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OPENSEQ.org
cI_A_20_cIII_cytb_40_Pdenitr_corr
Genes: A B A+B
Length: 121 440 493
Sequences: 4481 3285 2607
Seq/Len: 37.03 7.47 5.29
MirrorTree (Pazo et al. 2001) 0.74
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 0.07
2 0.00 0.00 0.21
5 0.00 0.00 3.43
10 0.00 0.00 3.79
20 0.00 0.00 3.82
100 0.01 0.00 3.95
∞ 0.02 0.01 4.65
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
79_F 343_M 1.47 0.98 0.82
19_S 242_L 1.12 0.89 0.52
75_L 360_R 1.11 0.89 0.52
101_F 281_I 1.05 0.84 0.45
35_R 41_L 1.03 0.83 0.43
93_V 261_V 0.95 0.75 0.34
72_I 403_Y 0.90 0.70 0.29
91_S 29_V 0.89 0.69 0.29
20_A 19_L 0.89 0.69 0.28
21_L 33_L 0.89 0.68 0.28
100_V 138_M 0.87 0.66 0.26
45_Y 261_V 0.86 0.65 0.26
83_W 360_R 0.86 0.65 0.26
78_A 145_M 0.86 0.65 0.25
55_A 197_L 0.86 0.65 0.25
66_V 390_P 0.84 0.62 0.23
71_I 99_N 0.83 0.61 0.23
34_V 360_R 0.83 0.60 0.23
67_S 128_T 0.81 0.58 0.21
60_D 276_H 0.81 0.58 0.21
93_V 398_A 0.81 0.57 0.21
16_G 57_L 0.80 0.56 0.20
64_Y 20_H 0.79 0.55 0.20
115_K 43_W 0.79 0.55 0.20
26_I 208_L 0.79 0.55 0.19
80_L 394_L 0.79 0.54 0.19
93_V 369_L 0.77 0.53 0.18
101_F 243_P 0.76 0.51 0.17
91_S 180_L 0.76 0.51 0.17
84_A 158_G 0.76 0.50 0.17
106_T 40_N 0.76 0.50 0.17
50_N 115_G 0.76 0.50 0.17
93_V 260_L 0.75 0.49 0.16
27_L 405_L 0.74 0.48 0.16
30_A 63_I 0.74 0.47 0.15
115_K 66_V 0.73 0.47 0.15
116_G 92_M 0.73 0.47 0.15
59_F 381_G 0.73 0.47 0.15
40_E 275_G 0.73 0.47 0.15
29_A 145_M 0.72 0.46 0.15
78_A 171_G 0.72 0.46 0.15
101_F 76_A 0.72 0.46 0.15
96_W 338_G 0.72 0.45 0.14
11_I 19_L 0.72 0.45 0.14
67_S 139_M 0.72 0.45 0.14
16_G 134_L 0.72 0.45 0.14
19_S 348_W 0.72 0.45 0.14
45_Y 386_E 0.71 0.44 0.14
19_S 249_V 0.71 0.44 0.14
72_I 397_S 0.71 0.44 0.14
119_E 255_A 0.71 0.43 0.14
20_A 410_L 0.71 0.43 0.14
23_I 211_V 0.70 0.43 0.13
26_I 328_A 0.70 0.42 0.13
95_F 81_E 0.70 0.41 0.13
71_I 377_L 0.69 0.41 0.13
114_K 348_W 0.69 0.41 0.12
72_I 411_L 0.69 0.40 0.12
67_S 116_L 0.69 0.40 0.12
26_I 392_I 0.69 0.40 0.12
29_A 172_V 0.68 0.40 0.12
98_L 176_I 0.68 0.40 0.12
111_Y 78_A 0.68 0.39 0.12
39_P 185_A 0.68 0.39 0.12
62_R 94_R 0.68 0.39 0.12
38_D 106_L 0.67 0.38 0.11
79_F 178_T 0.67 0.38 0.11
77_V 46_I 0.67 0.38 0.11
39_P 107_A 0.67 0.38 0.11
53_D 350_D 0.67 0.38 0.11
69_L 116_L 0.67 0.38 0.11
18_A 406_I 0.67 0.37 0.11
27_L 369_L 0.66 0.37 0.11
115_K 240_D 0.66 0.37 0.11
14_F 41_L 0.66 0.37 0.11
22_A 127_V 0.66 0.36 0.11
117_A 374_F 0.66 0.36 0.11
107_V 338_G 0.66 0.36 0.11
72_I 127_V 0.66 0.36 0.11
56_R 91_Y 0.66 0.36 0.11
43_S 379_W 0.66 0.36 0.11
45_Y 415_E 0.65 0.36 0.10
79_F 336_M 0.65 0.35 0.10
83_W 269_F 0.65 0.35 0.10
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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