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OPENSEQ.org
cIV_B_40_cIII_cytb_4_Pdenitr
Genes: A B A+B
Length: 252 440 622
Sequences: 4089 3282 2598
Seq/Len: 16.23 7.46 4.18
MirrorTree (Pazo et al. 2001) 0.90
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 0.27
5 0.00 0.00 0.89
10 0.00 0.00 3.13
20 0.01 0.00 3.24
100 0.01 0.00 3.32
∞ 0.03 0.01 3.75
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 1.03 0.77 0.03
112_L 180_L 0.95 0.68 0.02
15_N 415_E 0.93 0.67 0.02
23_A 364_K 0.92 0.66 0.02
176_A 259_V 0.91 0.64 0.02
79_V 376_V 0.91 0.64 0.02
49_V 195_F 0.89 0.61 0.02
184_T 185_A 0.88 0.60 0.02
43_T 345_L 0.86 0.57 0.02
104_Q 189_P 0.85 0.56 0.01
15_N 397_S 0.85 0.56 0.01
170_V 168_A 0.85 0.56 0.01
225_A 276_H 0.85 0.56 0.01
225_A 51_L 0.84 0.55 0.01
127_Y 409_P 0.83 0.53 0.01
29_H 192_N 0.81 0.51 0.01
79_V 180_L 0.81 0.50 0.01
163_V 348_W 0.80 0.49 0.01
46_T 156_F 0.80 0.49 0.01
68_P 200_L 0.80 0.49 0.01
15_N 293_V 0.80 0.49 0.01
117_I 406_I 0.79 0.47 0.01
92_I 43_W 0.78 0.47 0.01
22_P 168_A 0.78 0.47 0.01
112_L 362_L 0.78 0.46 0.01
206_V 254_F 0.78 0.46 0.01
204_F 61_T 0.77 0.46 0.01
87_L 351_T 0.77 0.46 0.01
174_V 119_G 0.77 0.46 0.01
120_Q 305_L 0.77 0.45 0.01
164_V 307_A 0.77 0.45 0.01
74_N 69_Y 0.77 0.45 0.01
185_I 270_M 0.76 0.44 0.01
231_V 75_L 0.76 0.44 0.01
30_D 240_D 0.76 0.44 0.01
17_G 43_W 0.75 0.43 0.01
157_A 343_M 0.75 0.42 0.01
54_L 56_V 0.74 0.42 0.01
48_F 259_V 0.74 0.42 0.01
116_A 373_D 0.73 0.41 0.01
87_L 138_M 0.73 0.40 0.01
195_V 211_V 0.73 0.40 0.01
13_P 84_M 0.73 0.40 0.01
41_I 392_I 0.72 0.39 0.01
57_I 344_A 0.72 0.39 0.01
212_Y 92_M 0.71 0.38 0.01
104_Q 69_Y 0.71 0.38 0.01
158_T 205_I 0.71 0.38 0.01
84_V 197_L 0.71 0.38 0.01
174_V 59_I 0.71 0.37 0.01
54_L 365_W 0.71 0.37 0.01
20_F 70_T 0.70 0.37 0.01
133_A 391_Y 0.70 0.36 0.01
28_A 103_L 0.70 0.36 0.01
176_A 23_L 0.70 0.36 0.01
143_A 267_V 0.70 0.36 0.01
31_Q 71_P 0.70 0.36 0.01
52_L 246_P 0.69 0.35 0.01
151_E 369_L 0.69 0.35 0.01
117_I 136_Y 0.69 0.35 0.01
79_V 156_F 0.69 0.35 0.01
210_G 201_L 0.69 0.35 0.01
24_S 269_F 0.69 0.34 0.01
15_N 360_R 0.68 0.34 0.01
74_N 80_V 0.68 0.34 0.01
113_V 352_S 0.68 0.34 0.01
42_I 303_A 0.68 0.34 0.01
48_F 285_P 0.68 0.33 0.01
13_P 43_W 0.68 0.33 0.01
72_T 360_R 0.68 0.33 0.01
180_I 371_A 0.68 0.33 0.01
88_I 338_G 0.68 0.33 0.01
166_V 355_R 0.67 0.33 0.01
162_V 95_Y 0.67 0.33 0.01
52_L 37_T 0.67 0.33 0.01
143_A 411_L 0.67 0.33 0.01
106_M 60_A 0.67 0.33 0.01
176_A 272_N 0.67 0.33 0.01
241_A 121_Y 0.67 0.33 0.01
114_I 205_I 0.67 0.33 0.01
204_F 108_V 0.67 0.33 0.01
184_T 50_V 0.67 0.32 0.01
18_M 372_V 0.66 0.32 0.01
19_N 192_N 0.66 0.32 0.01
97_L 280_Y 0.66 0.31 0.01
92_I 240_D 0.66 0.31 0.01
111_D 268_G 0.66 0.31 0.01
121_W 306_R 0.66 0.31 0.01
213_F 344_A 0.66 0.31 0.01
243_L 267_V 0.66 0.31 0.01
98_P 187_D 0.65 0.31 0.01
180_I 135_I 0.65 0.30 0.01
74_N 116_L 0.65 0.30 0.01
50_C 383_M 0.65 0.30 0.01
160_N 26_V 0.65 0.30 0.01
169_K 185_A 0.65 0.30 0.01
243_L 145_M 0.65 0.30 0.01
46_T 349_L 0.65 0.30 0.01
89_L 401_F 0.65 0.30 0.01
161_P 277_P 0.65 0.30 0.01
220_C 155_S 0.65 0.30 0.01
242_W 385_A 0.64 0.29 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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