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OPENSEQ.org
cI_A_10_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 147 440 505
Sequences: 3460 3303 1953
Seq/Len: 23.54 7.51 3.87
MirrorTree (Pazo et al. 2001) 0.72
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 0.19
5 0.00 0.00 2.27
10 0.01 0.00 2.51
20 0.01 0.00 2.58
100 0.01 0.00 2.65
∞ 0.02 0.01 3.33
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 1.33 0.94 0.50
80_V 360_R 1.11 0.83 0.31
50_F 261_V 1.09 0.81 0.29
77_I 403_Y 1.09 0.81 0.29
83_L 145_M 1.07 0.79 0.27
77_I 397_S 1.07 0.79 0.27
25_G 19_L 1.07 0.79 0.27
113_G 121_Y 1.05 0.77 0.25
84_Y 343_M 1.02 0.74 0.23
103_A 257_A 0.98 0.70 0.20
105_I 25_I 0.98 0.69 0.20
106_F 281_I 0.94 0.65 0.18
40_R 41_L 0.91 0.62 0.16
34_G 145_M 0.91 0.62 0.16
43_A 106_L 0.90 0.61 0.15
120_I 66_V 0.90 0.60 0.15
71_V 390_P 0.89 0.60 0.15
106_F 76_A 0.89 0.59 0.15
100_F 349_L 0.88 0.58 0.14
26_L 355_R 0.87 0.56 0.14
69_Y 20_H 0.86 0.56 0.14
88_W 124_P 0.86 0.55 0.13
112_A 145_M 0.85 0.55 0.13
72_A 128_T 0.85 0.55 0.13
45_S 275_G 0.85 0.54 0.13
84_Y 336_M 0.85 0.54 0.13
72_A 76_A 0.84 0.53 0.12
50_F 415_E 0.84 0.52 0.12
66_A 57_L 0.83 0.51 0.12
69_Y 39_K 0.82 0.50 0.11
124_D 364_K 0.82 0.50 0.11
34_G 272_N 0.81 0.49 0.11
37_L 197_L 0.81 0.48 0.11
44_R 107_A 0.80 0.47 0.10
47_N 180_L 0.80 0.47 0.10
120_I 43_W 0.80 0.47 0.10
85_L 351_T 0.80 0.47 0.10
31_L 243_P 0.80 0.47 0.10
107_I 260_L 0.80 0.47 0.10
21_I 265_A 0.80 0.47 0.10
112_A 108_V 0.79 0.46 0.10
47_N 22_R 0.79 0.46 0.10
107_I 290_A 0.79 0.46 0.10
111_L 40_N 0.79 0.46 0.10
22_V 228_E 0.78 0.45 0.10
94_E 261_V 0.78 0.45 0.10
84_Y 263_F 0.78 0.45 0.10
93_R 60_A 0.78 0.45 0.10
30_M 74_D 0.78 0.45 0.10
16_F 385_A 0.78 0.44 0.10
88_W 269_F 0.78 0.44 0.09
76_V 99_N 0.78 0.44 0.09
107_I 258_V 0.78 0.44 0.09
49_P 76_A 0.77 0.44 0.09
105_I 138_M 0.77 0.44 0.09
40_R 390_P 0.77 0.44 0.09
29_L 362_L 0.77 0.43 0.09
84_Y 40_N 0.77 0.43 0.09
77_I 404_F 0.77 0.43 0.09
31_L 253_L 0.77 0.43 0.09
21_I 410_L 0.77 0.43 0.09
115_V 392_I 0.76 0.42 0.09
125_W 291_H 0.76 0.42 0.09
67_K 364_K 0.76 0.42 0.09
101_V 362_L 0.76 0.42 0.09
83_L 171_G 0.76 0.42 0.09
74_F 116_L 0.76 0.41 0.09
69_Y 95_Y 0.75 0.41 0.09
84_Y 44_W 0.75 0.41 0.08
96_G 180_L 0.75 0.40 0.08
84_Y 178_T 0.74 0.40 0.08
88_W 268_G 0.74 0.40 0.08
80_V 415_E 0.74 0.40 0.08
27_C 127_V 0.74 0.39 0.08
16_F 168_A 0.74 0.39 0.08
88_W 72_H 0.73 0.39 0.08
28_C 211_V 0.73 0.38 0.08
72_A 139_M 0.73 0.38 0.08
98_V 398_A 0.73 0.38 0.08
67_K 350_D 0.73 0.38 0.08
120_I 39_K 0.72 0.38 0.07
50_F 360_R 0.72 0.37 0.07
106_F 287_V 0.72 0.37 0.07
74_F 256_L 0.72 0.37 0.07
25_G 60_A 0.71 0.36 0.07
114_L 301_F 0.71 0.36 0.07
26_L 33_L 0.71 0.36 0.07
112_A 371_A 0.71 0.36 0.07
122_A 396_G 0.71 0.35 0.07
31_L 254_F 0.71 0.35 0.07
73_M 372_V 0.71 0.35 0.07
17_A 166_F 0.71 0.35 0.07
34_G 196_S 0.71 0.35 0.07
74_F 70_T 0.71 0.35 0.07
69_Y 171_G 0.71 0.35 0.07
17_A 346_V 0.71 0.35 0.07
29_L 61_T 0.71 0.35 0.07
105_I 402_A 0.70 0.35 0.07
104_A 89_G 0.70 0.34 0.07
74_F 156_F 0.70 0.34 0.07
92_I 402_A 0.70 0.34 0.07
40_R 387_G 0.70 0.34 0.07
74_F 71_P 0.70 0.34 0.07
19_F 41_L 0.70 0.34 0.07
84_Y 81_E 0.69 0.34 0.07
68_F 163_T 0.69 0.33 0.06
67_K 141_G 0.69 0.33 0.06
115_V 95_Y 0.69 0.33 0.06
116_Y 415_E 0.69 0.33 0.06
36_F 135_I 0.69 0.33 0.06
100_F 22_R 0.69 0.33 0.06
112_A 174_E 0.69 0.33 0.06
57_V 116_L 0.69 0.33 0.06
85_L 178_T 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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