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OPENSEQ.org
cIV_B_20_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 252 440 619
Sequences: 4606 3303 2666
Seq/Len: 18.28 7.51 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 3.26
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 1.07 0.82 0.05
23_A 364_K 1.00 0.75 0.04
15_N 415_E 0.96 0.71 0.04
127_Y 409_P 0.93 0.67 0.03
176_A 259_V 0.90 0.63 0.03
104_Q 189_P 0.89 0.63 0.03
29_H 192_N 0.87 0.59 0.03
184_T 185_A 0.86 0.59 0.03
41_I 392_I 0.85 0.57 0.03
225_A 51_L 0.85 0.57 0.03
225_A 276_H 0.83 0.54 0.02
58_V 270_M 0.83 0.54 0.02
49_V 195_F 0.82 0.53 0.02
142_E 337_F 0.81 0.52 0.02
185_I 270_M 0.81 0.52 0.02
164_V 307_A 0.81 0.52 0.02
15_N 397_S 0.81 0.51 0.02
117_I 406_I 0.80 0.50 0.02
30_D 240_D 0.79 0.49 0.02
79_V 180_L 0.79 0.49 0.02
195_V 211_V 0.78 0.48 0.02
116_A 373_D 0.78 0.48 0.02
163_V 348_W 0.76 0.45 0.02
15_N 293_V 0.76 0.44 0.02
48_F 259_V 0.75 0.44 0.02
15_N 360_R 0.75 0.44 0.02
46_T 156_F 0.75 0.43 0.02
170_V 168_A 0.74 0.42 0.02
174_V 119_G 0.74 0.42 0.02
174_V 267_V 0.73 0.41 0.02
114_I 205_I 0.73 0.41 0.02
79_V 376_V 0.73 0.41 0.02
20_F 70_T 0.73 0.41 0.02
209_E 346_V 0.73 0.41 0.02
28_A 103_L 0.72 0.40 0.02
231_V 269_F 0.72 0.40 0.02
49_V 180_L 0.72 0.39 0.02
68_P 200_L 0.72 0.39 0.02
139_L 270_M 0.72 0.39 0.02
112_L 180_L 0.71 0.39 0.02
16_G 71_P 0.71 0.39 0.02
111_D 268_G 0.71 0.38 0.02
146_D 80_V 0.71 0.38 0.02
42_I 303_A 0.70 0.38 0.01
52_L 246_P 0.70 0.37 0.01
18_M 392_I 0.70 0.37 0.01
45_V 284_N 0.70 0.36 0.01
46_T 171_G 0.69 0.36 0.01
160_N 26_V 0.69 0.36 0.01
241_A 121_Y 0.69 0.36 0.01
92_I 43_W 0.69 0.36 0.01
206_V 254_F 0.69 0.35 0.01
79_V 156_F 0.69 0.35 0.01
184_T 103_L 0.68 0.35 0.01
205_S 242_L 0.68 0.35 0.01
46_T 349_L 0.68 0.34 0.01
57_I 344_A 0.68 0.34 0.01
84_V 197_L 0.68 0.34 0.01
74_N 116_L 0.68 0.34 0.01
43_T 31_D 0.68 0.34 0.01
233_A 258_V 0.68 0.34 0.01
104_Q 69_Y 0.68 0.34 0.01
106_M 355_R 0.67 0.34 0.01
162_V 95_Y 0.67 0.33 0.01
17_G 43_W 0.67 0.33 0.01
53_L 248_F 0.67 0.33 0.01
22_P 67_M 0.67 0.33 0.01
236_Q 61_T 0.67 0.33 0.01
164_V 180_L 0.66 0.32 0.01
210_G 201_L 0.66 0.32 0.01
117_I 136_Y 0.66 0.32 0.01
142_E 371_A 0.66 0.32 0.01
120_Q 305_L 0.66 0.32 0.01
74_N 69_Y 0.66 0.32 0.01
219_L 156_F 0.66 0.32 0.01
134_F 42_N 0.65 0.31 0.01
225_A 35_I 0.65 0.31 0.01
50_C 383_M 0.65 0.31 0.01
31_Q 71_P 0.65 0.31 0.01
127_Y 209_V 0.65 0.31 0.01
98_P 187_D 0.65 0.31 0.01
71_F 364_K 0.65 0.30 0.01
152_D 121_Y 0.65 0.30 0.01
157_A 343_M 0.65 0.30 0.01
113_V 352_S 0.65 0.30 0.01
142_E 176_I 0.65 0.30 0.01
182_A 250_I 0.65 0.30 0.01
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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