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OPENSEQ.org
cI_I_20_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 163 440 579
Sequences: 1244 3285 426
Seq/Len: 7.63 7.47 0.74
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.00 0.00
2 0.01 0.00 0.01
5 0.01 0.00 0.01
10 0.01 0.00 0.01
20 0.02 0.00 0.01
100 0.03 0.00 0.07
∞ 0.06 0.01 0.71
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
23_L 355_R 1.33 0.55 0.00
20_G 49_I 1.28 0.50 0.00
13_L 369_L 1.27 0.49 0.00
33_P 60_A 1.25 0.47 0.00
21_F 384_P 1.22 0.45 0.00
10_K 122_K 1.20 0.43 0.00
30_S 136_Y 1.15 0.40 0.00
28_F 15_F 1.11 0.36 0.00
156_L 406_I 1.10 0.35 0.00
21_F 96_L 1.10 0.35 0.00
20_G 211_V 1.09 0.34 0.00
28_F 172_V 1.07 0.33 0.00
13_L 61_T 1.06 0.33 0.00
101_T 57_L 1.06 0.32 0.00
21_F 63_I 1.05 0.31 0.00
8_A 30_Y 1.05 0.31 0.00
30_S 369_L 1.04 0.31 0.00
139_Q 396_G 1.03 0.30 0.00
110_Q 276_H 1.02 0.30 0.00
83_A 142_T 1.02 0.29 0.00
41_K 166_F 1.02 0.29 0.00
9_T 134_L 1.02 0.29 0.00
160_A 44_W 1.01 0.29 0.00
19_K 345_L 1.01 0.29 0.00
33_P 242_L 1.01 0.28 0.00
84_E 33_L 0.97 0.26 0.00
48_F 211_V 0.97 0.26 0.00
108_F 136_Y 0.97 0.26 0.00
155_N 276_H 0.96 0.26 0.00
30_S 27_S 0.94 0.24 0.00
154_R 89_G 0.94 0.24 0.00
98_I 71_P 0.93 0.23 0.00
36_N 411_L 0.93 0.23 0.00
134_L 361_P 0.93 0.23 0.00
28_F 133_M 0.93 0.23 0.00
137_D 130_I 0.93 0.23 0.00
137_D 330_F 0.93 0.23 0.00
18_I 171_G 0.92 0.23 0.00
27_Y 167_G 0.92 0.23 0.00
8_A 64_V 0.91 0.22 0.00
39_H 290_A 0.91 0.22 0.00
134_L 133_M 0.91 0.22 0.00
112_A 57_L 0.91 0.22 0.00
158_L 7_D 0.90 0.22 0.00
140_K 15_F 0.90 0.22 0.00
124_F 405_L 0.90 0.21 0.00
116_D 150_P 0.90 0.21 0.00
124_F 122_K 0.88 0.20 0.00
30_S 166_F 0.88 0.20 0.00
11_Y 408_L 0.88 0.20 0.00
9_T 96_L 0.88 0.20 0.00
20_G 27_S 0.87 0.20 0.00
35_L 380_V 0.87 0.20 0.00
43_P 176_I 0.87 0.20 0.00
19_K 409_P 0.86 0.20 0.00
139_Q 171_G 0.86 0.20 0.00
157_Q 123_A 0.86 0.19 0.00
27_Y 200_L 0.85 0.19 0.00
161_P 108_V 0.85 0.19 0.00
35_L 136_Y 0.85 0.19 0.00
124_F 108_V 0.84 0.18 0.00
26_R 143_A 0.84 0.18 0.00
127_A 29_V 0.84 0.18 0.00
105_Y 197_L 0.84 0.18 0.00
62_E 271_P 0.84 0.18 0.00
21_F 33_L 0.83 0.18 0.00
108_F 363_F 0.83 0.18 0.00
43_P 392_I 0.83 0.18 0.00
122_P 415_E 0.83 0.18 0.00
11_Y 425_E 0.83 0.18 0.00
31_P 360_R 0.83 0.18 0.00
9_T 395_A 0.83 0.18 0.00
108_F 418_D 0.83 0.18 0.00
5_F 410_L 0.83 0.18 0.00
88_D 165_L 0.82 0.17 0.00
105_Y 23_L 0.82 0.17 0.00
140_K 340_I 0.82 0.17 0.00
65_I 344_A 0.82 0.17 0.00
48_F 19_L 0.82 0.17 0.00
139_Q 406_I 0.82 0.17 0.00
62_E 144_F 0.82 0.17 0.00
18_I 235_E 0.82 0.17 0.00
54_L 90_G 0.81 0.17 0.00
132_E 176_I 0.81 0.17 0.00
140_K 385_A 0.81 0.17 0.00
37_Y 298_F 0.81 0.17 0.00
5_F 345_L 0.81 0.17 0.00
30_S 269_F 0.81 0.17 0.00
44_L 413_I 0.81 0.17 0.00
14_M 379_W 0.81 0.17 0.00
158_L 89_G 0.81 0.17 0.00
115_V 100_G 0.80 0.17 0.00
37_Y 295_E 0.80 0.17 0.00
19_K 376_V 0.80 0.16 0.00
52_H 180_L 0.80 0.16 0.00
82_D 174_E 0.80 0.16 0.00
24_G 51_L 0.80 0.16 0.00
124_F 266_I 0.80 0.16 0.00
58_P 273_Y 0.79 0.16 0.00
147_R 392_I 0.79 0.16 0.00
17_F 49_I 0.79 0.16 0.00
105_Y 244_F 0.79 0.16 0.00
25_M 116_L 0.79 0.16 0.00
159_D 209_V 0.79 0.16 0.00
108_F 227_V 0.78 0.15 0.00
75_P 114_R 0.78 0.15 0.00
27_Y 131_V 0.78 0.15 0.00
105_Y 351_T 0.78 0.15 0.00
11_Y 379_W 0.78 0.15 0.00
88_D 161_V 0.78 0.15 0.00
33_P 93_L 0.78 0.15 0.00
130_T 204_V 0.78 0.15 0.00
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
3054 0.6 cI_I_40_cIII_cytb_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3053 0.74 cI_I_20_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3052 0.98 cI_I_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3051 0.6 cI_I_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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