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OPENSEQ.org
iscuiscs
Genes: A B A+B
Length: 128 404 527
Sequences: 951 9826 870
Seq/Len: 7.43 24.32 1.65
MirrorTree (Pazo et al. 2001) 0.84
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 0.05 1.60
2 0.00 0.06 1.64
5 0.00 0.08 1.65
10 0.00 0.08 1.65
20 0.00 0.09 1.67
100 0.00 0.13 1.73
∞ 0.01 0.18 1.83
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
61_Y 162_D 1.03 0.50 0.00
45_I 285_E 0.99 0.46 0.00
67_I 312_S 0.98 0.45 0.00
59_K 304_S 0.98 0.45 0.00
13_N 361_T 0.93 0.39 0.00
108_I 148_V 0.89 0.35 0.00
13_N 191_D 0.86 0.33 0.00
12_E 318_K 0.85 0.32 0.00
69_S 344_L 0.84 0.30 0.00
36_A 334_E 0.82 0.29 0.00
114_I 81_L 0.81 0.28 0.00
65_S 360_F 0.78 0.26 0.00
112_D 227_E 0.78 0.26 0.00
31_M 58_I 0.78 0.25 0.00
42_K 388_E 0.78 0.25 0.00
124_K 176_I 0.77 0.25 0.00
73_V 70_V 0.77 0.25 0.00
19_S 388_E 0.77 0.24 0.00
82_L 36_P 0.76 0.24 0.00
112_D 187_K 0.76 0.24 0.00
9_D 313_L 0.76 0.24 0.00
8_I 308_V 0.75 0.23 0.00
45_I 389_M 0.74 0.23 0.00
90_N 324_S 0.74 0.22 0.00
45_I 220_R 0.74 0.22 0.00
59_K 388_E 0.73 0.22 0.00
65_S 266_E 0.73 0.22 0.00
23_N 213_I 0.72 0.21 0.00
83_D 97_I 0.72 0.21 0.00
13_N 285_E 0.71 0.20 0.00
69_S 266_E 0.71 0.20 0.00
22_N 392_Q 0.70 0.20 0.00
109_L 358_G 0.69 0.19 0.00
49_D 60_D 0.68 0.19 0.00
34_A 346_D 0.68 0.18 0.00
15_R 230_M 0.68 0.18 0.00
66_A 314_I 0.68 0.18 0.00
65_S 246_V 0.68 0.18 0.00
116_A 191_D 0.68 0.18 0.00
67_I 44_G 0.67 0.18 0.00
101_P 247_H 0.67 0.18 0.00
64_G 135_K 0.67 0.18 0.00
9_D 111_C 0.67 0.17 0.00
88_I 348_L 0.66 0.17 0.00
42_K 215_A 0.66 0.17 0.00
101_P 123_Y 0.66 0.17 0.00
4_S 307_Y 0.66 0.17 0.00
122_K 197_V 0.65 0.17 0.00
28_G 46_Q 0.65 0.17 0.00
67_I 124_L 0.65 0.16 0.00
110_A 234_G 0.65 0.16 0.00
78_K 166_I 0.65 0.16 0.00
83_D 184_S 0.64 0.16 0.00
90_N 314_I 0.64 0.16 0.00
73_V 187_K 0.64 0.16 0.00
115_K 93_K 0.64 0.16 0.00
87_A 270_L 0.64 0.16 0.00
112_D 62_V 0.63 0.16 0.00
13_N 171_R 0.63 0.16 0.00
94_A 167_G 0.63 0.15 0.00
66_A 35_N 0.63 0.15 0.00
29_S 202_F 0.62 0.15 0.00
112_D 73_S 0.62 0.15 0.00
53_I 41_H 0.62 0.15 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
2042 3.61 IscUIscSmaxdist2 Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1966 1.65 iscuiscs Δgene:(1, 2) A:(1E-20, 2) B:(1E-20, 2) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1493 3.64 iscuiscs Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1474 3.72 iscuiscs Δgene:(1, ∞) A:(1E-10, 4) B:(1E-20, 4) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1460 2.84 iscuiscs Δgene:(1, 1) A:(1E-20, 4) B:(1E-20, 4) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1448 3.45 iscuiscs Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
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