S 0.84 0.25 0.01
99_V 186_V 0.84 0.25 0.01
158_M 196_S 0.84 0.25 0.01
179_E 375_V 0.84 0.25 0.01
54_M 374_F 0.83 0.24 0.01
15_V 414_I 0.83 0.24 0.01
2_M 27_S 0.83 0.24 0.01
46_L 344_A 0.83 0.24 0.01
172_V 134_L 0.82 0.24 0.01
173_K 341_L 0.82 0.24 0.01
154_L 296_W 0.82 0.23 0.01
102_A 19_L 0.82 0.23 0.01
59_V 402_A 0.82 0.23 0.01
66_V 171_G 0.82 0.23 0.01
57_V 143_A 0.82 0.23 0.01
26_P 396_G 0.82 0.23 0.01
144_V 348_W 0.81 0.23 0.01
30_V 380_V 0.81 0.23 0.01
31_L 266_I 0.81 0.23 0.01
97_G 207_A 0.81 0.23 0.01
21_V 96_L 0.81 0.23 0.01
37_F 224_P 0.81 0.22 0.01
82_L 398_A 0.80 0.22 0.01
173_K 380_V 0.80 0.22 0.01
65_A 148_V 0.80 0.22 0.01
147_F 399_Y 0.80 0.22 0.01
165_T 56_V 0.80 0.22 0.01
29_S 376_V 0.80 0.22 0.01
189_M 273_Y 0.80 0.22 0.01
14_C 242_L 0.79 0.21 0.01
80_A 243_P 0.79 0.21 0.01
159_I 110_I 0.79 0.21 0.01
132_T 148_V 0.79 0.21 0.01
50_E 151_W 0.79 0.21 0.01
135_L 388_I 0.79 0.21 0.01
9_F 205_I 0.79 0.21 0.01
15_V 354_V 0.79 0.21 0.01
45_V 214_W 0.79 0.21 0.01
55_L 175_A 0.79 0.21 0.01
141_D 28_L 0.79 0.21 0.01
81_E 138_M 0.79 0.21 0.01
176_N 204_V 0.79 0.21 0.01
48_G 407_I 0.79 0.21 0.01
70_F 305_L 0.79 0.21 0.01
46_L 360_R 0.78 0.21 0.00
32_W 32_T 0.78 0.21 0.00
101_L 330_F 0.78 0.21 0.00
37_F 271_P 0.78 0.21 0.00
99_V 405_L 0.78 0.21 0.00
127_A 204_V 0.78 0.21 0.00
147_F 103_L 0.78 0.21 0.00
8_L 14_G 0.78 0.21 0.00
108_F 416_K 0.78 0.20 0.00
116_Q 172_V 0.78 0.20 0.00
36_A 167_G 0.78 0.20 0.00
136_G 80_V 0.78 0.20 0.00
119_S 106_L 0.78 0.20 0.00
76_D 80_V 0.78 0.20 0.00
27_V 123_A 0.78 0.20 0.00
167_R 248_F 0.78 0.20 0.00
96_I 134_L 0.77 0.20 0.00
10_A 204_V 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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