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OPENSEQ.org
cI_A_10_cIII_cytb_20_Pdenitr
Genes: A B A+B
Length: 147 440 504
Sequences: 3460 3290 1946
Seq/Len: 23.54 7.48 3.86
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 2.23
10 0.01 0.00 2.50
20 0.01 0.00 2.55
100 0.01 0.00 2.63
∞ 0.02 0.01 3.32
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 1.32 0.93 0.46
80_V 360_R 1.10 0.82 0.28
50_F 261_V 1.09 0.81 0.27
77_I 403_Y 1.05 0.77 0.24
84_Y 343_M 1.04 0.76 0.23
83_L 145_M 1.02 0.75 0.22
77_I 397_S 1.00 0.72 0.20
113_G 121_Y 0.99 0.71 0.20
103_A 257_A 0.95 0.67 0.17
43_A 106_L 0.95 0.66 0.17
106_F 281_I 0.94 0.66 0.17
25_G 19_L 0.92 0.63 0.15
34_G 145_M 0.91 0.61 0.15
85_L 351_T 0.90 0.60 0.14
69_Y 20_H 0.89 0.59 0.14
93_R 60_A 0.88 0.58 0.13
40_R 41_L 0.88 0.58 0.13
66_A 57_L 0.87 0.56 0.13
94_E 261_V 0.86 0.56 0.12
105_I 25_I 0.86 0.55 0.12
106_F 76_A 0.86 0.55 0.12
34_G 272_N 0.85 0.54 0.12
112_A 145_M 0.85 0.54 0.12
71_V 390_P 0.83 0.52 0.11
72_A 76_A 0.83 0.51 0.11
100_F 349_L 0.83 0.51 0.11
107_I 260_L 0.83 0.51 0.11
112_A 371_A 0.83 0.51 0.11
30_M 74_D 0.82 0.50 0.11
112_A 108_V 0.82 0.50 0.10
31_L 243_P 0.82 0.49 0.10
74_F 116_L 0.81 0.49 0.10
120_I 66_V 0.81 0.49 0.10
72_A 128_T 0.81 0.49 0.10
45_S 275_G 0.81 0.49 0.10
47_N 180_L 0.81 0.48 0.10
104_A 89_G 0.80 0.48 0.10
44_R 107_A 0.80 0.47 0.10
69_Y 39_K 0.80 0.47 0.10
120_I 43_W 0.80 0.47 0.10
84_Y 336_M 0.80 0.47 0.10
21_I 265_A 0.79 0.46 0.09
28_C 211_V 0.79 0.46 0.09
96_G 180_L 0.78 0.45 0.09
92_I 402_A 0.78 0.44 0.09
111_L 40_N 0.78 0.44 0.09
47_N 22_R 0.78 0.44 0.09
98_V 398_A 0.78 0.44 0.09
69_Y 95_Y 0.78 0.44 0.09
83_L 171_G 0.77 0.43 0.09
124_D 364_K 0.77 0.42 0.08
67_K 141_G 0.76 0.42 0.08
76_V 99_N 0.76 0.42 0.08
22_V 228_E 0.76 0.42 0.08
84_Y 44_W 0.76 0.42 0.08
125_W 291_H 0.76 0.41 0.08
84_Y 263_F 0.75 0.41 0.08
105_I 138_M 0.75 0.41 0.08
26_L 33_L 0.75 0.41 0.08
101_V 362_L 0.75 0.41 0.08
67_K 350_D 0.75 0.41 0.08
92_I 71_P 0.75 0.40 0.08
49_P 76_A 0.74 0.40 0.08
21_I 22_R 0.74 0.40 0.08
121_G 374_F 0.74 0.39 0.07
88_W 269_F 0.74 0.39 0.07
62_L 80_V 0.74 0.39 0.07
26_L 355_R 0.73 0.39 0.07
107_I 258_V 0.73 0.38 0.07
107_I 290_A 0.73 0.38 0.07
77_I 404_F 0.73 0.38 0.07
72_A 139_M 0.73 0.38 0.07
88_W 72_H 0.73 0.38 0.07
24_I 273_Y 0.73 0.38 0.07
120_I 39_K 0.73 0.38 0.07
37_L 197_L 0.72 0.37 0.07
105_I 402_A 0.72 0.37 0.07
16_F 385_A 0.72 0.37 0.07
115_V 392_I 0.72 0.37 0.07
77_I 411_L 0.72 0.37 0.07
84_Y 81_E 0.72 0.37 0.07
115_V 269_F 0.72 0.36 0.07
84_Y 178_T 0.72 0.36 0.07
88_W 268_G 0.72 0.36 0.07
127_P 353_R 0.72 0.36 0.07
84_Y 40_N 0.71 0.36 0.07
80_V 256_L 0.71 0.36 0.07
85_L 178_T 0.71 0.36 0.07
74_F 70_T 0.71 0.36 0.07
122_A 374_F 0.71 0.36 0.07
66_A 56_V 0.71 0.36 0.07
32_V 405_L 0.71 0.35 0.07
69_Y 171_G 0.71 0.35 0.07
27_C 127_V 0.70 0.35 0.06
67_K 364_K 0.70 0.35 0.06
34_G 196_S 0.70 0.35 0.06
50_F 185_A 0.70 0.35 0.06
16_F 168_A 0.70 0.34 0.06
17_A 166_F 0.70 0.34 0.06
42_R 267_V 0.70 0.34 0.06
92_I 346_V 0.70 0.34 0.06
118_V 143_A 0.70 0.34 0.06
74_F 95_Y 0.70 0.34 0.06
108_F 93_L 0.70 0.34 0.06
31_L 253_L 0.69 0.34 0.06
50_F 415_E 0.69 0.34 0.06
103_A 261_V 0.69 0.34 0.06
114_L 301_F 0.69 0.33 0.06
40_R 390_P 0.69 0.33 0.06
25_G 410_L 0.69 0.33 0.06
72_A 37_T 0.69 0.33 0.06
29_L 362_L 0.68 0.32 0.06
120_I 240_D 0.68 0.32 0.06
66_A 29_V 0.68 0.32 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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