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OPENSEQ.org
cytb_80_cIV_C_80_human
Genes: A B A+B
Length: 378 261 636
Sequences: 3785 3199 2878
Seq/Len: 10.01 12.26 4.53
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 0.39
5 0.00 0.00 0.98
10 0.00 0.00 3.87
20 0.00 0.00 3.93
100 0.00 0.00 4.03
∞ 0.00 0.00 4.50
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
297_S 250_L 1.15 0.88 0.14
75_Y 35_F 1.02 0.79 0.09
195_L 192_I 0.98 0.74 0.08
276_F 250_L 0.98 0.74 0.08
142_G 253_Y 0.97 0.74 0.08
262_L 95_A 0.91 0.66 0.06
158_T 25_L 0.89 0.64 0.06
188_I 187_T 0.88 0.62 0.06
251_G 183_E 0.86 0.60 0.05
319_P 209_I 0.85 0.59 0.05
318_R 228_T 0.84 0.57 0.05
111_E 128_E 0.83 0.56 0.05
274_F 151_L 0.83 0.56 0.05
118_I 65_S 0.83 0.56 0.05
294_L 250_L 0.82 0.55 0.05
20_D 260_G 0.81 0.54 0.04
39_A 174_T 0.81 0.53 0.04
184_I 254_V 0.81 0.53 0.04
263_N 78_G 0.80 0.52 0.04
47_T 135_S 0.79 0.51 0.04
104_Y 61_V 0.78 0.50 0.04
30_W 223_L 0.77 0.48 0.04
45_I 238_A 0.77 0.48 0.04
254_D 179_S 0.77 0.48 0.04
30_W 101_F 0.77 0.47 0.04
269_K 96_G 0.77 0.47 0.04
308_H 127_L 0.77 0.47 0.04
49_L 144_I 0.76 0.47 0.04
298_I 142_V 0.76 0.47 0.04
362_I 96_G 0.76 0.46 0.04
303_M 26_L 0.76 0.46 0.04
47_T 195_S 0.76 0.46 0.04
301_L 101_F 0.75 0.45 0.04
318_R 254_V 0.75 0.45 0.04
260_N 131_L 0.75 0.45 0.04
343_V 134_T 0.75 0.45 0.04
322_Q 154_N 0.75 0.45 0.04
353_V 44_M 0.75 0.44 0.04
107_F 225_F 0.75 0.44 0.04
134_P 240_W 0.74 0.43 0.03
129_M 37_F 0.73 0.42 0.03
107_F 37_F 0.73 0.42 0.03
156_I 7_A 0.72 0.41 0.03
55_Y 254_V 0.72 0.41 0.03
17_S 199_V 0.72 0.41 0.03
79_I 255_S 0.72 0.41 0.03
277_A 253_Y 0.72 0.40 0.03
120_L 256_I 0.71 0.40 0.03
135_W 240_W 0.71 0.39 0.03
363_L 157_N 0.71 0.39 0.03
32_N 127_L 0.70 0.38 0.03
328_L 154_N 0.70 0.38 0.03
111_E 38_H 0.70 0.38 0.03
191_A 23_S 0.70 0.38 0.03
77_W 80_R 0.70 0.38 0.03
47_T 235_F 0.70 0.38 0.03
188_I 144_I 0.70 0.38 0.03
267_H 240_W 0.69 0.38 0.03
319_P 146_W 0.69 0.38 0.03
26_N 80_R 0.69 0.37 0.03
102_L 40_M 0.69 0.37 0.03
305_P 237_A 0.69 0.37 0.03
333_L 216_T 0.69 0.36 0.03
57_P 23_S 0.69 0.36 0.03
44_Q 194_G 0.69 0.36 0.03
71_R 260_G 0.68 0.36 0.03
30_W 127_L 0.68 0.36 0.03
47_T 106_L 0.68 0.35 0.03
234_L 47_L 0.68 0.35 0.03
50_F 149_H 0.68 0.35 0.03
162_Q 193_Y 0.67 0.35 0.03
66_I 40_M 0.67 0.34 0.03
115_I 229_S 0.67 0.34 0.03
9_P 218_C 0.67 0.34 0.03
181_F 129_V 0.66 0.33 0.03
302_A 162_A 0.66 0.33 0.02
37_L 250_L 0.66 0.33 0.02
371_L 47_L 0.66 0.33 0.02
376_M 170_G 0.66 0.33 0.02
300_I 195_S 0.66 0.33 0.02
84_A 184_S 0.66 0.33 0.02
262_L 112_L 0.66 0.33 0.02
118_I 226_H 0.65 0.32 0.02
153_I 62_T 0.65 0.32 0.02
183_F 112_L 0.65 0.32 0.02
322_Q 4_Q 0.65 0.32 0.02
119_L 152_M 0.65 0.32 0.02
316_M 136_V 0.65 0.32 0.02
61_T 184_S 0.65 0.32 0.02
102_L 143_S 0.65 0.32 0.02
90_F 248_V 0.65 0.32 0.02
164_I 217_I 0.64 0.31 0.02
292_L 81_Y 0.64 0.31 0.02
85_N 214_F 0.64 0.31 0.02
293_A 162_A 0.64 0.31 0.02
365_L 230_K 0.64 0.31 0.02
194_T 51_T 0.64 0.31 0.02
14_I 48_L 0.64 0.31 0.02
226_I 8_Y 0.64 0.31 0.02
297_S 198_F 0.64 0.30 0.02
75_Y 48_L 0.64 0.30 0.02
23_T 8_Y 0.64 0.30 0.02
240_M 27_M 0.64 0.30 0.02
269_K 78_G 0.64 0.30 0.02
213_S 80_R 0.64 0.30 0.02
158_T 49_T 0.64 0.30 0.02
100_R 240_W 0.64 0.30 0.02
121_L 8_Y 0.63 0.30 0.02
374_N 199_V 0.63 0.30 0.02
46_T 220_I 0.63 0.30 0.02
243_T 39_S 0.63 0.30 0.02
120_L 32_T 0.63 0.30 0.02
158_T 8_Y 0.63 0.29 0.02
96_L 253_Y 0.63 0.29 0.02
103_Y 113_G 0.63 0.29 0.02
216_D 109_T 0.63 0.29 0.02
79_I 160_I 0.63 0.29 0.02
127_A 23_S 0.63 0.29 0.02
267_H 87_I 0.63 0.29 0.02
108_L 61_V 0.63 0.29 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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