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OPENSEQ.org
cI_K_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 101 440 518
Sequences: 1319 3290 574
Seq/Len: 13.06 7.48 1.11
MirrorTree (Pazo et al. 2001) 0.59
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 0.05
5 0.00 0.00 0.16
10 0.01 0.00 0.23
20 0.01 0.00 0.29
100 0.02 0.00 0.37
∞ 0.03 0.01 1.06
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
61_V 205_I 1.67 0.88 0.22
42_A 71_P 1.63 0.86 0.20
61_V 113_F 1.38 0.71 0.10
39_M 26_V 1.23 0.58 0.07
38_L 180_L 1.23 0.57 0.06
39_M 242_L 1.21 0.56 0.06
16_V 342_V 1.19 0.54 0.06
90_T 64_V 1.14 0.49 0.05
81_L 168_A 1.11 0.47 0.04
39_M 134_L 1.11 0.47 0.04
47_F 369_L 1.10 0.46 0.04
91_I 404_F 1.09 0.44 0.04
35_S 385_A 1.08 0.44 0.04
36_I 61_T 1.06 0.42 0.04
88_R 131_V 1.05 0.41 0.04
64_M 34_M 1.04 0.40 0.03
100_K 367_F 1.02 0.38 0.03
47_F 298_F 1.01 0.37 0.03
50_F 180_L 0.98 0.35 0.03
42_A 354_V 0.98 0.35 0.03
35_S 262_V 0.97 0.34 0.03
90_T 93_L 0.97 0.33 0.03
11_G 277_P 0.96 0.33 0.03
76_I 211_V 0.96 0.33 0.03
77_G 143_A 0.96 0.33 0.03
28_N 260_L 0.96 0.33 0.02
100_K 262_V 0.95 0.32 0.02
53_H 376_V 0.94 0.32 0.02
65_F 158_G 0.94 0.31 0.02
48_V 328_A 0.93 0.30 0.02
10_V 348_W 0.93 0.30 0.02
9_V 156_F 0.93 0.30 0.02
86_R 131_V 0.92 0.30 0.02
65_F 208_L 0.92 0.29 0.02
19_I 134_L 0.91 0.29 0.02
100_K 214_W 0.91 0.29 0.02
42_A 411_L 0.91 0.29 0.02
85_F 284_N 0.90 0.28 0.02
34_M 140_M 0.90 0.28 0.02
49_A 270_M 0.89 0.28 0.02
5_T 169_I 0.89 0.28 0.02
71_A 356_S 0.89 0.27 0.02
57_L 57_L 0.88 0.27 0.02
22_I 143_A 0.88 0.27 0.02
94_E 20_H 0.88 0.27 0.02
80_I 42_N 0.88 0.27 0.02
66_V 83_I 0.88 0.26 0.02
30_I 254_F 0.87 0.26 0.02
48_V 239_K 0.87 0.26 0.02
99_M 174_E 0.87 0.26 0.02
88_R 201_L 0.86 0.25 0.02
47_F 138_M 0.86 0.25 0.02
63_T 410_L 0.85 0.25 0.02
80_I 300_P 0.85 0.24 0.02
74_A 15_F 0.85 0.24 0.02
87_N 23_L 0.85 0.24 0.02
24_V 75_L 0.85 0.24 0.02
66_V 105_F 0.84 0.24 0.01
74_A 207_A 0.84 0.24 0.01
42_A 72_H 0.84 0.24 0.01
79_A 344_A 0.84 0.24 0.01
87_N 18_W 0.84 0.24 0.01
57_L 116_L 0.83 0.23 0.01
39_M 406_I 0.83 0.23 0.01
43_V 260_L 0.83 0.23 0.01
32_I 128_T 0.83 0.23 0.01
33_L 356_S 0.82 0.23 0.01
33_L 220_G 0.82 0.23 0.01
97_N 17_R 0.82 0.22 0.01
4_L 375_V 0.81 0.22 0.01
53_H 427_D 0.81 0.22 0.01
61_V 213_I 0.81 0.22 0.01
30_I 287_V 0.81 0.22 0.01
56_D 93_L 0.81 0.22 0.01
35_S 145_M 0.81 0.22 0.01
38_L 59_I 0.81 0.21 0.01
39_M 11_P 0.81 0.21 0.01
5_T 201_L 0.81 0.21 0.01
61_V 410_L 0.80 0.21 0.01
34_M 358_Q 0.80 0.21 0.01
47_F 131_V 0.80 0.21 0.01
63_T 112_I 0.80 0.21 0.01
30_I 340_I 0.80 0.21 0.01
62_F 61_T 0.80 0.21 0.01
19_I 355_R 0.79 0.21 0.01
35_S 340_I 0.79 0.21 0.01
83_V 205_I 0.79 0.20 0.01
61_V 186_V 0.79 0.20 0.01
18_G 183_G 0.79 0.20 0.01
29_V 351_T 0.79 0.20 0.01
90_T 341_L 0.78 0.20 0.01
83_V 25_I 0.78 0.20 0.01
53_H 396_G 0.78 0.20 0.01
29_V 261_V 0.78 0.20 0.01
10_V 204_V 0.78 0.20 0.01
84_F 122_K 0.78 0.20 0.01
24_V 105_F 0.77 0.20 0.01
44_N 41_L 0.77 0.19 0.01
27_K 246_P 0.77 0.19 0.01
27_K 61_T 0.77 0.19 0.01
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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