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OPENSEQ.org
cI_A_10_cIII_isp_10_pdenitr
Genes: A B A+B
Length: 121 190 303
Sequences: 4764 1539 475
Seq/Len: 39.37 8.1 1.57
MirrorTree (Pazo et al. 2001) 0.60
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.02
10 0.00 0.01 0.02
20 0.00 0.01 0.03
100 0.01 0.01 0.12
∞ 0.02 0.04 1.53
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
11_I 131_V 2.34 1.00 0.98
28_A 176_I 1.51 0.88 0.76
13_V 42_M 1.38 0.80 0.65
28_A 67_L 1.35 0.79 0.62
31_V 22_A 1.28 0.73 0.55
89_S 22_A 1.28 0.73 0.55
28_A 36_W 1.18 0.64 0.44
36_N 174_L 1.10 0.56 0.35
27_L 101_S 1.10 0.55 0.35
72_I 126_L 1.07 0.53 0.33
69_L 131_V 1.07 0.53 0.33
32_I 24_A 1.06 0.51 0.31
85_V 23_T 1.03 0.48 0.28
13_V 65_T 1.02 0.48 0.28
33_A 28_T 1.01 0.47 0.27
15_L 58_V 1.01 0.46 0.26
15_L 10_D 1.00 0.45 0.25
35_R 19_L 0.99 0.45 0.25
51_A 176_I 0.99 0.44 0.24
85_V 159_Y 0.98 0.44 0.24
119_E 107_K 0.98 0.44 0.24
51_A 185_T 0.98 0.43 0.24
103_A 32_G 0.97 0.42 0.23
23_I 58_V 0.96 0.42 0.22
75_L 179_A 0.96 0.41 0.22
98_L 89_G 0.96 0.41 0.22
114_K 175_H 0.96 0.41 0.22
28_A 131_V 0.93 0.39 0.20
24_V 60_G 0.92 0.37 0.19
67_S 53_S 0.92 0.37 0.19
20_A 47_D 0.92 0.37 0.18
20_A 31_A 0.91 0.36 0.18
85_V 13_A 0.91 0.36 0.18
23_I 32_G 0.90 0.35 0.17
24_V 184_D 0.90 0.35 0.17
51_A 188_K 0.90 0.35 0.17
36_N 189_L 0.89 0.34 0.16
5_L 33_A 0.89 0.34 0.16
13_V 144_A 0.87 0.33 0.15
112_E 156_G 0.87 0.33 0.15
103_A 48_V 0.87 0.32 0.15
45_Y 166_R 0.86 0.32 0.15
96_W 39_V 0.86 0.32 0.15
21_L 48_V 0.86 0.32 0.14
32_I 27_G 0.85 0.30 0.14
19_S 174_L 0.84 0.30 0.13
114_K 40_N 0.84 0.30 0.13
81_F 71_W 0.83 0.29 0.13
18_A 18_F 0.83 0.29 0.13
17_M 187_I 0.82 0.28 0.12
18_A 125_W 0.82 0.28 0.12
50_N 26_A 0.82 0.28 0.12
17_M 165_I 0.82 0.28 0.12
33_A 168_G 0.81 0.28 0.12
31_V 105_S 0.81 0.27 0.12
35_R 32_G 0.81 0.27 0.12
16_G 47_D 0.81 0.27 0.12
62_R 157_S 0.81 0.27 0.11
26_I 47_D 0.81 0.27 0.11
87_F 10_D 0.81 0.27 0.11
32_I 112_A 0.81 0.27 0.11
15_L 24_A 0.80 0.27 0.11
103_A 93_D 0.80 0.27 0.11
86_S 10_D 0.80 0.26 0.11
110_A 35_A 0.80 0.26 0.11
16_G 98_I 0.80 0.26 0.11
117_A 130_G 0.80 0.26 0.11
87_F 24_A 0.80 0.26 0.11
100_V 88_A 0.80 0.26 0.11
19_S 23_T 0.79 0.26 0.11
11_I 10_D 0.79 0.26 0.10
104_V 25_G 0.77 0.24 0.10
119_E 35_A 0.77 0.24 0.10
103_A 12_G 0.77 0.24 0.10
26_I 34_A 0.77 0.24 0.10
42_V 55_Q 0.76 0.23 0.09
19_S 90_R 0.76 0.23 0.09
95_F 150_W 0.76 0.23 0.09
6_Q 66_Q 0.76 0.23 0.09
19_S 29_V 0.76 0.23 0.09
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
3485 1.57 cI_A_10_cIII_isp_10_pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
2518 1.59 cI_A_cIII_isp_Pnitri Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
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