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OPENSEQ.org
BR
Genes: A B A+B
Length: 229 431 641
Sequences: 36550 22676 4330
Seq/Len: 159.61 52.61 6.76
MirrorTree (Pazo et al. 2001) 0.58
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 0.01 0.03 6.56
2 0.01 0.04 7.35
5 0.04 0.05 8.20
10 0.08 0.06 9.20
20 0.12 0.08 10.46
100 0.23 0.16 14.69
∞ 0.29 0.23 16.40
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
14_I 220_T 2.91 1.00 1.00
16_E 241_K 2.44 1.00 1.00
17_M 224_G 2.30 1.00 1.00
13_P 249_Q 1.78 1.00 0.97
108_S 227_E 1.46 0.99 0.92
21_V 228_M 1.45 0.99 0.92
23_E 238_V 1.40 0.99 0.90
20_F 242_A 1.27 0.97 0.84
16_E 245_T 1.27 0.97 0.84
17_M 225_Y 1.11 0.93 0.72
107_F 220_T 0.91 0.78 0.49
88_E 227_E 0.86 0.72 0.42
110_K 231_E 0.86 0.71 0.42
13_P 248_E 0.85 0.71 0.41
20_F 238_V 0.84 0.69 0.40
84_A 216_R 0.80 0.64 0.35
109_P 227_E 0.80 0.64 0.34
11_E 252_R 0.79 0.62 0.33
83_T 214_E 0.78 0.61 0.32
109_P 224_G 0.75 0.57 0.29
14_I 224_G 0.74 0.56 0.28
11_E 382_R 0.74 0.55 0.28
9_E 225_Y 0.74 0.55 0.28
24_Q 232_Q 0.71 0.50 0.24
158_T 249_Q 0.70 0.49 0.24
24_Q 231_E 0.70 0.49 0.23
65_I 208_F 0.67 0.45 0.21
185_G 204_R 0.66 0.42 0.19
113_V 231_E 0.66 0.42 0.19
87_E 200_L 0.65 0.41 0.18
16_E 225_Y 0.64 0.40 0.18
11_E 219_L 0.64 0.40 0.17
25_N 231_E 0.64 0.39 0.17
13_P 245_T 0.63 0.38 0.16
87_E 260_L 0.62 0.37 0.16
219_R 228_M 0.62 0.36 0.15
60_S 103_G 0.61 0.35 0.15
17_M 245_T 0.61 0.35 0.15
27_F 421_I 0.59 0.33 0.14
202_L 214_E 0.59 0.33 0.14
13_P 221_V 0.59 0.33 0.13
84_A 372_R 0.59 0.32 0.13
55_M 377_D 0.59 0.32 0.13
110_K 227_E 0.58 0.32 0.13
56_L 225_Y 0.58 0.31 0.13
14_I 219_L 0.58 0.31 0.12
109_P 231_E 0.57 0.30 0.12
196_D 207_F 0.57 0.30 0.12
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
10827 6.6 PhoB-PHoR Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.68 Done - Shared
0714 6.76 BR Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 1.00 Done
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