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OPENSEQ.org
cytb_80_1_cIV_C_80_1_human
Genes: A B A+B
Length: 378 261 639
Sequences: 3706 2215 1961
Seq/Len: 9.8 8.49 3.07
MirrorTree (Pazo et al. 2001) 0.86
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 0.17
2 0.02 0.01 0.29
5 0.02 0.01 0.73
10 0.02 0.01 2.66
20 0.02 0.01 2.70
100 0.02 0.01 2.77
∞ 0.02 0.01 3.07
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
269_K 96_G 1.25 0.86 0.18
119_L 136_V 1.24 0.86 0.18
142_G 253_Y 1.06 0.72 0.10
308_H 127_L 1.03 0.68 0.09
99_G 253_Y 1.01 0.66 0.09
109_Y 32_T 0.99 0.64 0.08
75_Y 35_F 0.99 0.64 0.08
195_L 192_I 0.99 0.64 0.08
134_P 240_W 0.96 0.61 0.07
71_R 260_G 0.96 0.61 0.07
179_F 147_A 0.94 0.58 0.07
122_A 178_A 0.94 0.58 0.07
93_C 80_R 0.94 0.58 0.07
318_R 228_T 0.93 0.57 0.07
158_T 65_S 0.92 0.56 0.07
30_W 101_F 0.92 0.56 0.07
75_Y 48_L 0.92 0.56 0.07
79_I 255_S 0.92 0.56 0.07
102_L 217_I 0.92 0.55 0.06
230_L 187_T 0.91 0.55 0.06
360_T 22_L 0.91 0.54 0.06
323_S 23_S 0.90 0.54 0.06
307_L 65_S 0.90 0.54 0.06
46_T 254_V 0.90 0.53 0.06
66_I 187_T 0.90 0.53 0.06
297_S 250_L 0.89 0.52 0.06
46_T 171_L 0.89 0.51 0.06
114_N 212_S 0.88 0.51 0.06
30_W 127_L 0.88 0.51 0.06
79_I 26_L 0.88 0.51 0.06
239_L 151_L 0.87 0.50 0.05
118_I 224_M 0.86 0.49 0.05
256_Y 32_T 0.86 0.49 0.05
96_L 184_S 0.85 0.47 0.05
85_N 214_F 0.85 0.47 0.05
242_L 49_T 0.85 0.47 0.05
129_M 21_A 0.85 0.47 0.05
51_L 198_F 0.84 0.46 0.05
333_L 216_T 0.84 0.45 0.05
160_L 19_T 0.83 0.45 0.05
320_L 48_L 0.83 0.45 0.05
286_N 174_T 0.83 0.44 0.05
245_F 124_L 0.81 0.42 0.04
52_A 227_F 0.81 0.42 0.04
260_N 131_L 0.81 0.42 0.04
298_I 142_V 0.81 0.42 0.04
162_Q 21_A 0.81 0.41 0.04
362_I 96_G 0.80 0.41 0.04
107_F 30_G 0.80 0.41 0.04
301_L 80_R 0.80 0.41 0.04
49_L 144_I 0.79 0.40 0.04
59_A 210_I 0.79 0.40 0.04
318_R 76_Q 0.79 0.40 0.04
286_N 35_F 0.79 0.39 0.04
254_D 179_S 0.79 0.39 0.04
316_M 136_V 0.78 0.38 0.04
315_M 254_V 0.78 0.38 0.04
191_A 3_H 0.78 0.38 0.04
304_I 80_R 0.77 0.38 0.04
277_A 253_Y 0.77 0.38 0.04
193_A 65_S 0.77 0.37 0.04
261_P 19_T 0.77 0.37 0.04
303_M 198_F 0.77 0.37 0.04
164_I 217_I 0.77 0.37 0.04
234_L 47_L 0.76 0.36 0.04
115_I 206_L 0.76 0.36 0.04
218_I 65_S 0.76 0.36 0.04
301_L 101_F 0.76 0.36 0.04
119_L 115_H 0.76 0.36 0.04
199_F 172_Y 0.76 0.36 0.04
66_I 10_M 0.76 0.36 0.04
6_K 28_T 0.76 0.36 0.03
108_L 21_A 0.75 0.35 0.03
26_N 80_R 0.75 0.35 0.03
164_I 165_I 0.75 0.35 0.03
312_Q 96_G 0.75 0.35 0.03
340_G 198_F 0.75 0.35 0.03
92_I 104_S 0.74 0.34 0.03
222_P 261_S 0.74 0.34 0.03
319_P 146_W 0.74 0.34 0.03
121_L 8_Y 0.74 0.34 0.03
306_I 182_F 0.74 0.34 0.03
243_T 31_L 0.74 0.34 0.03
156_I 91_V 0.74 0.34 0.03
239_L 224_M 0.73 0.33 0.03
159_D 88_T 0.73 0.33 0.03
263_N 61_V 0.73 0.33 0.03
50_F 258_W 0.73 0.33 0.03
276_F 250_L 0.73 0.33 0.03
340_G 250_L 0.73 0.33 0.03
329_A 154_N 0.73 0.33 0.03
333_L 95_A 0.73 0.32 0.03
254_D 80_R 0.72 0.32 0.03
297_S 37_F 0.72 0.32 0.03
188_I 144_I 0.72 0.32 0.03
224_Y 168_L 0.72 0.32 0.03
81_Y 81_Y 0.72 0.32 0.03
79_I 28_T 0.72 0.32 0.03
224_Y 254_V 0.72 0.32 0.03
197_L 21_A 0.72 0.32 0.03
153_I 136_V 0.72 0.32 0.03
89_M 2_T 0.72 0.32 0.03
245_F 123_P 0.72 0.32 0.03
368_T 65_S 0.72 0.32 0.03
250_L 108_P 0.72 0.31 0.03
347_F 91_V 0.72 0.31 0.03
37_L 250_L 0.72 0.31 0.03
238_S 8_Y 0.72 0.31 0.03
216_D 225_F 0.72 0.31 0.03
269_K 76_Q 0.72 0.31 0.03
127_A 23_S 0.71 0.31 0.03
269_K 68_Q 0.71 0.30 0.03
189_I 88_T 0.71 0.30 0.03
368_T 161_Q 0.71 0.30 0.03
150_L 80_R 0.71 0.30 0.03
176_T 92_F 0.71 0.30 0.03
279_T 102_Y 0.71 0.30 0.03
117_I 78_G 0.70 0.30 0.03
303_M 182_F 0.70 0.30 0.03
28_S 129_V 0.70 0.30 0.03
237_L 216_T 0.70 0.30 0.03
18_L 136_V 0.70 0.29 0.03
313_Q 160_I 0.70 0.29 0.03
111_E 128_E 0.70 0.29 0.03
318_R 254_V 0.70 0.29 0.03
243_T 50_N 0.70 0.29 0.03
305_P 232_H 0.70 0.29 0.03
111_E 144_I 0.70 0.29 0.03
220_F 208_V 0.69 0.29 0.03
82_L 122_T 0.69 0.29 0.03
319_P 72_T 0.69 0.29 0.03
246_S 209_I 0.69 0.28 0.03
79_I 260_G 0.69 0.28 0.03
173_P 35_F 0.69 0.28 0.03
56_S 127_L 0.69 0.28 0.03
331_D 32_T 0.69 0.28 0.03
274_F 151_L 0.69 0.28 0.03
162_Q 193_Y 0.69 0.28 0.03
98_I 45_L 0.69 0.28 0.03
319_P 209_I 0.69 0.28 0.03
77_W 80_R 0.68 0.28 0.03
118_I 45_L 0.68 0.28 0.03
212_T 13_P 0.68 0.28 0.03
314_S 195_S 0.68 0.28 0.03
156_I 51_T 0.68 0.28 0.03
241_T 25_L 0.68 0.28 0.03
256_Y 199_V 0.68 0.27 0.03
58_D 254_V 0.68 0.27 0.03
316_M 168_L 0.68 0.27 0.03
299_L 24_A 0.68 0.27 0.03
119_L 152_M 0.68 0.27 0.03
213_S 112_L 0.68 0.27 0.02
27_I 3_H 0.68 0.27 0.02
44_Q 194_G 0.68 0.27 0.02
231_G 100_A 0.67 0.27 0.02
276_F 68_Q 0.67 0.27 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
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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