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OPENSEQ.org
cI_I_40_cIII_cytb_60_Pdenitr
Genes: A B A+B
Length: 163 440 581
Sequences: 644 3220 351
Seq/Len: 3.95 7.32 0.6
MirrorTree (Pazo et al. 2001) 0.80
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 0.00
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.01
100 0.00 0.00 0.05
∞ 0.01 0.00 0.58
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
124_F 207_A 1.42 0.56 0.00
23_L 355_R 1.39 0.53 0.00
108_F 418_D 1.31 0.47 0.00
10_K 122_K 1.28 0.44 0.00
18_I 330_F 1.23 0.41 0.00
156_L 406_I 1.20 0.38 0.00
5_F 410_L 1.18 0.36 0.00
160_A 44_W 1.15 0.34 0.00
20_G 27_S 1.14 0.33 0.00
13_L 135_I 1.13 0.33 0.00
33_P 60_A 1.12 0.33 0.00
11_Y 425_E 1.12 0.32 0.00
134_L 409_P 1.12 0.32 0.00
8_A 30_Y 1.11 0.32 0.00
112_A 57_L 1.11 0.31 0.00
122_P 415_E 1.09 0.30 0.00
21_F 63_I 1.09 0.30 0.00
139_Q 406_I 1.07 0.29 0.00
123_N 408_L 1.07 0.29 0.00
124_F 304_I 1.06 0.28 0.00
84_E 33_L 1.05 0.28 0.00
21_F 96_L 1.05 0.27 0.00
30_S 284_N 1.04 0.27 0.00
140_K 262_V 1.03 0.26 0.00
133_E 340_I 1.02 0.26 0.00
110_Q 276_H 1.02 0.26 0.00
37_Y 201_L 1.02 0.26 0.00
139_Q 171_G 1.02 0.26 0.00
155_N 276_H 1.02 0.25 0.00
83_A 142_T 1.01 0.25 0.00
155_N 138_M 1.01 0.25 0.00
124_F 122_K 1.01 0.25 0.00
33_P 242_L 1.01 0.25 0.00
84_E 134_L 1.00 0.24 0.00
25_M 116_L 1.00 0.24 0.00
98_I 71_P 0.99 0.24 0.00
157_Q 123_A 0.99 0.24 0.00
9_T 262_V 0.99 0.23 0.00
26_R 265_A 0.98 0.23 0.00
147_R 51_L 0.98 0.23 0.00
24_G 11_P 0.98 0.23 0.00
160_A 260_L 0.98 0.23 0.00
48_F 211_V 0.98 0.23 0.00
26_R 394_L 0.98 0.23 0.00
25_M 211_V 0.97 0.23 0.00
29_V 172_V 0.97 0.22 0.00
158_L 7_D 0.97 0.22 0.00
25_M 46_I 0.96 0.22 0.00
13_L 369_L 0.96 0.22 0.00
105_Y 64_V 0.96 0.22 0.00
5_F 13_T 0.95 0.21 0.00
26_R 136_Y 0.94 0.21 0.00
130_T 280_Y 0.94 0.21 0.00
143_A 358_Q 0.94 0.21 0.00
105_Y 331_F 0.94 0.21 0.00
31_P 360_R 0.93 0.20 0.00
134_L 133_M 0.93 0.20 0.00
139_Q 396_G 0.92 0.20 0.00
134_L 207_A 0.92 0.20 0.00
112_A 406_I 0.92 0.20 0.00
117_A 280_Y 0.92 0.20 0.00
21_F 384_P 0.91 0.20 0.00
100_M 188_N 0.91 0.20 0.00
10_K 93_L 0.91 0.19 0.00
58_P 405_L 0.91 0.19 0.00
20_G 9_Y 0.91 0.19 0.00
57_Y 168_A 0.91 0.19 0.00
105_Y 23_L 0.90 0.19 0.00
82_D 290_A 0.90 0.19 0.00
48_F 270_M 0.90 0.19 0.00
87_E 395_A 0.90 0.19 0.00
82_D 136_Y 0.90 0.19 0.00
36_N 186_V 0.90 0.19 0.00
65_I 105_F 0.90 0.19 0.00
19_K 16_E 0.90 0.19 0.00
28_F 133_M 0.89 0.18 0.00
24_G 136_Y 0.89 0.18 0.00
11_Y 408_L 0.89 0.18 0.00
161_P 108_V 0.89 0.18 0.00
8_A 394_L 0.88 0.18 0.00
65_I 326_I 0.88 0.18 0.00
132_E 330_F 0.88 0.18 0.00
136_Y 135_I 0.87 0.18 0.00
12_F 265_A 0.87 0.18 0.00
37_Y 295_E 0.87 0.17 0.00
18_I 262_V 0.87 0.17 0.00
6_A 425_E 0.87 0.17 0.00
44_L 177_Q 0.87 0.17 0.00
24_G 51_L 0.87 0.17 0.00
34_T 297_Y 0.86 0.17 0.00
150_A 9_Y 0.86 0.17 0.00
157_Q 75_L 0.86 0.17 0.00
5_F 206_A 0.86 0.17 0.00
118_I 121_Y 0.86 0.17 0.00
37_Y 412_G 0.86 0.17 0.00
19_K 345_L 0.86 0.17 0.00
35_L 92_M 0.86 0.17 0.00
155_N 220_G 0.86 0.17 0.00
140_K 106_L 0.85 0.17 0.00
25_M 148_V 0.85 0.17 0.00
25_M 172_V 0.85 0.17 0.00
135_F 52_A 0.85 0.17 0.00
44_L 413_I 0.85 0.17 0.00
154_R 357_G 0.85 0.17 0.00
151_E 210_V 0.85 0.16 0.00
116_D 150_P 0.85 0.16 0.00
4_D 353_R 0.84 0.16 0.00
158_L 44_W 0.84 0.16 0.00
88_D 161_V 0.84 0.16 0.00
27_Y 242_L 0.84 0.16 0.00
157_Q 127_V 0.84 0.16 0.00
20_G 49_I 0.84 0.16 0.00
9_T 395_A 0.84 0.16 0.00
147_R 108_V 0.84 0.16 0.00
12_F 61_T 0.84 0.16 0.00
30_S 269_F 0.84 0.16 0.00
84_E 127_V 0.84 0.16 0.00
6_A 213_I 0.84 0.16 0.00
155_N 398_A 0.84 0.16 0.00
117_A 305_L 0.84 0.16 0.00
40_E 105_F 0.83 0.16 0.00
12_F 68_H 0.83 0.16 0.00
100_M 122_K 0.83 0.16 0.00
139_Q 335_A 0.83 0.16 0.00
139_Q 134_L 0.82 0.15 0.00
30_S 403_Y 0.82 0.15 0.00
100_M 415_E 0.82 0.15 0.00
31_P 372_V 0.82 0.15 0.00
132_E 176_I 0.82 0.15 0.00
159_D 209_V 0.82 0.15 0.00
135_F 385_A 0.82 0.15 0.00
7_R 422_Q 0.82 0.15 0.00
136_Y 117_Y 0.82 0.15 0.00
11_Y 308_F 0.82 0.15 0.00
43_P 392_I 0.81 0.15 0.00
49_R 47_W 0.81 0.15 0.00
157_Q 256_L 0.81 0.15 0.00
108_F 227_V 0.81 0.15 0.00
135_F 72_H 0.81 0.15 0.00
28_F 415_E 0.81 0.15 0.00
39_H 351_T 0.81 0.15 0.00
88_D 288_T 0.81 0.15 0.00
13_L 250_I 0.80 0.14 0.00
8_A 64_V 0.80 0.14 0.00
57_Y 279_N 0.80 0.14 0.00
37_Y 232_G 0.80 0.14 0.00
25_M 28_L 0.80 0.14 0.00
42_G 72_H 0.80 0.14 0.00
41_K 166_F 0.80 0.14 0.00
135_F 28_L 0.80 0.14 0.00
20_G 7_D 0.80 0.14 0.00
57_Y 163_T 0.80 0.14 0.00
161_P 379_W 0.80 0.14 0.00
28_F 171_G 0.80 0.14 0.00
110_Q 238_K 0.80 0.14 0.00
152_I 93_L 0.80 0.14 0.00
112_A 335_A 0.79 0.14 0.00
7_R 133_M 0.79 0.14 0.00
18_I 156_F 0.79 0.14 0.00
5_F 75_L 0.79 0.14 0.00
92_R 126_E 0.79 0.14 0.00
57_Y 378_M 0.79 0.14 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
3054 0.6 cI_I_40_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3053 0.74 cI_I_20_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3052 0.98 cI_I_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3051 0.6 cI_I_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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