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OPENSEQ.org
cI_A_10_cIII_isp_6_Pdenitr
Genes: A B A+B
Length: 147 190 305
Sequences: 3460 1587 487
Seq/Len: 23.54 8.35 1.6
MirrorTree (Pazo et al. 2001) 0.61
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 1.45
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 2.04 0.98 0.94
36_F 22_A 1.48 0.86 0.69
33_G 36_W 1.45 0.85 0.67
33_G 67_L 1.38 0.81 0.59
94_E 22_A 1.35 0.79 0.57
18_I 42_M 1.35 0.79 0.56
41_A 174_L 1.22 0.68 0.43
108_F 32_G 1.22 0.68 0.43
33_G 176_I 1.16 0.63 0.38
40_R 19_L 1.13 0.59 0.34
20_L 10_D 1.13 0.59 0.34
24_I 174_L 1.07 0.53 0.28
39_G 98_I 1.04 0.50 0.26
99_G 56_V 1.01 0.47 0.23
16_F 42_M 1.00 0.46 0.22
91_S 109_D 0.99 0.44 0.21
24_I 23_T 0.98 0.44 0.21
41_A 189_L 0.98 0.43 0.20
98_V 38_L 0.95 0.41 0.18
80_V 179_A 0.94 0.40 0.18
37_L 27_G 0.94 0.40 0.17
112_A 140_I 0.92 0.38 0.16
29_L 184_D 0.92 0.37 0.16
37_L 24_A 0.91 0.36 0.15
29_L 31_A 0.91 0.36 0.15
24_I 115_E 0.88 0.34 0.14
119_R 40_N 0.87 0.33 0.13
119_R 140_I 0.87 0.33 0.13
24_I 58_V 0.87 0.33 0.13
77_I 126_L 0.86 0.32 0.13
37_L 140_I 0.86 0.32 0.12
37_L 185_T 0.86 0.32 0.12
112_A 120_D 0.85 0.31 0.12
92_I 10_D 0.85 0.31 0.12
86_F 32_G 0.85 0.31 0.12
36_F 107_K 0.85 0.31 0.12
23_A 18_F 0.84 0.31 0.12
108_F 12_G 0.84 0.31 0.12
55_D 26_A 0.84 0.30 0.11
100_F 13_A 0.84 0.30 0.11
26_L 48_V 0.83 0.30 0.11
23_A 125_W 0.83 0.30 0.11
90_T 159_Y 0.83 0.29 0.11
8_E 12_G 0.82 0.29 0.11
90_T 13_A 0.82 0.28 0.10
74_F 131_V 0.82 0.28 0.10
50_F 166_R 0.81 0.28 0.10
24_I 183_D 0.81 0.28 0.10
115_V 83_E 0.81 0.28 0.10
18_I 65_T 0.81 0.28 0.10
41_A 142_D 0.80 0.27 0.10
24_I 124_E 0.80 0.27 0.10
29_L 24_A 0.80 0.26 0.09
77_I 66_Q 0.79 0.26 0.09
44_R 9_G 0.79 0.26 0.09
112_A 69_V 0.78 0.25 0.09
38_G 168_G 0.78 0.25 0.09
37_L 175_H 0.78 0.25 0.09
10_I 33_A 0.78 0.25 0.09
38_G 28_T 0.77 0.24 0.08
112_A 86_I 0.76 0.24 0.08
77_I 87_Q 0.76 0.24 0.08
27_C 31_A 0.76 0.24 0.08
69_Y 32_G 0.76 0.23 0.08
88_W 174_L 0.76 0.23 0.08
94_E 161_T 0.75 0.23 0.08
68_F 178_V 0.75 0.23 0.07
25_G 47_D 0.75 0.23 0.07
24_I 180_E 0.74 0.22 0.07
89_S 172_Q 0.74 0.22 0.07
20_L 58_V 0.74 0.22 0.07
29_L 159_Y 0.74 0.22 0.07
91_S 10_D 0.74 0.22 0.07
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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