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OPENSEQ.org
cIV_B_10_cIII_cytb_4_Pdenitr
Genes: A B A+B
Length: 252 440 618
Sequences: 4618 3282 2666
Seq/Len: 18.33 7.46 4.31
MirrorTree (Pazo et al. 2001) 0.87
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 0.18
2 0.00 0.00 0.28
5 0.00 0.00 0.90
10 0.01 0.00 3.16
20 0.01 0.00 3.27
100 0.02 0.00 3.37
∞ 0.04 0.01 3.85
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_A 44_W 1.11 0.85 0.09
15_N 415_E 1.00 0.76 0.06
23_A 364_K 0.96 0.71 0.05
127_Y 409_P 0.94 0.68 0.05
184_T 185_A 0.89 0.62 0.04
176_A 259_V 0.89 0.62 0.04
29_H 192_N 0.88 0.61 0.04
104_Q 189_P 0.85 0.58 0.04
49_V 195_F 0.85 0.58 0.04
142_E 337_F 0.85 0.57 0.04
225_A 51_L 0.84 0.56 0.04
79_V 180_L 0.84 0.55 0.04
79_V 376_V 0.82 0.53 0.03
15_N 360_R 0.82 0.53 0.03
41_I 392_I 0.80 0.50 0.03
43_T 345_L 0.80 0.50 0.03
225_A 276_H 0.79 0.49 0.03
57_I 344_A 0.79 0.49 0.03
15_N 397_S 0.79 0.49 0.03
164_V 307_A 0.79 0.49 0.03
147_A 269_F 0.79 0.48 0.03
234_V 262_V 0.78 0.48 0.03
46_T 156_F 0.78 0.48 0.03
53_L 248_F 0.78 0.47 0.03
30_D 240_D 0.77 0.47 0.03
206_V 254_F 0.77 0.46 0.03
116_A 373_D 0.76 0.45 0.03
15_N 293_V 0.74 0.42 0.02
52_L 246_P 0.74 0.42 0.02
68_P 200_L 0.73 0.41 0.02
195_V 211_V 0.73 0.41 0.02
84_V 197_L 0.73 0.41 0.02
28_A 103_L 0.73 0.41 0.02
114_I 205_I 0.73 0.41 0.02
209_E 346_V 0.73 0.41 0.02
42_I 303_A 0.73 0.41 0.02
163_V 348_W 0.73 0.40 0.02
174_V 119_G 0.73 0.40 0.02
112_L 180_L 0.73 0.40 0.02
180_I 135_I 0.72 0.40 0.02
20_F 70_T 0.72 0.40 0.02
92_I 43_W 0.72 0.40 0.02
104_Q 69_Y 0.72 0.40 0.02
45_V 284_N 0.72 0.40 0.02
87_L 351_T 0.72 0.40 0.02
231_V 75_L 0.71 0.39 0.02
111_D 268_G 0.71 0.39 0.02
164_V 180_L 0.71 0.38 0.02
170_V 168_A 0.71 0.38 0.02
157_A 343_M 0.70 0.37 0.02
117_I 406_I 0.70 0.37 0.02
185_I 270_M 0.70 0.37 0.02
48_F 259_V 0.70 0.37 0.02
58_V 270_M 0.70 0.37 0.02
219_L 156_F 0.70 0.36 0.02
112_L 362_L 0.69 0.36 0.02
142_E 176_I 0.69 0.36 0.02
243_L 145_M 0.69 0.36 0.02
139_L 122_K 0.68 0.35 0.02
184_T 50_V 0.68 0.35 0.02
204_F 61_T 0.68 0.35 0.02
213_F 344_A 0.68 0.34 0.02
16_G 56_V 0.68 0.34 0.02
17_G 43_W 0.68 0.34 0.02
230_V 201_L 0.67 0.34 0.02
120_Q 305_L 0.67 0.33 0.02
133_A 391_Y 0.67 0.33 0.02
48_F 285_P 0.67 0.33 0.02
225_A 35_I 0.67 0.33 0.02
174_V 267_V 0.67 0.33 0.02
16_G 71_P 0.66 0.32 0.02
143_A 267_V 0.66 0.32 0.02
210_G 201_L 0.66 0.32 0.02
117_I 136_Y 0.66 0.32 0.02
24_S 269_F 0.66 0.32 0.02
139_L 270_M 0.66 0.32 0.02
160_N 26_V 0.66 0.32 0.02
22_P 67_M 0.66 0.31 0.02
87_L 138_M 0.65 0.31 0.02
185_I 265_A 0.65 0.31 0.02
166_V 351_T 0.65 0.31 0.02
176_A 256_L 0.65 0.31 0.02
185_I 261_V 0.65 0.31 0.02
46_T 171_G 0.65 0.30 0.02
74_N 69_Y 0.65 0.30 0.02
43_T 31_D 0.65 0.30 0.02
233_A 258_V 0.65 0.30 0.02
92_I 79_S 0.65 0.30 0.02
18_M 392_I 0.65 0.30 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
3470 4.31 cIV_B_10_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3125 4.31 cIV_B_20_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3124 4.18 cIV_B_40_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3123 4.32 cIV_B_20_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
3122 4.34 cIV_B_6_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
3121 4.33 cIV_B_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3120 4.18 cIV_B_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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