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OPENSEQ.org
cI_A_10_cIII_cytb_6_Pdenitr
Genes: A B A+B
Length: 147 440 505
Sequences: 3460 3299 1958
Seq/Len: 23.54 7.5 3.88
MirrorTree (Pazo et al. 2001) 0.73
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 0.20
5 0.00 0.00 2.26
10 0.01 0.00 2.50
20 0.01 0.00 2.57
100 0.01 0.00 2.65
∞ 0.02 0.01 3.34
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
71_V 80_V 1.30 0.93 0.43
77_I 403_Y 1.10 0.82 0.26
113_G 121_Y 1.10 0.82 0.26
50_F 261_V 1.09 0.81 0.25
80_V 360_R 1.08 0.80 0.24
25_G 19_L 1.04 0.77 0.22
77_I 397_S 1.04 0.77 0.22
103_A 257_A 1.03 0.76 0.21
83_L 145_M 1.03 0.76 0.21
84_Y 343_M 1.00 0.73 0.19
34_G 145_M 0.95 0.66 0.16
40_R 41_L 0.93 0.65 0.15
106_F 76_A 0.92 0.63 0.15
100_F 349_L 0.91 0.62 0.14
105_I 25_I 0.91 0.61 0.14
66_A 57_L 0.90 0.61 0.14
50_F 415_E 0.90 0.61 0.14
106_F 281_I 0.90 0.61 0.14
112_A 145_M 0.88 0.57 0.12
120_I 66_V 0.86 0.56 0.12
45_S 275_G 0.86 0.55 0.12
94_E 261_V 0.86 0.55 0.12
71_V 390_P 0.86 0.55 0.12
101_V 362_L 0.86 0.55 0.12
88_W 126_E 0.86 0.55 0.12
69_Y 20_H 0.85 0.55 0.11
72_A 128_T 0.84 0.53 0.11
69_Y 39_K 0.84 0.52 0.10
47_N 180_L 0.83 0.52 0.10
34_G 272_N 0.83 0.51 0.10
31_L 243_P 0.82 0.51 0.10
72_A 76_A 0.82 0.50 0.10
112_A 108_V 0.82 0.50 0.10
43_A 106_L 0.82 0.50 0.10
30_M 74_D 0.81 0.49 0.10
84_Y 336_M 0.81 0.48 0.09
88_W 268_G 0.80 0.48 0.09
93_R 60_A 0.80 0.47 0.09
124_D 364_K 0.80 0.47 0.09
44_R 107_A 0.80 0.47 0.09
77_I 411_L 0.80 0.47 0.09
26_L 355_R 0.80 0.47 0.09
29_L 362_L 0.80 0.47 0.09
120_I 43_W 0.80 0.47 0.09
85_L 351_T 0.79 0.46 0.09
84_Y 44_W 0.79 0.46 0.09
84_Y 40_N 0.79 0.46 0.09
111_L 40_N 0.79 0.45 0.09
22_V 228_E 0.78 0.45 0.09
40_R 390_P 0.78 0.45 0.08
28_C 211_V 0.78 0.45 0.08
84_Y 263_F 0.78 0.44 0.08
107_I 260_L 0.77 0.44 0.08
72_A 139_M 0.77 0.44 0.08
88_W 269_F 0.77 0.44 0.08
49_P 76_A 0.77 0.43 0.08
96_G 180_L 0.77 0.43 0.08
25_G 60_A 0.77 0.43 0.08
47_N 22_R 0.77 0.43 0.08
76_V 99_N 0.77 0.43 0.08
125_W 291_H 0.76 0.42 0.08
85_L 178_T 0.75 0.41 0.07
107_I 258_V 0.75 0.41 0.07
21_I 265_A 0.75 0.41 0.07
100_F 22_R 0.75 0.40 0.07
21_I 410_L 0.74 0.40 0.07
67_K 364_K 0.74 0.40 0.07
106_F 287_V 0.74 0.40 0.07
69_Y 95_Y 0.74 0.40 0.07
21_I 22_R 0.74 0.40 0.07
112_A 371_A 0.74 0.39 0.07
107_I 290_A 0.74 0.39 0.07
16_F 385_A 0.74 0.39 0.07
74_F 116_L 0.74 0.39 0.07
88_W 72_H 0.74 0.39 0.07
115_V 392_I 0.73 0.39 0.07
112_A 346_V 0.73 0.39 0.07
120_I 39_K 0.73 0.38 0.07
92_I 402_A 0.73 0.38 0.07
77_I 404_F 0.73 0.38 0.07
80_V 415_E 0.73 0.38 0.07
26_L 33_L 0.73 0.38 0.07
83_L 171_G 0.72 0.37 0.07
24_I 273_Y 0.72 0.37 0.07
37_L 197_L 0.72 0.37 0.07
105_I 402_A 0.72 0.37 0.07
50_F 360_R 0.72 0.37 0.06
116_Y 415_E 0.72 0.37 0.06
105_I 138_M 0.72 0.36 0.06
27_C 127_V 0.72 0.36 0.06
16_F 168_A 0.72 0.36 0.06
69_Y 171_G 0.71 0.36 0.06
84_Y 178_T 0.71 0.36 0.06
72_A 98_A 0.71 0.36 0.06
115_V 95_Y 0.71 0.36 0.06
74_F 256_L 0.71 0.36 0.06
42_R 267_V 0.71 0.35 0.06
17_A 346_V 0.71 0.35 0.06
98_V 398_A 0.70 0.35 0.06
67_K 350_D 0.70 0.35 0.06
122_A 396_G 0.70 0.35 0.06
66_A 56_V 0.70 0.34 0.06
103_A 261_V 0.70 0.34 0.06
62_L 80_V 0.70 0.34 0.06
114_L 301_F 0.70 0.34 0.06
104_A 89_G 0.69 0.34 0.06
31_L 254_F 0.69 0.34 0.06
67_K 141_G 0.69 0.34 0.06
31_L 253_L 0.69 0.34 0.06
90_T 345_L 0.69 0.34 0.06
36_F 116_L 0.69 0.33 0.06
36_F 135_I 0.69 0.33 0.06
50_F 185_A 0.69 0.33 0.06
74_F 70_T 0.69 0.33 0.06
100_F 81_E 0.69 0.33 0.06
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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