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OPENSEQ.org
cIm_K_40_cytb_40_human
Genes: A B A+B
Length: 98 378 476
Sequences: 189 4493 123
Seq/Len: 1.93 11.89 0.26
MirrorTree (Pazo et al. 2001) 0.41
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.26
10 0.00 0.00 0.26
20 0.00 0.00 0.26
100 0.00 0.00 0.26
∞ 0.00 0.00 0.26
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
15_S 310_S 1.90 0.63 0.01
26_L 235_F 1.52 0.40 0.00
43_M 236_I 1.43 0.34 0.00
26_L 95_F 1.36 0.30 0.00
79_V 57_P 1.33 0.28 0.00
79_V 123_T 1.31 0.27 0.00
56_A 360_T 1.30 0.27 0.00
22_Y 376_M 1.28 0.26 0.00
80_S 56_S 1.28 0.26 0.00
19_M 102_L 1.27 0.25 0.00
54_L 321_S 1.20 0.22 0.00
79_V 111_E 1.20 0.22 0.00
91_H 8_N 1.18 0.21 0.00
19_M 211_I 1.18 0.21 0.00
43_M 233_L 1.17 0.21 0.00
54_L 325_Y 1.16 0.20 0.00
58_I 215_S 1.15 0.20 0.00
73_V 235_F 1.14 0.19 0.00
14_I 7_I 1.13 0.19 0.00
43_M 4_M 1.13 0.19 0.00
91_H 172_S 1.13 0.19 0.00
55_L 98_I 1.11 0.18 0.00
90_V 170_V 1.11 0.18 0.00
21_V 313_Q 1.10 0.18 0.00
59_V 212_T 1.09 0.18 0.00
57_N 209_L 1.08 0.17 0.00
79_V 313_Q 1.07 0.17 0.00
87_L 123_T 1.06 0.17 0.00
62_A 313_Q 1.06 0.17 0.00
90_V 313_Q 1.06 0.16 0.00
43_M 310_S 1.05 0.16 0.00
57_N 236_I 1.04 0.16 0.00
91_H 168_Y 1.03 0.15 0.00
81_I 181_F 1.03 0.15 0.00
79_V 121_L 1.02 0.15 0.00
81_I 180_T 1.02 0.15 0.00
62_A 240_M 1.02 0.15 0.00
43_M 70_T 1.02 0.15 0.00
51_T 235_F 1.02 0.15 0.00
21_V 107_F 1.02 0.15 0.00
56_A 190_A 1.01 0.15 0.00
87_L 108_L 1.00 0.14 0.00
21_V 195_L 1.00 0.14 0.00
54_L 4_M 0.99 0.14 0.00
47_M 313_Q 0.99 0.14 0.00
57_N 370_S 0.99 0.14 0.00
53_S 236_I 0.99 0.14 0.00
54_L 95_F 0.98 0.14 0.00
17_L 96_L 0.98 0.14 0.00
56_A 370_S 0.98 0.14 0.00
6_M 330_A 0.98 0.14 0.00
59_V 102_L 0.97 0.14 0.00
59_V 159_D 0.97 0.13 0.00
80_S 8_N 0.96 0.13 0.00
81_I 3_P 0.96 0.13 0.00
21_V 4_M 0.95 0.13 0.00
43_M 162_Q 0.95 0.13 0.00
87_L 235_F 0.95 0.13 0.00
57_N 321_S 0.94 0.13 0.00
43_M 95_F 0.94 0.13 0.00
80_S 170_V 0.94 0.13 0.00
19_M 109_Y 0.94 0.12 0.00
17_L 349_I 0.94 0.12 0.00
51_T 108_L 0.93 0.12 0.00
54_L 357_L 0.93 0.12 0.00
40_L 57_P 0.93 0.12 0.00
63_M 325_Y 0.92 0.12 0.00
19_M 345_Y 0.91 0.12 0.00
55_L 376_M 0.91 0.12 0.00
64_L 254_D 0.91 0.12 0.00
19_M 173_P 0.91 0.12 0.00
45_T 260_N 0.91 0.12 0.00
8_I 109_Y 0.91 0.12 0.00
43_M 180_T 0.91 0.12 0.00
19_M 249_L 0.90 0.12 0.00
56_A 173_P 0.90 0.12 0.00
47_M 29_A 0.90 0.11 0.00
56_A 363_L 0.90 0.11 0.00
22_Y 316_M 0.90 0.11 0.00
54_L 236_I 0.90 0.11 0.00
45_T 245_F 0.89 0.11 0.00
56_A 357_L 0.89 0.11 0.00
64_L 310_S 0.89 0.11 0.00
6_M 340_G 0.89 0.11 0.00
36_M 239_L 0.89 0.11 0.00
45_T 371_L 0.89 0.11 0.00
6_M 209_L 0.88 0.11 0.00
29_S 215_S 0.88 0.11 0.00
43_M 67_A 0.88 0.11 0.00
58_I 16_H 0.88 0.11 0.00
56_A 321_S 0.88 0.11 0.00
2_P 209_L 0.88 0.11 0.00
63_M 215_S 0.88 0.11 0.00
57_N 168_Y 0.88 0.11 0.00
55_L 229_A 0.87 0.11 0.00
6_M 369_I 0.87 0.11 0.00
2_P 159_D 0.87 0.11 0.00
17_L 364_I 0.87 0.11 0.00
29_S 159_D 0.87 0.11 0.00
6_M 320_L 0.86 0.10 0.00
36_M 343_V 0.86 0.10 0.00
26_L 16_H 0.86 0.10 0.00
19_M 376_M 0.86 0.10 0.00
80_S 96_L 0.86 0.10 0.00
81_I 23_T 0.86 0.10 0.00
55_L 57_P 0.86 0.10 0.00
79_V 108_L 0.86 0.10 0.00
58_I 102_L 0.86 0.10 0.00
52_H 243_T 0.86 0.10 0.00
19_M 46_T 0.86 0.10 0.00
91_H 356_V 0.85 0.10 0.00
42_I 180_T 0.85 0.10 0.00
80_S 168_Y 0.85 0.10 0.00
2_P 92_I 0.85 0.10 0.00
21_V 109_Y 0.85 0.10 0.00
59_V 304_I 0.85 0.10 0.00
26_L 11_M 0.85 0.10 0.00
73_V 95_F 0.85 0.10 0.00
63_M 232_L 0.84 0.10 0.00
56_A 234_L 0.84 0.10 0.00
87_L 313_Q 0.84 0.10 0.00
48_T 102_L 0.84 0.10 0.00
71_A 245_F 0.84 0.10 0.00
17_L 347_F 0.84 0.10 0.00
61_I 150_L 0.84 0.10 0.00
81_I 123_T 0.84 0.10 0.00
52_H 368_T 0.84 0.10 0.00
73_V 108_L 0.83 0.10 0.00
19_M 122_A 0.83 0.10 0.00
55_L 314_S 0.83 0.10 0.00
14_I 195_L 0.83 0.10 0.00
21_V 309_M 0.83 0.10 0.00
26_L 323_S 0.82 0.10 0.00
2_P 78_I 0.82 0.10 0.00
43_M 240_M 0.82 0.10 0.00
5_Y 98_I 0.82 0.10 0.00
46_F 121_L 0.82 0.10 0.00
62_A 321_S 0.82 0.10 0.00
5_Y 159_D 0.82 0.10 0.00
58_I 110_S 0.82 0.10 0.00
63_M 376_M 0.82 0.10 0.00
21_V 46_T 0.82 0.10 0.00
91_H 13_L 0.82 0.10 0.00
38_L 10_L 0.82 0.09 0.00
59_V 229_A 0.82 0.09 0.00
59_V 78_I 0.81 0.09 0.00
62_A 236_I 0.81 0.09 0.00
15_S 195_L 0.81 0.09 0.00
40_L 194_T 0.81 0.09 0.00
36_M 254_D 0.81 0.09 0.00
12_F 309_M 0.81 0.09 0.00
19_M 371_L 0.81 0.09 0.00
22_Y 229_A 0.81 0.09 0.00
87_L 353_V 0.81 0.09 0.00
90_V 172_S 0.81 0.09 0.00
26_L 377_L 0.81 0.09 0.00
71_A 181_F 0.81 0.09 0.00
58_I 313_Q 0.81 0.09 0.00
6_M 7_I 0.81 0.09 0.00
55_L 325_Y 0.81 0.09 0.00
22_Y 314_S 0.80 0.09 0.00
22_Y 57_P 0.80 0.09 0.00
29_S 232_L 0.80 0.09 0.00
47_M 215_S 0.80 0.09 0.00
45_T 372_I 0.80 0.09 0.00
80_S 209_L 0.80 0.09 0.00
12_F 366_M 0.80 0.09 0.00
14_I 320_L 0.80 0.09 0.00
56_A 236_I 0.80 0.09 0.00
90_V 10_L 0.80 0.09 0.00
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
5753 7.43 cIm_K_2_cytb_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.20 Done - Shared
5751 7.22 cIm_K_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.04 Done - Shared
5750 0.26 cIm_K_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
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