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OPENSEQ.org
cI_A_40_cytb_6_human
Genes: A B A+B
Length: 115 378 493
Sequences: 1496 4489 966
Seq/Len: 13.01 11.88 1.96
MirrorTree (Pazo et al. 2001) 0.67
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 0.00
2 0.00 0.00 0.01
5 0.00 0.00 1.93
10 0.00 0.00 1.96
20 0.00 0.00 1.96
100 0.00 0.00 1.96
∞ 0.00 0.00 1.96
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
80_Q 232_L 1.79 0.97 0.88
29_G 248_D 1.56 0.93 0.76
51_F 322_Q 1.55 0.92 0.74
78_A 99_G 1.49 0.90 0.70
45_S 49_L 1.42 0.88 0.65
61_T 256_Y 1.42 0.87 0.64
78_A 371_L 1.38 0.85 0.60
78_A 341_Q 1.37 0.85 0.60
21_T 206_N 1.37 0.85 0.60
92_L 164_I 1.33 0.82 0.56
75_L 59_A 1.33 0.82 0.56
16_L 330_A 1.33 0.82 0.56
13_L 238_S 1.33 0.82 0.56
26_Q 94_L 1.32 0.81 0.55
102_L 244_L 1.31 0.81 0.54
49_V 339_G 1.26 0.77 0.49
19_I 170_V 1.26 0.77 0.48
14_A 310_S 1.25 0.77 0.48
51_F 244_L 1.25 0.77 0.48
63_L 121_L 1.25 0.76 0.48
78_A 112_T 1.23 0.75 0.46
97_I 122_A 1.23 0.75 0.46
95_I 89_M 1.21 0.73 0.44
75_L 300_I 1.21 0.73 0.43
10_N 94_L 1.20 0.72 0.43
103_A 246_S 1.20 0.72 0.42
100_L 79_I 1.19 0.72 0.42
80_Q 332_L 1.18 0.71 0.41
13_L 98_I 1.17 0.69 0.40
95_I 170_V 1.16 0.68 0.39
109_K 256_Y 1.15 0.68 0.38
25_P 49_L 1.15 0.67 0.37
97_I 109_Y 1.14 0.67 0.37
46_P 74_N 1.14 0.67 0.37
64_L 30_W 1.14 0.67 0.37
53_M 59_A 1.14 0.67 0.37
51_F 75_Y 1.14 0.66 0.36
53_M 99_G 1.13 0.66 0.36
53_M 107_F 1.12 0.65 0.35
53_M 254_D 1.11 0.64 0.34
18_M 102_L 1.11 0.64 0.34
109_K 334_I 1.09 0.62 0.32
7_L 160_L 1.09 0.61 0.32
2_N 370_S 1.09 0.61 0.32
54_K 95_F 1.08 0.61 0.31
97_I 129_M 1.08 0.60 0.31
80_Q 371_L 1.08 0.60 0.30
95_I 324_L 1.07 0.60 0.30
51_F 339_G 1.07 0.60 0.30
84_L 95_F 1.07 0.59 0.29
100_L 181_F 1.06 0.58 0.29
9_I 302_A 1.06 0.58 0.29
32_E 339_G 1.06 0.58 0.29
73_L 308_H 1.06 0.58 0.29
95_I 266_P 1.05 0.58 0.28
109_K 122_A 1.05 0.58 0.28
32_E 258_L 1.04 0.56 0.28
11_T 361_T 1.04 0.56 0.27
30_Y 122_A 1.04 0.56 0.27
102_L 322_Q 1.03 0.55 0.26
114_A 132_V 1.03 0.55 0.26
17_L 203_T 1.03 0.55 0.26
49_V 38_G 1.02 0.54 0.26
13_L 159_D 1.02 0.54 0.25
51_F 153_I 1.02 0.54 0.25
54_K 80_R 1.01 0.53 0.25
13_L 357_L 1.01 0.53 0.25
14_A 117_I 1.00 0.52 0.24
91_S 324_L 1.00 0.52 0.24
30_Y 57_P 1.00 0.52 0.24
90_S 19_I 1.00 0.52 0.24
18_M 202_E 1.00 0.52 0.24
97_I 11_M 1.00 0.52 0.24
107_L 320_L 1.00 0.52 0.24
80_Q 74_N 1.00 0.51 0.23
8_M 153_I 1.00 0.51 0.23
58_V 25_S 0.99 0.50 0.23
109_K 248_D 0.98 0.49 0.22
63_L 172_S 0.98 0.49 0.22
46_P 66_I 0.98 0.49 0.22
45_S 185_L 0.98 0.49 0.22
95_I 362_I 0.98 0.49 0.22
53_M 376_M 0.97 0.48 0.21
76_P 179_F 0.97 0.48 0.21
58_V 64_S 0.97 0.48 0.21
75_L 369_I 0.97 0.48 0.21
112_D 123_T 0.96 0.48 0.21
79_X 232_L 0.96 0.47 0.21
23_W 59_A 0.96 0.47 0.21
61_T 254_D 0.96 0.47 0.20
23_W 171_D 0.95 0.47 0.20
26_Q 303_M 0.95 0.46 0.20
53_M 322_Q 0.95 0.46 0.20
51_F 206_N 0.95 0.46 0.20
80_Q 370_S 0.95 0.46 0.20
103_A 184_I 0.94 0.45 0.19
110_G 64_S 0.94 0.45 0.19
95_I 46_T 0.94 0.45 0.19
18_M 353_V 0.94 0.45 0.19
80_Q 369_I 0.94 0.45 0.19
6_I 94_L 0.94 0.45 0.19
90_S 331_D 0.94 0.45 0.19
80_Q 329_A 0.93 0.44 0.18
29_G 256_Y 0.92 0.43 0.18
88_V 7_I 0.92 0.43 0.18
30_Y 224_Y 0.92 0.43 0.18
63_L 85_N 0.92 0.42 0.17
46_P 4_M 0.92 0.42 0.17
35_T 374_N 0.91 0.42 0.17
58_V 40_C 0.91 0.42 0.17
81_T 248_D 0.91 0.42 0.17
51_F 202_E 0.91 0.42 0.17
75_L 121_L 0.91 0.42 0.17
54_K 173_P 0.91 0.42 0.17
81_T 232_L 0.91 0.42 0.17
78_A 125_A 0.91 0.41 0.17
46_P 180_T 0.91 0.41 0.17
6_I 117_I 0.90 0.41 0.16
75_L 57_P 0.89 0.40 0.16
4_A 43_L 0.89 0.40 0.16
61_T 242_L 0.89 0.40 0.16
21_T 241_T 0.89 0.40 0.16
88_V 304_I 0.89 0.40 0.16
25_P 74_N 0.89 0.39 0.15
53_M 296_L 0.89 0.39 0.15
44_M 209_L 0.88 0.39 0.15
20_I 123_T 0.88 0.39 0.15
95_I 375_K 0.88 0.38 0.15
89_M 61_T 0.88 0.38 0.15
61_T 248_D 0.87 0.38 0.15
77_W 269_K 0.87 0.38 0.14
86_L 303_M 0.87 0.38 0.14
88_V 229_A 0.87 0.37 0.14
61_T 40_C 0.86 0.36 0.14
21_T 47_T 0.86 0.36 0.14
79_X 191_A 0.86 0.36 0.14
30_Y 256_Y 0.86 0.36 0.14
3_F 102_L 0.86 0.36 0.14
88_V 219_T 0.86 0.36 0.14
75_L 61_T 0.86 0.36 0.14
92_L 314_S 0.85 0.36 0.13
21_T 184_I 0.85 0.36 0.13
61_T 81_Y 0.85 0.36 0.13
91_S 108_L 0.85 0.36 0.13
13_L 366_M 0.85 0.36 0.13
22_F 49_L 0.85 0.35 0.13
87_M 1_M 0.85 0.35 0.13
92_L 321_S 0.85 0.35 0.13
7_L 333_L 0.84 0.35 0.13
94_L 256_Y 0.84 0.35 0.13
47_A 325_Y 0.84 0.35 0.13
15_L 304_I 0.84 0.35 0.13
84_L 81_Y 0.84 0.34 0.13
76_P 55_Y 0.84 0.34 0.13
19_I 241_T 0.84 0.34 0.12
53_M 365_L 0.83 0.34 0.12
88_V 121_L 0.83 0.34 0.12
97_I 191_A 0.83 0.33 0.12
11_T 190_A 0.83 0.33 0.12
89_M 372_I 0.83 0.33 0.12
24_L 354_A 0.83 0.33 0.12
80_Q 254_D 0.82 0.33 0.12
13_L 69_I 0.82 0.33 0.12
58_V 375_K 0.82 0.33 0.12
114_A 256_Y 0.82 0.33 0.12
1_M 59_A 0.82 0.33 0.12
11_T 99_G 0.82 0.32 0.12
97_I 160_L 0.82 0.32 0.12
30_Y 263_N 0.82 0.32 0.12
26_Q 27_I 0.82 0.32 0.11
95_I 226_I 0.82 0.32 0.11
95_I 329_A 0.82 0.32 0.11
91_S 232_L 0.82 0.32 0.11
109_K 81_Y 0.82 0.32 0.11
6_I 159_D 0.82 0.32 0.11
88_V 66_I 0.81 0.32 0.11
81_T 295_L 0.81 0.32 0.11
2_N 310_S 0.81 0.32 0.11
91_S 299_L 0.81 0.31 0.11
49_V 318_R 0.81 0.31 0.11
58_V 214_H 0.81 0.31 0.11
32_E 197_L 0.81 0.31 0.11
24_L 149_L 0.81 0.31 0.11
49_V 341_Q 0.81 0.31 0.11
61_T 263_N 0.81 0.31 0.11
114_A 181_F 0.81 0.31 0.11
49_V 119_L 0.81 0.31 0.11
95_I 29_A 0.80 0.31 0.11
92_L 11_M 0.80 0.31 0.11
22_F 377_L 0.80 0.31 0.11
18_M 333_L 0.80 0.30 0.10
95_I 302_A 0.80 0.30 0.10
75_L 184_I 0.80 0.30 0.10
93_L 284_V 0.80 0.30 0.10
81_T 122_A 0.80 0.30 0.10
27_L 218_I 0.80 0.30 0.10
8_M 241_T 0.79 0.30 0.10
29_G 313_Q 0.79 0.30 0.10
61_T 340_G 0.79 0.30 0.10
90_S 354_A 0.79 0.30 0.10
10_N 256_Y 0.79 0.30 0.10
95_I 94_L 0.79 0.30 0.10
87_M 295_L 0.79 0.30 0.10
90_S 310_S 0.79 0.30 0.10
12_L 211_I 0.79 0.30 0.10
63_L 151_S 0.79 0.30 0.10
80_Q 10_L 0.79 0.29 0.10
91_S 27_I 0.79 0.29 0.10
84_L 172_S 0.79 0.29 0.10
103_A 243_T 0.79 0.29 0.10
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
5614 1.96 cI_A_40_cytb_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2016_06b) 0.88 Done - Shared
5613 1.95 cI_A_40_cytb_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.92 Done - Shared
5612 7.03 cI_A_20_cytb_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.21 Done - Shared
5611 1.93 cI_A_40_cytb_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.89 Done - Shared
5610 1.94 cI_A_40_cytb_60_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) 0.85 Done - Shared
5596 0 cI_A_60_cytb_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5593 0 cI_A_80_cytb_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5591 1.95 cI_A_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.85 Done - Shared
5586 7.85 cI_A_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.03 Done - Shared
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