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OPENSEQ.org
cytb_4_cIV_C_4_human
Genes: A B A+B
Length: 378 261 639
Sequences: 3773 2413 2089
Seq/Len: 9.98 9.25 3.27
MirrorTree (Pazo et al. 2001) 0.88
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 0.26
2 0.02 0.01 0.41
5 0.02 0.01 0.87
10 0.02 0.01 2.83
20 0.02 0.01 2.86
100 0.02 0.01 2.93
∞ 0.02 0.01 3.27
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
119_L 136_V 1.14 0.81 0.07
269_K 96_G 1.10 0.77 0.06
160_L 19_T 1.01 0.68 0.04
308_H 127_L 0.99 0.66 0.04
142_G 253_Y 0.98 0.66 0.04
179_F 147_A 0.98 0.65 0.04
195_L 192_I 0.92 0.58 0.03
85_N 214_F 0.92 0.58 0.03
119_L 115_H 0.91 0.56 0.03
93_C 80_R 0.90 0.56 0.03
99_G 253_Y 0.90 0.55 0.03
158_T 65_S 0.90 0.55 0.03
333_L 216_T 0.89 0.54 0.03
307_L 65_S 0.89 0.53 0.03
75_Y 35_F 0.88 0.53 0.03
134_P 240_W 0.88 0.53 0.03
30_W 101_F 0.88 0.52 0.03
129_M 21_A 0.87 0.51 0.03
297_S 250_L 0.86 0.50 0.03
66_I 187_T 0.86 0.50 0.03
49_L 144_I 0.85 0.48 0.03
318_R 228_T 0.84 0.48 0.03
241_T 168_L 0.84 0.48 0.03
71_R 260_G 0.84 0.47 0.03
118_I 224_M 0.83 0.47 0.03
250_L 108_P 0.83 0.46 0.02
319_P 209_I 0.82 0.45 0.02
261_P 19_T 0.82 0.45 0.02
75_Y 48_L 0.81 0.44 0.02
46_T 171_L 0.81 0.44 0.02
30_W 127_L 0.80 0.43 0.02
51_L 198_F 0.80 0.43 0.02
122_A 178_A 0.80 0.43 0.02
364_I 26_L 0.80 0.43 0.02
301_L 101_F 0.80 0.42 0.02
230_L 187_T 0.80 0.42 0.02
295_L 206_L 0.80 0.42 0.02
18_L 136_V 0.79 0.42 0.02
170_V 9_H 0.79 0.41 0.02
242_L 49_T 0.79 0.41 0.02
96_L 184_S 0.79 0.41 0.02
323_S 23_S 0.79 0.41 0.02
59_A 210_I 0.79 0.41 0.02
333_L 95_A 0.79 0.41 0.02
191_A 3_H 0.78 0.41 0.02
319_P 146_W 0.78 0.40 0.02
179_F 138_L 0.78 0.40 0.02
142_G 122_T 0.78 0.40 0.02
218_I 160_I 0.78 0.40 0.02
276_F 250_L 0.78 0.40 0.02
118_I 45_L 0.78 0.40 0.02
238_S 8_Y 0.78 0.40 0.02
66_I 10_M 0.77 0.39 0.02
121_L 8_Y 0.77 0.38 0.02
254_D 80_R 0.77 0.38 0.02
333_L 220_I 0.77 0.38 0.02
267_H 203_F 0.76 0.38 0.02
81_Y 81_Y 0.76 0.38 0.02
193_A 65_S 0.76 0.38 0.02
46_T 79_L 0.76 0.37 0.02
239_L 224_M 0.76 0.37 0.02
164_I 88_T 0.76 0.37 0.02
283_S 22_L 0.75 0.37 0.02
298_I 142_V 0.75 0.37 0.02
79_I 255_S 0.75 0.36 0.02
156_I 51_T 0.75 0.36 0.02
238_S 171_L 0.75 0.36 0.02
329_A 144_I 0.74 0.36 0.02
245_F 123_P 0.74 0.36 0.02
216_D 225_F 0.74 0.35 0.02
109_Y 32_T 0.74 0.35 0.02
316_M 136_V 0.74 0.35 0.02
318_R 76_Q 0.74 0.35 0.02
243_T 50_N 0.74 0.35 0.02
92_I 104_S 0.73 0.34 0.02
118_I 65_S 0.73 0.34 0.02
162_Q 21_A 0.73 0.34 0.02
47_T 81_Y 0.73 0.34 0.02
360_T 22_L 0.72 0.34 0.02
117_I 78_G 0.72 0.33 0.02
26_N 80_R 0.72 0.33 0.02
286_N 35_F 0.72 0.33 0.02
66_I 62_T 0.72 0.33 0.02
56_S 127_L 0.72 0.33 0.02
123_T 193_Y 0.72 0.33 0.02
153_I 136_V 0.72 0.33 0.02
79_I 26_L 0.72 0.33 0.02
61_T 220_I 0.72 0.33 0.02
50_F 258_W 0.72 0.33 0.02
300_I 195_S 0.71 0.33 0.02
245_F 124_L 0.71 0.33 0.02
188_I 144_I 0.71 0.32 0.02
313_Q 160_I 0.71 0.32 0.02
52_A 227_F 0.71 0.32 0.02
158_T 47_L 0.71 0.32 0.02
164_I 224_M 0.71 0.32 0.02
329_A 154_N 0.70 0.31 0.01
197_L 21_A 0.70 0.31 0.01
111_E 144_I 0.70 0.31 0.01
320_L 48_L 0.70 0.31 0.01
243_T 31_L 0.70 0.31 0.01
224_Y 168_L 0.70 0.31 0.01
224_Y 96_G 0.70 0.30 0.01
234_L 47_L 0.70 0.30 0.01
159_D 88_T 0.70 0.30 0.01
27_I 3_H 0.69 0.30 0.01
251_G 26_L 0.69 0.30 0.01
134_P 245_V 0.69 0.30 0.01
89_M 2_T 0.69 0.30 0.01
173_P 35_F 0.69 0.30 0.01
27_I 139_A 0.69 0.30 0.01
346_P 85_L 0.69 0.30 0.01
102_L 217_I 0.69 0.30 0.01
362_I 96_G 0.69 0.30 0.01
46_T 254_V 0.69 0.30 0.01
127_A 23_S 0.69 0.30 0.01
239_L 151_L 0.69 0.30 0.01
331_D 32_T 0.69 0.29 0.01
222_P 261_S 0.69 0.29 0.01
169_S 5_S 0.69 0.29 0.01
368_T 161_Q 0.68 0.29 0.01
28_S 129_V 0.68 0.29 0.01
32_N 127_L 0.68 0.29 0.01
213_S 112_L 0.68 0.29 0.01
220_F 208_V 0.68 0.29 0.01
107_F 30_G 0.68 0.29 0.01
171_D 238_A 0.68 0.29 0.01
114_N 212_S 0.68 0.29 0.01
119_L 112_L 0.68 0.29 0.01
269_K 68_Q 0.68 0.29 0.01
60_S 13_P 0.68 0.29 0.01
212_T 13_P 0.68 0.29 0.01
58_D 12_K 0.68 0.29 0.01
199_F 151_L 0.68 0.29 0.01
221_H 170_G 0.68 0.28 0.01
111_E 128_E 0.68 0.28 0.01
101_G 18_L 0.68 0.28 0.01
336_T 170_G 0.68 0.28 0.01
279_T 102_Y 0.68 0.28 0.01
315_M 254_V 0.68 0.28 0.01
45_I 188_I 0.68 0.28 0.01
47_T 30_G 0.67 0.28 0.01
82_L 79_L 0.67 0.28 0.01
234_L 26_L 0.67 0.28 0.01
254_D 179_S 0.67 0.28 0.01
80_R 142_V 0.67 0.28 0.01
189_I 88_T 0.67 0.28 0.01
79_I 260_G 0.67 0.28 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
6081 4.53 cytb_80_cIV_C_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b) 0.14 Done - Shared
5385 3.07 cytb_80_1_cIV_C_80_1_human Δgene:(1, ∞) A:(1E-80, 1) B:(1E-80, 1) msa: HHblits (2015_06) 0.18 Done - Shared
5384 3.07 cytb_80_cIV_C_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.19 Done - Shared
5383 3.27 cytb_4_cIV_C_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.07 Done - Shared
5381 3.26 cytb_4_cIV_C_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.05 Done - Shared
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