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OPENSEQ.org
cI_A_10_cIII_cytb_20_Pdenitr_corr
Genes: A B A+B
Length: 121 440 493
Sequences: 4764 3290 2800
Seq/Len: 39.37 7.48 5.68
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 0.08
2 0.00 0.00 0.27
5 0.00 0.00 3.63
10 0.00 0.00 4.08
20 0.00 0.00 4.17
100 0.01 0.00 4.25
∞ 0.02 0.01 4.99
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 1.36 0.97 0.66
72_I 403_Y 1.05 0.86 0.37
45_Y 386_E 1.01 0.83 0.32
19_S 242_L 1.01 0.83 0.32
75_L 360_R 0.95 0.78 0.27
55_A 197_L 0.94 0.77 0.27
93_V 398_A 0.94 0.76 0.26
101_F 281_I 0.92 0.74 0.25
35_R 41_L 0.87 0.68 0.21
64_Y 20_H 0.87 0.68 0.20
27_L 405_L 0.85 0.65 0.19
115_K 43_W 0.85 0.65 0.19
116_G 112_I 0.85 0.65 0.19
83_W 360_R 0.84 0.65 0.19
72_I 411_L 0.83 0.63 0.18
99_M 89_G 0.82 0.62 0.17
21_L 123_A 0.81 0.61 0.17
66_V 390_P 0.81 0.60 0.16
20_A 19_L 0.81 0.59 0.16
29_A 145_M 0.78 0.56 0.14
78_A 145_M 0.78 0.55 0.14
39_P 107_A 0.77 0.54 0.14
50_N 115_G 0.77 0.54 0.14
77_V 46_I 0.77 0.54 0.14
68_I 59_I 0.76 0.53 0.13
100_V 138_M 0.76 0.53 0.13
21_L 33_L 0.76 0.52 0.13
98_L 257_A 0.73 0.48 0.12
71_I 99_N 0.73 0.48 0.12
98_L 176_I 0.72 0.47 0.11
91_S 22_R 0.72 0.46 0.11
87_F 206_A 0.71 0.46 0.11
27_L 338_G 0.71 0.46 0.11
62_R 94_R 0.71 0.46 0.11
11_I 371_A 0.71 0.46 0.11
21_L 166_F 0.71 0.45 0.11
66_V 80_V 0.70 0.45 0.10
108_G 121_Y 0.70 0.44 0.10
80_L 394_L 0.70 0.44 0.10
83_W 269_F 0.70 0.44 0.10
12_L 410_L 0.70 0.44 0.10
107_V 338_G 0.69 0.43 0.10
60_D 276_H 0.69 0.43 0.10
15_L 265_A 0.69 0.42 0.10
99_M 410_L 0.69 0.42 0.10
67_S 76_A 0.69 0.42 0.10
80_L 96_L 0.68 0.42 0.09
52_F 267_V 0.68 0.42 0.09
79_F 336_M 0.68 0.41 0.09
87_F 264_F 0.68 0.41 0.09
24_V 206_A 0.68 0.40 0.09
64_Y 39_K 0.67 0.40 0.09
26_I 208_L 0.67 0.40 0.09
30_A 63_I 0.67 0.40 0.09
113_W 143_A 0.67 0.39 0.09
28_A 344_A 0.67 0.39 0.09
91_S 19_L 0.66 0.38 0.08
40_E 275_G 0.66 0.38 0.08
20_A 362_L 0.66 0.38 0.08
81_F 246_P 0.66 0.38 0.08
110_A 392_I 0.65 0.37 0.08
34_V 360_R 0.65 0.37 0.08
89_S 261_V 0.65 0.37 0.08
25_L 70_T 0.65 0.37 0.08
27_L 345_L 0.65 0.37 0.08
101_F 76_A 0.65 0.37 0.08
110_A 204_V 0.65 0.37 0.08
118_L 136_Y 0.65 0.36 0.08
16_G 134_L 0.65 0.36 0.08
67_S 128_T 0.65 0.36 0.08
18_A 406_I 0.64 0.36 0.08
45_Y 397_S 0.64 0.36 0.08
75_L 382_A 0.64 0.36 0.08
23_I 19_L 0.64 0.36 0.08
87_F 402_A 0.64 0.35 0.08
79_F 178_T 0.64 0.35 0.08
23_I 257_A 0.64 0.35 0.08
20_A 410_L 0.64 0.35 0.08
68_I 222_N 0.64 0.35 0.07
116_G 374_F 0.64 0.35 0.07
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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