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OPENSEQ.org
cI_A_10_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 147 190 305
Sequences: 3460 1539 468
Seq/Len: 23.54 8.1 1.53
MirrorTree (Pazo et al. 2001) 0.62
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 0.01
10 0.01 0.01 0.02
20 0.01 0.01 0.03
100 0.01 0.01 0.11
∞ 0.02 0.04 1.39
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
16_F 131_V 2.28 0.99 0.98
33_G 176_I 1.43 0.82 0.67
33_G 67_L 1.38 0.79 0.63
18_I 42_M 1.36 0.78 0.61
94_E 22_A 1.32 0.76 0.57
36_F 22_A 1.24 0.69 0.49
41_A 174_L 1.16 0.61 0.40
77_I 126_L 1.09 0.54 0.33
33_G 36_W 1.07 0.52 0.31
40_R 19_L 1.07 0.51 0.30
20_L 10_D 1.06 0.51 0.30
24_I 23_T 1.05 0.50 0.29
108_F 32_G 1.04 0.49 0.28
18_I 65_T 1.04 0.49 0.28
37_L 24_A 1.01 0.45 0.25
90_T 159_Y 1.00 0.45 0.25
37_L 112_A 1.00 0.44 0.24
32_V 101_S 0.99 0.44 0.24
119_R 40_N 0.97 0.42 0.22
74_F 131_V 0.96 0.41 0.21
90_T 23_T 0.96 0.41 0.21
20_L 58_V 0.96 0.41 0.21
26_L 48_V 0.96 0.40 0.21
80_V 179_A 0.95 0.40 0.20
23_A 125_W 0.90 0.35 0.17
56_S 185_T 0.90 0.34 0.16
25_G 47_D 0.88 0.33 0.15
40_R 32_G 0.88 0.33 0.15
29_L 24_A 0.88 0.33 0.15
56_S 176_I 0.88 0.33 0.15
55_D 26_A 0.88 0.33 0.15
72_A 53_S 0.87 0.32 0.15
23_A 18_F 0.87 0.32 0.14
25_G 31_A 0.86 0.32 0.14
103_A 89_G 0.86 0.31 0.14
105_I 88_A 0.86 0.31 0.14
34_G 47_D 0.85 0.30 0.13
86_F 71_W 0.85 0.30 0.13
108_F 48_V 0.85 0.30 0.13
37_L 27_G 0.84 0.30 0.13
124_D 107_K 0.84 0.30 0.13
117_L 156_G 0.84 0.29 0.13
39_G 98_I 0.84 0.29 0.13
20_L 24_A 0.83 0.28 0.12
18_I 144_A 0.83 0.28 0.12
90_T 13_A 0.82 0.28 0.12
56_S 188_K 0.82 0.28 0.12
31_L 47_D 0.81 0.27 0.11
29_L 60_G 0.81 0.27 0.11
22_V 187_I 0.80 0.26 0.11
50_F 166_R 0.80 0.26 0.10
29_L 31_A 0.80 0.26 0.10
41_A 189_L 0.80 0.26 0.10
112_A 161_T 0.80 0.26 0.10
124_D 35_A 0.79 0.25 0.10
22_V 165_I 0.79 0.25 0.10
94_E 161_T 0.79 0.25 0.10
44_R 9_G 0.78 0.25 0.10
92_I 10_D 0.78 0.25 0.10
24_I 90_R 0.78 0.24 0.10
29_L 184_D 0.78 0.24 0.09
38_G 168_G 0.77 0.24 0.09
16_F 42_M 0.77 0.24 0.09
24_I 178_V 0.77 0.24 0.09
24_I 29_V 0.77 0.24 0.09
28_C 58_V 0.77 0.23 0.09
108_F 93_D 0.77 0.23 0.09
110_L 71_W 0.77 0.23 0.09
67_K 157_S 0.77 0.23 0.09
77_I 89_G 0.76 0.23 0.09
69_Y 32_G 0.76 0.23 0.09
40_R 70_K 0.76 0.23 0.09
112_A 21_Y 0.76 0.23 0.09
100_F 156_G 0.76 0.23 0.09
47_N 55_Q 0.76 0.23 0.08
112_A 86_I 0.76 0.23 0.08
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
2955 1.6 cI_A_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
2954 1.55 cI_A_6_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
2953 1.53 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
2952 0.99 cI_A_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.54 Done - Shared
2951 0.1 cI_A_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
2950 0.99 cI_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
2434 1.48 cI_E_cIII_isp_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.97 Done - Shared
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