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OPENSEQ.org
cIp_9_4_cytb_40_human
Genes: A B A+B
Length: 210 378 579
Sequences: 1680 4493 154
Seq/Len: 8 11.89 0.27
MirrorTree (Pazo et al. 2001) 0.12
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 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.00 0.00 0.04
∞ 0.02 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
24_G 120_L 1.11 0.19 0.00
169_P 293_A 1.03 0.16 0.00
80_A 173_P 1.03 0.16 0.00
142_R 114_N 1.02 0.15 0.00
70_M 155_Y 1.02 0.15 0.00
142_R 204_G 1.01 0.15 0.00
25_R 302_A 1.00 0.15 0.00
12_A 191_A 0.97 0.14 0.00
43_D 114_N 0.97 0.14 0.00
19_A 119_L 0.96 0.13 0.00
13_L 181_F 0.96 0.13 0.00
100_A 96_L 0.95 0.13 0.00
53_D 238_S 0.95 0.13 0.00
36_Y 333_L 0.92 0.12 0.00
167_E 174_T 0.91 0.12 0.00
39_V 128_F 0.91 0.12 0.00
169_P 334_I 0.91 0.12 0.00
20_G 310_S 0.90 0.12 0.00
168_G 45_I 0.90 0.12 0.00
93_P 49_L 0.89 0.12 0.00
99_H 181_F 0.89 0.12 0.00
68_L 356_V 0.88 0.11 0.00
82_I 103_Y 0.86 0.11 0.00
118_E 229_A 0.86 0.11 0.00
162_V 190_A 0.85 0.10 0.00
39_V 87_A 0.85 0.10 0.00
24_G 156_I 0.84 0.10 0.00
112_I 181_F 0.84 0.10 0.00
164_A 10_L 0.83 0.10 0.00
52_T 245_F 0.83 0.10 0.00
143_Y 181_F 0.83 0.10 0.00
119_A 58_D 0.83 0.10 0.00
27_L 163_W 0.83 0.10 0.00
141_T 181_F 0.83 0.10 0.00
165_I 184_I 0.82 0.10 0.00
124_Q 122_A 0.82 0.10 0.00
115_K 194_T 0.82 0.10 0.00
72_L 185_L 0.82 0.10 0.00
65_F 343_V 0.81 0.10 0.00
59_L 46_T 0.80 0.09 0.00
116_L 151_S 0.80 0.09 0.00
13_L 261_P 0.80 0.09 0.00
93_P 245_F 0.79 0.09 0.00
32_V 198_L 0.79 0.09 0.00
178_H 94_L 0.79 0.09 0.00
142_R 229_A 0.79 0.09 0.00
94_R 260_N 0.79 0.09 0.00
169_P 82_L 0.78 0.09 0.00
202_N 319_P 0.78 0.09 0.00
32_V 364_I 0.78 0.09 0.00
19_A 45_I 0.78 0.09 0.00
47_D 189_I 0.77 0.09 0.00
92_S 333_L 0.77 0.09 0.00
90_P 243_T 0.76 0.09 0.00
33_A 219_T 0.76 0.08 0.00
94_R 236_I 0.76 0.08 0.00
159_A 300_I 0.76 0.08 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
5835 0.27 cIp_9_4_cytb_40_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5645 0.47 cIp_9_40_cIV_I_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5624 0.36 cIp_9_10_cIV_I_40_human Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5623 0.46 cIp_9_40_cIV_I_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
5622 0.47 cIp_9_4_cIV_I_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
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