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OPENSEQ.org
cIV_D_2_cI_N_10_1_Pdenitr
Genes: A B A+B
Length: 43 499 515
Sequences: 221 3881 95
Seq/Len: 5.14 7.78 0.18
MirrorTree (Pazo et al. 2001) 0.09
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 0.16 0.00
2 0.00 0.27 0.00
5 0.00 0.29 0.00
10 0.00 0.29 0.00
20 0.00 0.30 0.00
100 0.00 0.31 0.01
∞ 0.01 0.34 0.18
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
41_A 328_M 1.54 0.32 0.00
13_Q 323_N 1.47 0.28 0.00
32_I 90_A 1.35 0.23 0.00
13_Q 170_L 1.27 0.20 0.00
14_Q 154_S 1.27 0.20 0.00
40_L 17_G 1.26 0.20 0.00
33_A 150_S 1.26 0.20 0.00
38_L 182_A 1.21 0.18 0.00
13_Q 81_T 1.18 0.17 0.00
17_F 244_T 1.18 0.17 0.00
30_L 285_S 1.18 0.17 0.00
22_K 110_V 1.15 0.16 0.00
33_A 258_V 1.13 0.15 0.00
35_L 412_I 1.11 0.15 0.00
27_V 268_D 1.09 0.14 0.00
15_A 154_S 1.08 0.14 0.00
41_A 20_L 1.05 0.13 0.00
12_H 24_M 1.02 0.12 0.00
28_S 366_P 1.01 0.12 0.00
32_I 95_Y 1.00 0.12 0.00
17_F 300_Y 1.00 0.12 0.00
40_L 321_V 0.99 0.11 0.00
14_Q 65_H 0.98 0.11 0.00
38_L 97_Q 0.95 0.10 0.00
38_L 218_V 0.94 0.10 0.00
2_D 459_G 0.94 0.10 0.00
27_V 360_R 0.94 0.10 0.00
25_T 119_F 0.94 0.10 0.00
23_G 363_W 0.94 0.10 0.00
32_I 404_G 0.93 0.10 0.00
13_Q 157_G 0.92 0.10 0.00
18_A 277_A 0.92 0.10 0.00
33_A 111_A 0.91 0.10 0.00
36_V 305_H 0.91 0.10 0.00
26_W 192_S 0.91 0.10 0.00
13_Q 278_V 0.90 0.10 0.00
16_T 222_P 0.89 0.09 0.00
38_L 92_S 0.89 0.09 0.00
3_H 61_G 0.88 0.09 0.00
32_I 338_T 0.88 0.09 0.00
13_Q 300_Y 0.87 0.09 0.00
17_F 42_T 0.86 0.09 0.00
39_A 83_V 0.86 0.09 0.00
7_E 409_L 0.86 0.09 0.00
13_Q 255_A 0.86 0.09 0.00
26_W 338_T 0.86 0.09 0.00
10_I 409_L 0.86 0.09 0.00
21_I 425_V 0.85 0.09 0.00
7_E 194_I 0.84 0.08 0.00
13_Q 324_M 0.84 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)
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