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OPENSEQ.org
yech_iscs
Genes: A B A+B
Length: 79 404 455
Sequences: 162 17383 79
Seq/Len: 2.05 43.03 0.17
MirrorTree (Pazo et al. 2001) 0.25
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.03 0.00
2 0.00 0.03 0.00
5 0.00 0.04 0.00
10 0.00 0.05 0.02
20 0.00 0.06 0.02
100 0.00 0.11 0.03
∞ 0.00 0.21 0.16
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
12_M 174_G 1.66 0.37 0.00
17_G 179_V 1.40 0.24 0.00
47_M 301_L 1.30 0.20 0.00
59_K 53_I 1.28 0.19 0.00
16_S 78_S 1.23 0.18 0.00
13_M 58_I 1.20 0.17 0.00
47_M 191_D 1.14 0.15 0.00
11_N 189_P 1.14 0.15 0.00
8_E 174_G 1.11 0.14 0.00
37_A 119_F 1.10 0.14 0.00
34_G 180_D 1.08 0.13 0.00
34_G 206_K 1.08 0.13 0.00
42_C 180_D 1.08 0.13 0.00
42_C 206_K 1.08 0.13 0.00
61_K 180_D 1.08 0.13 0.00
61_K 206_K 1.08 0.13 0.00
77_C 180_D 1.08 0.13 0.00
77_C 206_K 1.08 0.13 0.00
16_S 245_P 1.07 0.13 0.00
71_T 97_I 1.04 0.12 0.00
52_L 180_D 1.03 0.12 0.00
52_L 206_K 1.03 0.12 0.00
47_M 175_I 1.03 0.12 0.00
66_K 120_E 1.02 0.12 0.00
6_G 146_I 1.02 0.12 0.00
3_S 97_I 1.01 0.12 0.00
12_M 303_V 1.01 0.12 0.00
47_M 24_M 1.00 0.11 0.00
14_I 245_P 0.97 0.11 0.00
25_L 180_D 0.97 0.10 0.00
25_L 206_K 0.97 0.10 0.00
75_K 85_G 0.95 0.10 0.00
4_I 177_Y 0.95 0.10 0.00
56_L 174_G 0.95 0.10 0.00
47_M 168_E 0.95 0.10 0.00
60_G 13_T 0.94 0.10 0.00
32_R 174_G 0.94 0.10 0.00
78_R 163_I 0.94 0.10 0.00
11_N 279_N 0.94 0.10 0.00
69_F 133_D 0.94 0.10 0.00
79_H 180_D 0.94 0.10 0.00
79_H 206_K 0.94 0.10 0.00
49_A 58_I 0.93 0.10 0.00
5_H 181_A 0.93 0.10 0.00
7_H 181_A 0.93 0.10 0.00
48_T 174_G 0.92 0.10 0.00
43_S 275_N 0.92 0.10 0.00
31_A 20_A 0.92 0.10 0.00
47_M 271_R 0.92 0.10 0.00
66_K 185_V 0.92 0.10 0.00
16_S 373_V 0.89 0.09 0.00
66_K 364_E 0.89 0.09 0.00
4_I 290_N 0.89 0.09 0.00
11_N 261_E 0.89 0.09 0.00
5_H 180_D 0.89 0.09 0.00
5_H 206_K 0.89 0.09 0.00
7_H 180_D 0.89 0.09 0.00
7_H 206_K 0.89 0.09 0.00
47_M 166_I 0.89 0.09 0.00
12_M 204_G 0.88 0.09 0.00
14_I 92_K 0.88 0.09 0.00
15_E 264_A 0.88 0.09 0.00
11_N 85_G 0.88 0.09 0.00
56_L 303_V 0.87 0.09 0.00
46_G 285_E 0.87 0.09 0.00
68_G 174_G 0.86 0.08 0.00
19_Q 272_G 0.86 0.08 0.00
63_I 344_L 0.85 0.08 0.00
4_I 168_E 0.85 0.08 0.00
34_G 354_R 0.85 0.08 0.00
42_C 354_R 0.85 0.08 0.00
61_K 354_R 0.85 0.08 0.00
77_C 354_R 0.85 0.08 0.00
6_G 200_M 0.84 0.08 0.00
52_L 198_D 0.84 0.08 0.00
41_T 180_D 0.84 0.08 0.00
41_T 206_K 0.84 0.08 0.00
20_Y 58_I 0.84 0.08 0.00
1_M 169_M 0.84 0.08 0.00
47_M 288_Y 0.84 0.08 0.00
15_E 368_Y 0.84 0.08 0.00
76_I 146_I 0.83 0.08 0.00
40_H 213_I 0.83 0.08 0.00
44_A 99_T 0.83 0.08 0.00
6_G 97_I 0.83 0.08 0.00
21_T 93_K 0.83 0.08 0.00
56_L 191_D 0.82 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
8072 0.17 yech_iscs Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7862 0.02 yech_iscs Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
7861 0.02 yech_iscs Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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