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OPENSEQ.org
cI_K_10_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 101 440 483
Sequences: 4172 3285 2072
Seq/Len: 41.31 7.47 4.29
MirrorTree (Pazo et al. 2001) 0.66
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 0.11
2 0.00 0.00 1.02
5 0.01 0.00 2.64
10 0.01 0.00 2.74
20 0.01 0.00 2.86
100 0.03 0.00 2.95
∞ 0.07 0.01 3.83
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
69_V 364_K 1.43 0.97 0.72
88_R 192_N 1.13 0.86 0.46
32_I 63_I 1.09 0.83 0.42
47_F 402_A 0.95 0.69 0.28
19_I 355_R 0.92 0.66 0.25
85_F 93_L 0.91 0.65 0.25
68_T 278_D 0.91 0.65 0.24
74_A 135_I 0.90 0.63 0.23
38_L 180_L 0.89 0.63 0.23
47_F 395_A 0.89 0.62 0.23
32_I 364_K 0.88 0.61 0.22
25_N 254_F 0.87 0.60 0.21
30_I 88_N 0.87 0.60 0.21
93_V 344_A 0.86 0.58 0.20
14_L 239_K 0.85 0.57 0.19
69_V 352_S 0.84 0.56 0.19
15_F 405_L 0.84 0.56 0.19
25_N 350_D 0.84 0.56 0.19
25_N 123_A 0.84 0.56 0.19
34_M 298_F 0.84 0.55 0.19
25_N 272_N 0.83 0.54 0.18
67_L 121_Y 0.81 0.51 0.17
75_A 397_S 0.81 0.51 0.17
17_T 119_G 0.80 0.51 0.16
64_M 103_L 0.80 0.51 0.16
25_N 267_V 0.79 0.49 0.15
36_I 278_D 0.79 0.48 0.15
45_I 371_A 0.79 0.48 0.15
8_L 71_P 0.79 0.48 0.15
32_I 25_I 0.78 0.48 0.15
51_S 338_G 0.78 0.47 0.15
49_A 270_M 0.78 0.47 0.15
74_A 196_S 0.78 0.47 0.14
75_A 134_L 0.77 0.45 0.14
69_V 176_I 0.77 0.45 0.14
36_I 178_T 0.76 0.45 0.14
74_A 403_Y 0.76 0.45 0.14
60_Q 412_G 0.76 0.44 0.13
42_A 103_L 0.75 0.44 0.13
48_V 209_V 0.75 0.43 0.13
45_I 139_M 0.75 0.43 0.13
59_G 207_A 0.75 0.43 0.13
70_A 352_S 0.75 0.43 0.13
35_S 385_A 0.74 0.43 0.13
96_V 250_I 0.74 0.43 0.13
19_I 362_L 0.74 0.42 0.12
80_I 80_V 0.74 0.42 0.12
83_V 376_V 0.74 0.42 0.12
48_V 135_I 0.73 0.41 0.12
13_I 59_I 0.73 0.41 0.12
50_F 370_L 0.73 0.41 0.12
34_M 285_P 0.73 0.40 0.12
63_T 166_F 0.73 0.40 0.12
48_V 239_K 0.72 0.40 0.12
61_V 383_M 0.72 0.40 0.12
22_I 143_A 0.72 0.40 0.11
94_E 204_V 0.72 0.40 0.11
38_L 344_A 0.72 0.40 0.11
65_F 44_W 0.72 0.39 0.11
93_V 272_N 0.72 0.39 0.11
46_N 356_S 0.71 0.39 0.11
18_G 248_F 0.71 0.39 0.11
64_M 180_L 0.71 0.38 0.11
72_A 215_A 0.71 0.38 0.11
88_R 375_V 0.71 0.38 0.11
18_G 243_P 0.71 0.38 0.11
45_I 253_L 0.70 0.37 0.10
80_I 56_V 0.70 0.37 0.10
65_F 293_V 0.70 0.37 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
2932 5.03 cI_K_6_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.62 Done - Shared
2930 4.29 cI_K_10_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.72 Done - Shared
2928 1.12 cI_K_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
2927 1.12 cI_K_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.52 Done - Shared
2926 1.11 cI_K_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
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