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OPENSEQ.org
cI_A_40_cIII_cytb_20_Pdenitr_corr
Genes: A B A+B
Length: 121 440 535
Sequences: 493 3290 325
Seq/Len: 4.07 7.48 0.61
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 0.02
2 0.00 0.00 0.04
5 0.00 0.00 0.10
10 0.00 0.00 0.16
20 0.00 0.00 0.18
100 0.00 0.00 0.23
∞ 0.00 0.01 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
88_A 359_Y 1.43 0.57 0.00
43_S 379_W 1.25 0.42 0.00
117_A 300_P 1.21 0.39 0.00
106_T 156_F 1.17 0.36 0.00
90_L 372_V 1.17 0.36 0.00
29_A 99_N 1.15 0.35 0.00
64_Y 35_I 1.15 0.34 0.00
77_V 187_D 1.15 0.34 0.00
107_V 177_Q 1.14 0.34 0.00
92_D 307_A 1.13 0.33 0.00
54_D 403_Y 1.11 0.32 0.00
67_S 35_I 1.11 0.32 0.00
61_V 244_F 1.10 0.31 0.00
15_L 390_P 1.10 0.31 0.00
25_L 156_F 1.09 0.31 0.00
10_P 126_E 1.09 0.30 0.00
110_A 341_L 1.09 0.30 0.00
21_L 261_V 1.07 0.29 0.00
64_Y 300_P 1.06 0.29 0.00
17_M 264_F 1.06 0.28 0.00
107_V 136_Y 1.05 0.28 0.00
23_I 370_L 1.05 0.27 0.00
104_V 131_V 1.04 0.27 0.00
38_D 136_Y 1.03 0.27 0.00
17_M 282_E 1.03 0.27 0.00
44_A 250_I 1.03 0.26 0.00
21_L 370_L 1.03 0.26 0.00
26_I 328_A 1.02 0.26 0.00
24_V 396_G 1.02 0.26 0.00
58_K 245_W 1.02 0.26 0.00
119_E 414_I 1.02 0.26 0.00
24_V 376_V 1.02 0.26 0.00
61_V 237_A 1.01 0.25 0.00
54_D 264_F 1.00 0.25 0.00
53_D 37_T 1.00 0.24 0.00
95_F 409_P 0.99 0.24 0.00
18_A 240_D 0.99 0.24 0.00
28_A 136_Y 0.98 0.23 0.00
90_L 15_F 0.98 0.23 0.00
63_F 177_Q 0.98 0.23 0.00
109_F 300_P 0.98 0.23 0.00
31_V 395_A 0.97 0.23 0.00
22_A 393_A 0.97 0.23 0.00
61_V 411_L 0.96 0.23 0.00
13_V 238_K 0.96 0.22 0.00
107_V 397_S 0.96 0.22 0.00
67_S 276_H 0.96 0.22 0.00
78_A 126_E 0.95 0.22 0.00
29_A 58_Q 0.95 0.22 0.00
24_V 211_V 0.94 0.21 0.00
39_P 172_V 0.94 0.21 0.00
64_Y 301_F 0.94 0.21 0.00
35_R 176_I 0.94 0.21 0.00
35_R 237_A 0.93 0.21 0.00
72_I 343_M 0.93 0.20 0.00
8_Y 124_P 0.93 0.20 0.00
20_A 370_L 0.92 0.20 0.00
63_F 424_I 0.92 0.20 0.00
8_Y 246_P 0.92 0.20 0.00
64_Y 246_P 0.92 0.20 0.00
72_I 330_F 0.92 0.20 0.00
72_I 197_L 0.92 0.20 0.00
63_F 163_T 0.92 0.20 0.00
33_A 353_R 0.92 0.20 0.00
15_L 57_L 0.92 0.20 0.00
119_E 136_Y 0.92 0.20 0.00
99_M 215_A 0.92 0.20 0.00
94_A 13_T 0.92 0.20 0.00
29_A 359_Y 0.92 0.20 0.00
104_V 75_L 0.91 0.20 0.00
93_V 262_V 0.91 0.19 0.00
27_L 133_M 0.91 0.19 0.00
24_V 184_P 0.91 0.19 0.00
117_A 35_I 0.91 0.19 0.00
21_L 373_D 0.90 0.19 0.00
22_A 390_P 0.89 0.19 0.00
85_V 334_I 0.89 0.19 0.00
56_R 108_V 0.89 0.19 0.00
71_I 259_V 0.89 0.19 0.00
15_L 133_M 0.89 0.19 0.00
63_F 415_E 0.89 0.18 0.00
78_A 259_V 0.89 0.18 0.00
52_F 137_L 0.89 0.18 0.00
60_D 356_S 0.88 0.18 0.00
25_L 418_D 0.88 0.18 0.00
32_I 84_M 0.88 0.18 0.00
14_F 22_R 0.88 0.18 0.00
20_A 61_T 0.88 0.18 0.00
107_V 339_A 0.88 0.18 0.00
91_S 215_A 0.88 0.18 0.00
31_V 335_A 0.87 0.18 0.00
13_V 240_D 0.87 0.18 0.00
87_F 19_L 0.87 0.18 0.00
18_A 416_K 0.87 0.17 0.00
28_A 371_A 0.87 0.17 0.00
114_K 103_L 0.87 0.17 0.00
21_L 308_F 0.86 0.17 0.00
64_Y 125_R 0.86 0.17 0.00
92_D 28_L 0.86 0.17 0.00
98_L 84_M 0.86 0.17 0.00
91_S 403_Y 0.86 0.17 0.00
61_V 53_F 0.86 0.17 0.00
31_V 31_D 0.86 0.17 0.00
107_V 342_V 0.86 0.17 0.00
64_Y 91_Y 0.85 0.17 0.00
115_K 192_N 0.85 0.17 0.00
99_M 393_A 0.84 0.16 0.00
21_L 355_R 0.84 0.16 0.00
99_M 352_S 0.84 0.16 0.00
112_E 259_V 0.84 0.16 0.00
61_V 269_F 0.84 0.16 0.00
10_P 22_R 0.84 0.16 0.00
44_A 284_N 0.84 0.16 0.00
87_F 53_F 0.84 0.16 0.00
93_V 13_T 0.84 0.16 0.00
51_A 348_W 0.83 0.16 0.00
55_A 266_I 0.83 0.16 0.00
17_M 108_V 0.83 0.16 0.00
110_A 286_L 0.83 0.16 0.00
33_A 304_I 0.83 0.16 0.00
85_V 53_F 0.83 0.16 0.00
107_V 269_F 0.82 0.16 0.00
31_V 63_I 0.82 0.15 0.00
10_P 350_D 0.82 0.15 0.00
12_L 137_L 0.82 0.15 0.00
86_S 309_T 0.82 0.15 0.00
30_A 257_A 0.81 0.15 0.00
61_V 266_I 0.81 0.15 0.00
20_A 110_I 0.81 0.15 0.00
64_Y 124_P 0.81 0.15 0.00
12_L 7_D 0.81 0.15 0.00
119_E 392_I 0.81 0.15 0.00
67_S 391_Y 0.81 0.15 0.00
90_L 171_G 0.81 0.15 0.00
11_I 362_L 0.81 0.15 0.00
16_G 376_V 0.81 0.15 0.00
42_V 339_A 0.81 0.15 0.00
78_A 113_F 0.80 0.15 0.00
8_Y 260_L 0.80 0.15 0.00
119_E 251_K 0.80 0.15 0.00
100_V 394_L 0.80 0.15 0.00
34_V 112_I 0.79 0.14 0.00
99_M 375_V 0.79 0.14 0.00
119_E 189_P 0.79 0.14 0.00
107_V 73_V 0.79 0.14 0.00
24_V 362_L 0.79 0.14 0.00
12_L 374_F 0.79 0.14 0.00
60_D 300_P 0.79 0.14 0.00
94_A 337_F 0.79 0.14 0.00
60_D 35_I 0.79 0.14 0.00
72_I 344_A 0.78 0.14 0.00
9_L 349_L 0.78 0.14 0.00
78_A 301_F 0.78 0.14 0.00
84_A 126_E 0.78 0.14 0.00
10_P 39_K 0.78 0.14 0.00
86_S 207_A 0.78 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
2988 5.32 cI_A_20_cIII_cytb_40_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
2987 5.29 cI_A_20_cIII_cytb_40_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.82 Done - Shared
2986 0.61 cI_A_40_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2985 5.32 cI_A_20_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.78 Done - Shared
2984 5.68 cI_A_10_cIII_cytb_20_Pdenitr_corr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.66 Done - Shared
2983 5.68 cI_A_10_cIII_cytb_10_Pdenitr_corr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.61 Done - Shared
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