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OPENSEQ.org
DI1210004_3C94
Genes: A B A+B
Length: 30 475 501
Sequences: 199 1321 55
Seq/Len: 6.63 2.78 0.11
MirrorTree (Pazo et al. 2001) 0.69
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 0.00
100 0.00 0.00 0.01
∞ 0.01 0.00 0.11
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
5_Q 358_T 1.40 0.18 0.00
4_A 34_I 1.39 0.18 0.00
4_A 313_N 1.35 0.17 0.00
16_P 34_I 1.32 0.16 0.00
15_A 209_F 1.29 0.15 0.00
6_S 474_I 1.25 0.14 0.00
9_Q 288_T 1.23 0.14 0.00
4_A 227_K 1.22 0.14 0.00
7_R 343_V 1.20 0.13 0.00
17_S 85_A 1.09 0.11 0.00
4_A 256_R 1.08 0.10 0.00
9_Q 153_N 1.07 0.10 0.00
17_S 75_R 1.07 0.10 0.00
16_P 207_Y 1.05 0.10 0.00
9_Q 275_D 1.04 0.10 0.00
15_A 165_R 1.03 0.09 0.00
4_A 425_Q 1.00 0.09 0.00
13_P 308_V 0.98 0.09 0.00
12_A 405_K 0.98 0.09 0.00
17_S 54_A 0.98 0.09 0.00
5_Q 438_E 0.98 0.09 0.00
16_P 325_I 0.98 0.09 0.00
12_A 193_M 0.98 0.09 0.00
3_G 192_A 0.95 0.08 0.00
5_Q 141_M 0.95 0.08 0.00
14_A 440_L 0.95 0.08 0.00
14_A 175_I 0.94 0.08 0.00
9_Q 12_L 0.94 0.08 0.00
16_P 165_R 0.93 0.08 0.00
9_Q 99_I 0.92 0.08 0.00
11_S 112_T 0.92 0.08 0.00
7_R 380_M 0.92 0.08 0.00
13_P 199_T 0.91 0.07 0.00
10_Q 89_H 0.90 0.07 0.00
24_F 164_F 0.89 0.07 0.00
13_P 175_I 0.89 0.07 0.00
15_A 13_F 0.89 0.07 0.00
9_Q 241_G 0.88 0.07 0.00
7_R 442_G 0.87 0.07 0.00
6_S 471_A 0.86 0.07 0.00
5_Q 401_K 0.86 0.07 0.00
17_S 436_T 0.86 0.07 0.00
16_P 446_E 0.85 0.07 0.00
4_A 203_R 0.85 0.07 0.00
18_N 77_K 0.84 0.07 0.00
7_R 34_I 0.84 0.07 0.00
15_A 295_A 0.84 0.07 0.00
12_A 461_V 0.83 0.07 0.00
12_A 80_N 0.83 0.07 0.00
2_G 29_A 0.82 0.06 0.00
14_A 449_M 0.82 0.06 0.00
9_Q 60_Q 0.81 0.06 0.00
6_S 439_F 0.81 0.06 0.00
15_A 246_V 0.81 0.06 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)
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