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OPENSEQ.org
cytb_80_cIV_B_80_human
Genes: A B A+B
Length: 378 227 598
Sequences: 3718 2066 1151
Seq/Len: 9.84 9.1 1.92
MirrorTree (Pazo et al. 2001) 0.83
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.01 0.10
2 0.02 0.01 0.17
5 0.02 0.01 0.50
10 0.02 0.01 1.62
20 0.02 0.01 1.69
100 0.02 0.01 1.73
∞ 0.02 0.01 1.90
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
283_S 144_L 1.25 0.76 0.03
322_Q 12_A 1.20 0.71 0.03
179_F 38_V 1.12 0.64 0.02
37_L 205_S 1.12 0.64 0.02
57_P 138_V 1.12 0.64 0.02
102_L 68_L 1.10 0.62 0.02
101_G 138_V 1.07 0.58 0.02
46_T 33_L 1.04 0.56 0.02
274_F 105_Y 1.03 0.54 0.02
355_S 4_A 1.00 0.51 0.01
55_Y 107_T 1.00 0.51 0.01
304_I 167_T 1.00 0.51 0.01
262_L 184_F 0.99 0.51 0.01
33_F 33_L 0.99 0.50 0.01
239_L 13_T 0.99 0.50 0.01
173_P 88_D 0.97 0.48 0.01
140_F 23_F 0.97 0.47 0.01
74_N 140_N 0.96 0.47 0.01
347_F 137_D 0.96 0.47 0.01
252_D 205_S 0.96 0.46 0.01
37_L 86_M 0.95 0.46 0.01
233_L 167_T 0.95 0.46 0.01
331_D 96_T 0.95 0.45 0.01
39_A 97_I 0.94 0.45 0.01
189_I 163_W 0.94 0.44 0.01
42_I 92_D 0.93 0.44 0.01
46_T 165_V 0.93 0.43 0.01
297_S 22_T 0.92 0.42 0.01
105_G 214_I 0.92 0.42 0.01
267_H 163_W 0.91 0.41 0.01
173_P 11_D 0.91 0.41 0.01
165_W 85_Y 0.91 0.41 0.01
89_M 45_A 0.90 0.41 0.01
118_I 47_T 0.90 0.41 0.01
72_D 144_L 0.89 0.40 0.01
239_L 30_I 0.89 0.39 0.01
318_R 4_A 0.89 0.39 0.01
245_F 150_I 0.89 0.39 0.01
245_F 211_L 0.89 0.39 0.01
64_S 60_E 0.88 0.38 0.01
229_A 29_M 0.88 0.38 0.01
158_T 192_Y 0.88 0.38 0.01
208_P 65_W 0.88 0.38 0.01
192_L 64_V 0.87 0.37 0.01
347_F 12_A 0.87 0.37 0.01
232_L 123_L 0.87 0.37 0.01
232_L 2_A 0.87 0.37 0.01
223_Y 155_T 0.87 0.37 0.01
78_I 160_L 0.87 0.37 0.01
82_L 46_L 0.87 0.37 0.01
316_M 32_F 0.86 0.36 0.01
102_L 143_V 0.86 0.36 0.01
202_E 144_L 0.86 0.36 0.01
189_I 143_V 0.86 0.36 0.01
45_I 155_T 0.85 0.35 0.01
197_L 211_L 0.85 0.35 0.01
190_A 155_T 0.85 0.35 0.01
121_L 41_A 0.85 0.35 0.01
234_L 215_P 0.84 0.34 0.01
193_A 186_A 0.84 0.34 0.01
308_H 8_G 0.84 0.34 0.01
302_A 156_S 0.83 0.34 0.01
340_G 58_A 0.83 0.33 0.01
39_A 56_S 0.83 0.33 0.01
237_L 211_L 0.82 0.32 0.01
102_L 211_L 0.82 0.32 0.01
163_W 203_N 0.82 0.32 0.01
299_L 7_V 0.82 0.32 0.01
65_S 93_P 0.82 0.32 0.01
181_F 21_I 0.81 0.32 0.01
71_R 93_P 0.81 0.31 0.01
94_L 153_M 0.81 0.31 0.01
193_A 110_Y 0.81 0.31 0.01
162_Q 63_T 0.81 0.31 0.01
328_L 192_Y 0.81 0.31 0.01
30_W 12_A 0.81 0.31 0.01
230_L 160_L 0.81 0.31 0.01
328_L 7_V 0.81 0.31 0.01
263_N 81_L 0.81 0.31 0.01
346_P 119_N 0.80 0.30 0.01
234_L 74_V 0.80 0.30 0.01
55_Y 37_L 0.80 0.30 0.01
66_I 165_V 0.80 0.30 0.01
122_A 128_L 0.80 0.30 0.01
329_A 167_T 0.80 0.30 0.01
89_M 164_A 0.80 0.30 0.01
331_D 9_L 0.80 0.30 0.01
135_W 206_F 0.80 0.30 0.01
318_R 42_L 0.80 0.30 0.01
82_L 155_T 0.80 0.30 0.01
256_Y 86_M 0.79 0.30 0.01
129_M 31_I 0.79 0.30 0.01
357_L 192_Y 0.79 0.29 0.01
119_L 160_L 0.79 0.29 0.01
304_I 97_I 0.79 0.29 0.01
304_I 6_Q 0.79 0.29 0.01
47_T 54_N 0.79 0.29 0.01
144_T 178_R 0.79 0.29 0.01
313_Q 23_F 0.79 0.29 0.01
164_I 95_L 0.78 0.28 0.01
75_Y 67_I 0.78 0.28 0.01
355_S 30_I 0.78 0.28 0.01
170_V 127_F 0.78 0.28 0.01
173_P 67_I 0.78 0.28 0.01
302_A 12_A 0.77 0.28 0.01
52_A 170_L 0.77 0.28 0.01
134_P 176_P 0.77 0.28 0.01
238_S 165_V 0.77 0.28 0.01
347_F 93_P 0.77 0.28 0.01
156_I 47_T 0.77 0.27 0.01
334_I 172_T 0.77 0.27 0.01
209_L 211_L 0.77 0.27 0.01
310_S 96_T 0.77 0.27 0.01
82_L 68_L 0.77 0.27 0.01
274_F 162_S 0.77 0.27 0.01
181_F 165_V 0.77 0.27 0.01
360_T 130_P 0.76 0.27 0.01
21_L 205_S 0.76 0.27 0.01
296_L 68_L 0.76 0.27 0.01
198_L 165_V 0.76 0.26 0.01
98_I 68_L 0.76 0.26 0.01
230_L 185_T 0.76 0.26 0.01
129_M 3_H 0.75 0.26 0.01
211_I 43_F 0.75 0.26 0.01
248_D 156_S 0.75 0.26 0.01
118_I 179_L 0.75 0.26 0.01
362_I 46_L 0.75 0.26 0.01
102_L 116_L 0.75 0.26 0.01
70_T 41_A 0.75 0.25 0.01
150_L 42_L 0.75 0.25 0.01
292_L 210_V 0.74 0.25 0.01
140_F 182_T 0.74 0.25 0.01
47_T 99_S 0.74 0.25 0.01
66_I 55_I 0.74 0.25 0.01
185_L 155_T 0.74 0.25 0.01
123_T 54_N 0.74 0.25 0.01
239_L 163_W 0.74 0.25 0.01
92_I 16_I 0.74 0.25 0.01
322_Q 55_I 0.74 0.24 0.01
353_V 126_L 0.74 0.24 0.01
285_P 24_H 0.73 0.24 0.01
171_D 23_F 0.73 0.24 0.01
164_I 76_I 0.73 0.24 0.01
329_A 34_I 0.73 0.24 0.01
343_V 210_V 0.73 0.24 0.01
300_I 47_T 0.73 0.24 0.01
329_A 192_Y 0.72 0.24 0.01
169_S 39_L 0.72 0.24 0.01
340_G 55_I 0.72 0.24 0.01
252_D 57_D 0.72 0.24 0.01
18_L 8_G 0.72 0.24 0.01
279_T 31_I 0.72 0.24 0.01
329_A 211_L 0.72 0.23 0.01
206_N 211_L 0.72 0.23 0.01
292_L 39_L 0.72 0.23 0.01
364_I 36_F 0.72 0.23 0.01
332_L 68_L 0.72 0.23 0.01
251_G 38_V 0.72 0.23 0.01
188_I 32_F 0.72 0.23 0.01
170_V 170_L 0.71 0.23 0.01
266_P 132_D 0.71 0.23 0.01
109_Y 54_N 0.71 0.23 0.01
193_A 179_L 0.71 0.23 0.01
258_L 26_H 0.71 0.23 0.01
238_S 123_L 0.71 0.23 0.01
294_L 199_I 0.71 0.23 0.01
208_P 66_T 0.71 0.23 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
5399 2.44 cytb_40_cIV_B_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.04 Done - Shared
5398 2.44 cytb_40_cIV_B_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.12 Done - Shared
5397 2.45 cytb_20_cIV_B_40_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5396 1.92 cytb_80_cIV_B_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5395 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.06 Done - Shared
5392 2.44 cytb_40_cIV_B_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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