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OPENSEQ.org
cI_A_40_cytb_40_human
Genes: A B A+B
Length: 115 378 493
Sequences: 1496 4493 960
Seq/Len: 13.01 11.89 1.95
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 1.95
20 0.00 0.00 1.95
100 0.00 0.00 1.95
∞ 0.00 0.00 1.95
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 1.77 0.97 0.85
51_F 322_Q 1.67 0.95 0.81
29_G 248_D 1.63 0.94 0.78
78_A 99_G 1.52 0.92 0.71
75_L 59_A 1.49 0.90 0.68
45_S 49_L 1.43 0.88 0.63
21_T 206_N 1.42 0.87 0.62
26_Q 94_L 1.37 0.85 0.58
61_T 256_Y 1.37 0.85 0.58
78_A 341_Q 1.36 0.84 0.57
51_F 244_L 1.32 0.82 0.53
78_A 371_L 1.31 0.81 0.53
102_L 244_L 1.31 0.81 0.52
10_N 94_L 1.29 0.80 0.50
53_M 99_G 1.27 0.78 0.48
49_V 339_G 1.26 0.77 0.47
14_A 310_S 1.25 0.77 0.46
16_L 330_A 1.24 0.76 0.45
13_L 238_S 1.24 0.76 0.45
95_I 170_V 1.23 0.75 0.44
53_M 254_D 1.23 0.74 0.44
51_F 206_N 1.21 0.73 0.42
63_L 121_L 1.21 0.73 0.42
100_L 79_I 1.20 0.72 0.41
109_K 334_I 1.16 0.69 0.37
11_T 361_T 1.15 0.68 0.36
2_N 370_S 1.14 0.67 0.35
80_Q 332_L 1.14 0.66 0.35
97_I 122_A 1.13 0.66 0.34
80_Q 371_L 1.13 0.65 0.34
13_L 357_L 1.13 0.65 0.34
13_L 159_D 1.12 0.64 0.33
45_S 185_L 1.12 0.64 0.33
102_L 322_Q 1.12 0.64 0.33
13_L 98_I 1.12 0.64 0.33
95_I 89_M 1.11 0.63 0.32
54_K 95_F 1.10 0.63 0.32
95_I 375_K 1.10 0.63 0.32
19_I 170_V 1.10 0.63 0.31
51_F 202_E 1.09 0.61 0.30
78_A 112_T 1.09 0.61 0.30
53_M 376_M 1.09 0.61 0.30
75_L 121_L 1.08 0.61 0.30
53_M 107_F 1.08 0.60 0.29
92_L 164_I 1.08 0.60 0.29
14_A 117_I 1.07 0.59 0.29
53_M 59_A 1.07 0.59 0.29
18_M 102_L 1.07 0.59 0.28
51_F 339_G 1.07 0.59 0.28
14_A 60_S 1.07 0.59 0.28
92_L 11_M 1.06 0.58 0.28
30_Y 57_P 1.06 0.58 0.28
95_I 266_P 1.06 0.58 0.28
46_P 74_N 1.06 0.58 0.27
109_K 256_Y 1.06 0.58 0.27
25_P 74_N 1.05 0.57 0.27
80_Q 74_N 1.05 0.57 0.27
73_L 308_H 1.05 0.57 0.27
97_I 129_M 1.05 0.57 0.27
32_E 339_G 1.05 0.57 0.27
13_L 366_M 1.05 0.57 0.27
109_K 122_A 1.04 0.56 0.26
7_L 160_L 1.04 0.56 0.26
109_K 248_D 1.04 0.56 0.26
103_A 246_S 1.03 0.55 0.25
32_E 258_L 1.03 0.55 0.25
100_L 181_F 1.03 0.55 0.25
75_L 369_I 1.03 0.54 0.25
95_I 324_L 1.02 0.54 0.25
91_S 324_L 1.02 0.54 0.24
49_V 38_G 1.01 0.53 0.24
51_F 75_Y 1.01 0.53 0.24
18_M 202_E 1.01 0.53 0.23
54_K 80_R 1.01 0.53 0.23
95_I 226_I 0.99 0.51 0.22
35_T 374_N 0.99 0.51 0.22
84_L 81_Y 0.99 0.50 0.22
79_X 232_L 0.98 0.49 0.21
46_P 66_I 0.98 0.49 0.21
76_P 179_F 0.98 0.49 0.21
64_L 30_W 0.98 0.49 0.21
114_A 132_V 0.98 0.49 0.21
17_L 203_T 0.97 0.49 0.20
90_S 310_S 0.97 0.48 0.20
110_G 64_S 0.97 0.48 0.20
23_W 171_D 0.97 0.48 0.20
53_M 322_Q 0.97 0.48 0.20
8_M 153_I 0.96 0.48 0.20
63_L 172_S 0.96 0.48 0.20
58_V 40_C 0.96 0.48 0.20
30_Y 122_A 0.96 0.47 0.20
58_V 25_S 0.96 0.47 0.20
88_V 7_I 0.96 0.47 0.19
80_Q 370_S 0.96 0.47 0.19
75_L 300_I 0.96 0.47 0.19
95_I 46_T 0.95 0.46 0.19
80_Q 254_D 0.95 0.46 0.19
79_X 11_M 0.94 0.45 0.18
27_L 218_I 0.94 0.45 0.18
61_T 248_D 0.94 0.45 0.18
95_I 94_L 0.94 0.45 0.18
61_T 40_C 0.94 0.44 0.18
78_A 125_A 0.93 0.44 0.17
23_W 59_A 0.92 0.43 0.17
97_I 109_Y 0.92 0.43 0.17
97_I 160_L 0.92 0.43 0.17
30_Y 224_Y 0.92 0.43 0.17
90_S 331_D 0.92 0.43 0.17
89_M 61_T 0.92 0.43 0.17
94_L 256_Y 0.92 0.42 0.16
61_T 254_D 0.92 0.42 0.16
1_M 59_A 0.91 0.42 0.16
63_L 85_N 0.91 0.41 0.16
29_G 256_Y 0.91 0.41 0.16
61_T 263_N 0.91 0.41 0.16
83_N 82_L 0.91 0.41 0.16
88_V 304_I 0.91 0.41 0.16
88_V 229_A 0.90 0.41 0.16
90_S 19_I 0.90 0.40 0.15
114_A 256_Y 0.89 0.40 0.15
3_F 102_L 0.89 0.40 0.15
30_Y 256_Y 0.89 0.40 0.15
61_T 242_L 0.89 0.40 0.15
77_W 269_K 0.89 0.40 0.15
87_M 295_L 0.89 0.39 0.15
16_L 348_T 0.89 0.39 0.15
97_I 224_Y 0.89 0.39 0.15
112_D 123_T 0.89 0.39 0.15
99_A 81_Y 0.88 0.39 0.14
75_L 57_P 0.88 0.38 0.14
80_Q 329_A 0.88 0.38 0.14
9_I 302_A 0.87 0.38 0.14
4_A 43_L 0.87 0.37 0.14
18_M 333_L 0.87 0.37 0.14
58_V 214_H 0.87 0.37 0.14
103_A 184_I 0.87 0.37 0.13
22_F 49_L 0.86 0.37 0.13
12_L 211_I 0.86 0.36 0.13
24_L 354_A 0.85 0.36 0.13
95_I 82_L 0.85 0.36 0.13
95_I 302_A 0.85 0.36 0.13
21_T 184_I 0.85 0.36 0.13
88_V 219_T 0.84 0.35 0.12
54_K 173_P 0.84 0.35 0.12
21_T 74_N 0.84 0.35 0.12
6_I 254_D 0.84 0.35 0.12
97_I 188_I 0.84 0.34 0.12
53_M 361_T 0.84 0.34 0.12
28_N 195_L 0.84 0.34 0.12
84_L 254_D 0.84 0.34 0.12
95_I 190_A 0.84 0.34 0.12
11_T 99_G 0.84 0.34 0.12
26_Q 303_M 0.84 0.34 0.12
20_I 225_T 0.83 0.34 0.12
99_A 212_T 0.83 0.34 0.12
84_L 95_F 0.83 0.34 0.12
18_M 321_S 0.83 0.33 0.11
49_V 318_R 0.83 0.33 0.11
25_P 49_L 0.83 0.33 0.11
90_S 354_A 0.83 0.33 0.11
100_L 55_Y 0.83 0.33 0.11
84_L 378_K 0.82 0.33 0.11
108_Q 235_F 0.82 0.33 0.11
92_L 321_S 0.82 0.33 0.11
82_T 329_A 0.82 0.33 0.11
75_L 61_T 0.82 0.33 0.11
87_M 1_M 0.82 0.33 0.11
90_S 122_A 0.82 0.33 0.11
30_Y 263_N 0.82 0.32 0.11
89_M 195_L 0.82 0.32 0.11
61_T 81_Y 0.82 0.32 0.11
81_T 248_D 0.82 0.32 0.11
13_L 94_L 0.81 0.32 0.11
46_P 4_M 0.81 0.32 0.11
61_T 156_I 0.81 0.32 0.11
75_L 184_I 0.81 0.32 0.11
32_E 338_I 0.81 0.32 0.11
76_P 55_Y 0.81 0.32 0.11
13_L 69_I 0.81 0.32 0.11
25_P 47_T 0.81 0.32 0.11
97_I 11_M 0.81 0.32 0.11
103_A 260_N 0.81 0.32 0.11
58_V 64_S 0.81 0.32 0.10
49_V 119_L 0.81 0.31 0.10
49_V 341_Q 0.81 0.31 0.10
58_V 194_T 0.81 0.31 0.10
18_M 353_V 0.81 0.31 0.10
84_L 172_S 0.81 0.31 0.10
97_I 191_A 0.81 0.31 0.10
7_L 333_L 0.81 0.31 0.10
29_G 313_Q 0.81 0.31 0.10
92_L 314_S 0.80 0.31 0.10
93_L 192_L 0.80 0.31 0.10
54_K 172_S 0.80 0.31 0.10
14_A 66_I 0.80 0.31 0.10
58_V 375_K 0.80 0.30 0.10
47_A 325_Y 0.80 0.30 0.10
107_L 320_L 0.80 0.30 0.10
2_N 310_S 0.79 0.30 0.10
80_Q 369_I 0.79 0.30 0.10
9_I 353_V 0.79 0.29 0.10
63_L 351_G 0.79 0.29 0.10
81_T 160_L 0.79 0.29 0.10
54_K 242_L 0.79 0.29 0.10
51_F 307_L 0.79 0.29 0.10
22_F 377_L 0.79 0.29 0.10
93_L 284_V 0.79 0.29 0.10
26_Q 27_I 0.79 0.29 0.09
91_S 232_L 0.79 0.29 0.09
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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