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OPENSEQ.org
cytb_80_cIV_C_80_human
Genes: A B A+B
Length: 378 261 639
Sequences: 3718 2219 1963
Seq/Len: 9.84 8.5 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 2.67
20 0.02 0.01 2.70
100 0.02 0.01 2.76
∞ 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 0.87 0.19
119_L 136_V 1.20 0.83 0.16
142_G 253_Y 1.09 0.75 0.12
99_G 253_Y 1.02 0.68 0.10
75_Y 35_F 1.01 0.67 0.09
308_H 127_L 1.00 0.66 0.09
307_L 65_S 0.97 0.62 0.08
134_P 240_W 0.96 0.61 0.08
122_A 178_A 0.96 0.61 0.08
297_S 250_L 0.96 0.61 0.08
109_Y 32_T 0.96 0.61 0.08
179_F 147_A 0.96 0.61 0.08
93_C 80_R 0.95 0.59 0.07
30_W 101_F 0.93 0.57 0.07
195_L 192_I 0.93 0.57 0.07
75_Y 48_L 0.93 0.56 0.07
71_R 260_G 0.92 0.56 0.07
318_R 228_T 0.92 0.56 0.07
323_S 23_S 0.91 0.55 0.07
239_L 151_L 0.91 0.55 0.07
158_T 65_S 0.90 0.53 0.06
230_L 187_T 0.89 0.52 0.06
30_W 127_L 0.88 0.50 0.06
79_I 255_S 0.87 0.49 0.06
160_L 19_T 0.86 0.49 0.05
162_Q 21_A 0.86 0.48 0.05
360_T 22_L 0.85 0.47 0.05
118_I 224_M 0.84 0.46 0.05
102_L 217_I 0.84 0.46 0.05
129_M 21_A 0.84 0.46 0.05
79_I 26_L 0.84 0.46 0.05
85_N 214_F 0.84 0.46 0.05
286_N 174_T 0.84 0.46 0.05
96_L 184_S 0.84 0.45 0.05
114_N 212_S 0.83 0.45 0.05
261_P 19_T 0.83 0.45 0.05
245_F 124_L 0.83 0.45 0.05
107_F 30_G 0.82 0.43 0.05
46_T 254_V 0.82 0.43 0.04
333_L 216_T 0.82 0.43 0.04
52_A 227_F 0.81 0.43 0.04
49_L 144_I 0.81 0.42 0.04
51_L 198_F 0.81 0.42 0.04
362_I 96_G 0.81 0.42 0.04
46_T 171_L 0.80 0.41 0.04
333_L 95_A 0.80 0.41 0.04
316_M 136_V 0.80 0.40 0.04
98_I 45_L 0.80 0.40 0.04
59_A 210_I 0.80 0.40 0.04
127_A 23_S 0.79 0.40 0.04
250_L 108_P 0.79 0.40 0.04
301_L 101_F 0.78 0.39 0.04
153_I 136_V 0.78 0.38 0.04
242_L 49_T 0.78 0.38 0.04
239_L 224_M 0.77 0.38 0.04
320_L 48_L 0.77 0.38 0.04
6_K 28_T 0.77 0.37 0.04
256_Y 32_T 0.77 0.37 0.04
238_S 8_Y 0.77 0.37 0.04
254_D 179_S 0.77 0.37 0.04
197_L 21_A 0.77 0.37 0.04
18_L 136_V 0.77 0.37 0.04
298_I 142_V 0.76 0.37 0.04
237_L 216_T 0.76 0.36 0.04
319_P 146_W 0.76 0.36 0.04
318_R 76_Q 0.76 0.36 0.04
173_P 35_F 0.76 0.36 0.04
260_N 131_L 0.75 0.35 0.04
286_N 35_F 0.75 0.35 0.04
199_F 172_Y 0.75 0.35 0.04
50_F 258_W 0.75 0.35 0.04
350_I 12_K 0.75 0.35 0.04
164_I 165_I 0.75 0.35 0.04
301_L 80_R 0.75 0.35 0.04
230_L 189_S 0.75 0.35 0.04
108_L 21_A 0.75 0.35 0.03
159_D 88_T 0.75 0.35 0.03
277_A 253_Y 0.75 0.35 0.03
368_T 161_Q 0.75 0.35 0.03
304_I 80_R 0.74 0.34 0.03
28_S 129_V 0.74 0.34 0.03
81_Y 81_Y 0.74 0.34 0.03
222_P 261_S 0.74 0.34 0.03
234_L 47_L 0.73 0.33 0.03
117_I 78_G 0.73 0.33 0.03
243_T 31_L 0.73 0.33 0.03
243_T 50_N 0.73 0.33 0.03
276_F 250_L 0.73 0.33 0.03
315_M 254_V 0.73 0.33 0.03
256_Y 199_V 0.73 0.33 0.03
340_G 198_F 0.73 0.33 0.03
245_F 123_P 0.73 0.33 0.03
269_K 76_Q 0.73 0.32 0.03
254_D 80_R 0.73 0.32 0.03
111_E 144_I 0.73 0.32 0.03
118_I 65_S 0.73 0.32 0.03
218_I 160_I 0.72 0.32 0.03
212_T 13_P 0.72 0.32 0.03
191_A 3_H 0.72 0.32 0.03
66_I 10_M 0.72 0.32 0.03
164_I 217_I 0.72 0.32 0.03
331_D 32_T 0.72 0.32 0.03
158_T 47_L 0.72 0.32 0.03
115_I 206_L 0.72 0.32 0.03
193_A 65_S 0.72 0.32 0.03
218_I 65_S 0.72 0.31 0.03
216_D 225_F 0.72 0.31 0.03
313_Q 160_I 0.71 0.31 0.03
119_L 152_M 0.71 0.31 0.03
269_K 68_Q 0.71 0.31 0.03
263_N 61_V 0.71 0.31 0.03
176_T 92_F 0.71 0.31 0.03
26_N 80_R 0.71 0.31 0.03
283_S 22_L 0.71 0.31 0.03
303_M 182_F 0.71 0.30 0.03
79_I 28_T 0.71 0.30 0.03
329_A 154_N 0.71 0.30 0.03
107_F 162_A 0.71 0.30 0.03
119_L 115_H 0.71 0.30 0.03
368_T 65_S 0.71 0.30 0.03
118_I 45_L 0.70 0.30 0.03
334_I 191_G 0.70 0.30 0.03
303_M 198_F 0.70 0.30 0.03
156_I 51_T 0.70 0.29 0.03
56_S 127_L 0.70 0.29 0.03
164_I 88_T 0.70 0.29 0.03
241_T 168_L 0.70 0.29 0.03
279_T 102_Y 0.70 0.29 0.03
89_M 2_T 0.70 0.29 0.03
220_F 208_V 0.70 0.29 0.03
254_D 38_H 0.69 0.29 0.03
23_T 22_L 0.69 0.29 0.03
74_N 150_S 0.69 0.29 0.03
224_Y 168_L 0.69 0.29 0.03
312_Q 96_G 0.69 0.29 0.03
181_F 120_G 0.69 0.29 0.03
111_E 128_E 0.69 0.29 0.03
44_Q 194_G 0.69 0.28 0.03
37_L 250_L 0.69 0.28 0.03
314_S 195_S 0.69 0.28 0.03
223_Y 78_G 0.69 0.28 0.03
340_G 250_L 0.69 0.28 0.03
274_F 151_L 0.69 0.28 0.03
66_I 120_G 0.69 0.28 0.03
318_R 254_V 0.69 0.28 0.03
79_I 165_I 0.68 0.28 0.03
213_S 112_L 0.68 0.28 0.03
100_R 240_W 0.68 0.28 0.03
238_S 25_L 0.68 0.28 0.03
184_I 253_Y 0.68 0.28 0.03
224_Y 254_V 0.68 0.28 0.03
350_I 213_T 0.68 0.28 0.03
92_I 104_S 0.68 0.28 0.03
66_I 187_T 0.68 0.28 0.03
241_T 25_L 0.68 0.28 0.03
305_P 232_H 0.68 0.28 0.03
162_Q 193_Y 0.68 0.28 0.03
179_F 138_L 0.68 0.27 0.03
77_W 80_R 0.68 0.27 0.03
121_L 8_Y 0.68 0.27 0.03
276_F 68_Q 0.68 0.27 0.03
189_I 115_H 0.68 0.27 0.03
316_M 168_L 0.68 0.27 0.03
150_L 80_R 0.68 0.27 0.03
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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