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OPENSEQ.org
cI_E_cIII_cytb
Genes: A B A+B
Length: 147 440 496
Sequences: 3696 3168 2162
Seq/Len: 25.14 7.2 4.36
MirrorTree (Pazo et al. 2001) 0.76
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 0.06
2 0.00 0.00 0.18
5 0.00 0.00 2.65
10 0.00 0.00 2.91
20 0.00 0.00 2.96
100 0.01 0.00 3.04
∞ 0.01 0.01 3.68
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
80_V 360_R 1.12 0.85 0.09
71_V 80_V 1.10 0.84 0.09
50_F 261_V 1.09 0.84 0.09
77_I 403_Y 1.09 0.84 0.09
83_L 145_M 1.02 0.77 0.07
84_Y 343_M 1.00 0.76 0.07
31_L 243_P 0.96 0.72 0.06
69_Y 95_Y 0.95 0.71 0.06
34_G 145_M 0.95 0.70 0.06
44_R 107_A 0.94 0.69 0.05
106_F 76_A 0.93 0.68 0.05
84_Y 178_T 0.93 0.68 0.05
25_G 19_L 0.93 0.68 0.05
106_F 281_I 0.92 0.66 0.05
92_I 169_I 0.92 0.66 0.05
24_I 258_V 0.90 0.64 0.05
84_Y 44_W 0.87 0.60 0.04
85_L 351_T 0.86 0.59 0.04
34_G 272_N 0.86 0.59 0.04
24_I 365_W 0.85 0.58 0.04
74_F 95_Y 0.85 0.58 0.04
35_W 63_I 0.85 0.57 0.04
32_V 405_L 0.85 0.57 0.04
26_L 33_L 0.85 0.57 0.04
29_L 362_L 0.84 0.57 0.04
125_W 291_H 0.84 0.56 0.04
69_Y 20_H 0.84 0.56 0.04
74_F 278_D 0.83 0.55 0.04
72_A 139_M 0.83 0.55 0.04
93_R 60_A 0.83 0.55 0.04
27_C 127_V 0.82 0.54 0.04
77_I 397_S 0.82 0.53 0.04
112_A 108_V 0.81 0.52 0.03
111_L 40_N 0.80 0.51 0.03
64_L 381_G 0.80 0.50 0.03
105_I 138_M 0.79 0.50 0.03
85_L 178_T 0.79 0.50 0.03
107_I 178_T 0.79 0.49 0.03
94_E 176_I 0.79 0.49 0.03
74_F 71_P 0.79 0.49 0.03
72_A 76_A 0.78 0.48 0.03
45_S 275_G 0.78 0.48 0.03
107_I 290_A 0.78 0.47 0.03
84_Y 81_E 0.77 0.47 0.03
32_V 369_L 0.77 0.47 0.03
67_K 141_G 0.77 0.47 0.03
50_F 404_F 0.77 0.46 0.03
96_G 180_L 0.77 0.46 0.03
94_E 211_V 0.76 0.46 0.03
67_K 94_R 0.76 0.45 0.03
39_G 360_R 0.76 0.45 0.03
25_G 138_M 0.76 0.45 0.03
74_F 256_L 0.76 0.45 0.03
72_A 98_A 0.75 0.44 0.03
55_D 64_V 0.75 0.44 0.03
122_A 374_F 0.75 0.44 0.03
114_L 121_Y 0.75 0.44 0.03
43_A 106_L 0.75 0.44 0.03
124_D 255_A 0.75 0.44 0.03
111_L 409_P 0.75 0.44 0.03
80_V 256_L 0.75 0.43 0.03
100_F 22_R 0.74 0.43 0.03
88_W 268_G 0.74 0.43 0.03
48_V 379_W 0.74 0.43 0.03
112_A 346_V 0.74 0.42 0.03
94_E 261_V 0.74 0.42 0.03
30_M 74_D 0.74 0.42 0.03
47_N 180_L 0.73 0.42 0.03
112_A 410_L 0.73 0.42 0.03
71_V 390_P 0.73 0.41 0.03
120_I 66_V 0.73 0.41 0.03
74_F 185_A 0.73 0.41 0.03
34_G 196_S 0.73 0.41 0.03
120_I 43_W 0.72 0.40 0.02
40_R 41_L 0.72 0.40 0.02
47_N 22_R 0.72 0.40 0.02
28_C 204_V 0.72 0.40 0.02
50_F 360_R 0.72 0.40 0.02
26_L 355_R 0.72 0.40 0.02
66_A 57_L 0.72 0.39 0.02
122_A 270_M 0.71 0.39 0.02
89_S 197_L 0.71 0.39 0.02
98_V 398_A 0.71 0.39 0.02
120_I 240_D 0.71 0.39 0.02
104_A 89_G 0.71 0.39 0.02
25_G 60_A 0.71 0.39 0.02
31_L 392_I 0.71 0.39 0.02
112_A 145_M 0.71 0.38 0.02
67_K 255_A 0.71 0.38 0.02
126_T 204_V 0.70 0.38 0.02
20_L 338_G 0.70 0.38 0.02
69_Y 39_K 0.70 0.38 0.02
36_F 262_V 0.70 0.38 0.02
106_F 185_A 0.70 0.38 0.02
69_Y 301_F 0.70 0.37 0.02
113_G 121_Y 0.70 0.37 0.02
92_I 402_A 0.70 0.37 0.02
107_I 260_L 0.70 0.37 0.02
67_K 364_K 0.70 0.37 0.02
92_I 207_A 0.70 0.37 0.02
92_I 346_V 0.70 0.37 0.02
74_F 116_L 0.69 0.36 0.02
45_S 156_F 0.69 0.36 0.02
28_C 410_L 0.69 0.36 0.02
50_F 185_A 0.69 0.36 0.02
105_I 402_A 0.69 0.36 0.02
76_V 50_V 0.69 0.36 0.02
66_A 56_V 0.69 0.36 0.02
90_T 166_F 0.69 0.36 0.02
21_I 57_L 0.69 0.36 0.02
42_R 267_V 0.69 0.36 0.02
122_A 81_E 0.68 0.35 0.02
84_Y 336_M 0.68 0.35 0.02
57_V 116_L 0.68 0.35 0.02
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
2967 4.45 cI_A_20_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
2965 4.54 cI_A_6_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
2964 3.88 cI_A_10_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.43 Done - Shared
2963 3.87 cI_A_10_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.50 Done - Shared
2961 3.86 cI_A_10_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.46 Done - Shared
2265 4.36 cI_E_cIII_cytb Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.09 Done - Shared
2264 0.07 cI_E_cIII_cytb Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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