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OPENSEQ.org
MFD_THETH_329_368-RPOB_THETH_17_392
Genes: A B A+B
Length: 40 182 202
Sequences: 4008 6630 204
Seq/Len: 100.2 36.43 1.01
MirrorTree (Pazo et al. 2001) 0.33
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 0.98 0.01
2 0.00 0.98 0.02
5 0.00 0.98 0.03
10 0.00 0.98 0.06
20 0.00 0.98 0.15
100 0.00 0.98 0.92
∞ 0.00 0.98 4.48
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
21_D 10_Y 2.08 0.97 0.85
9_G 80_L 1.68 0.87 0.59
26_R 5_I 1.58 0.82 0.51
31_G 91_D 1.40 0.70 0.34
25_L 142_G 1.38 0.68 0.33
12_T 97_H 1.24 0.56 0.22
7_Y 61_D 1.19 0.51 0.18
2_H 49_L 1.17 0.50 0.17
30_E 32_F 1.16 0.49 0.17
32_K 90_E 1.15 0.47 0.16
13_R 88_I 1.14 0.47 0.16
12_T 78_L 1.12 0.45 0.14
14_E 93_V 1.11 0.44 0.14
21_D 3_T 1.09 0.42 0.13
25_L 63_C 1.09 0.42 0.13
21_D 160_L 1.08 0.41 0.13
23_L 108_I 1.07 0.40 0.12
22_Y 54_G 1.06 0.40 0.12
17_G 126_E 1.04 0.38 0.11
28_K 63_C 1.04 0.38 0.11
40_L 125_G 1.04 0.38 0.11
15_V 94_F 1.04 0.38 0.11
2_H 48_F 1.03 0.36 0.10
34_Y 63_C 1.02 0.36 0.10
39_Q 98_L 1.02 0.36 0.10
40_L 42_G 0.99 0.34 0.09
13_R 79_Q 0.98 0.32 0.08
1_E 87_L 0.97 0.32 0.08
22_Y 127_L 0.97 0.32 0.08
13_R 116_I 0.97 0.32 0.08
25_L 17_D 0.97 0.32 0.08
7_Y 104_D 0.96 0.31 0.08
23_L 59_S 0.96 0.31 0.07
36_P 146_R 0.95 0.30 0.07
25_L 43_G 0.94 0.30 0.07
28_K 36_F 0.94 0.29 0.07
13_R 39_E 0.94 0.29 0.07
40_L 52_R 0.93 0.28 0.07
4_V 24_E 0.93 0.28 0.07
18_V 159_K 0.93 0.28 0.07
39_Q 57_P 0.92 0.28 0.07
31_G 43_G 0.92 0.28 0.07
37_V 131_Q 0.91 0.27 0.06
37_V 77_R 0.91 0.27 0.06
17_G 103_E 0.91 0.27 0.06
29_G 59_S 0.91 0.27 0.06
35_L 20_P 0.91 0.27 0.06
2_H 93_V 0.91 0.27 0.06
2_H 106_S 0.90 0.26 0.06
35_L 75_Y 0.89 0.26 0.06
25_L 76_A 0.89 0.26 0.06
24_V 155_L 0.89 0.25 0.06
37_V 98_L 0.88 0.25 0.06
21_D 141_R 0.88 0.25 0.05
2_H 105_G 0.88 0.25 0.05
11_E 104_D 0.88 0.25 0.05
7_Y 50_E 0.88 0.25 0.05
40_L 56_P 0.87 0.24 0.05
12_T 103_E 0.87 0.24 0.05
22_Y 30_A 0.86 0.24 0.05
4_V 98_L 0.86 0.24 0.05
22_Y 152_P 0.86 0.23 0.05
29_G 44_L 0.86 0.23 0.05
20_R 34_E 0.85 0.23 0.05
8_L 11_K 0.85 0.23 0.05
4_V 140_A 0.85 0.23 0.05
10_L 141_R 0.84 0.23 0.04
39_Q 116_I 0.84 0.22 0.04
16_L 28_I 0.84 0.22 0.04
7_Y 132_F 0.84 0.22 0.04
11_E 142_G 0.83 0.22 0.04
22_Y 82_H 0.83 0.22 0.04
25_L 132_F 0.83 0.21 0.04
21_D 40_E 0.82 0.21 0.04
10_L 140_A 0.82 0.21 0.04
22_Y 120_G 0.81 0.21 0.04
22_Y 86_G 0.81 0.21 0.04
6_Q 104_D 0.81 0.20 0.04
28_K 106_S 0.80 0.20 0.04
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)
WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.98 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
7851 1.01 MFD_THETH_329_368-RPOB_THETH_17_392 Δgene:(1, 100) A:(1E-02, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.85 Done - Shared
7850 0 MFD_THETH_329_368-RPOB_THETH_17_392 Δgene:(1, 100) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
7849 0 MFD_THETH_329_368-RPOB_THETH_17_392 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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