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OPENSEQ.org
cI_6_40_cI_9_20_tt
Genes: A B A+B
Length: 181 182 328
Sequences: 1163 979 681
Seq/Len: 6.43 5.38 2.08
MirrorTree (Pazo et al. 2001) 0.76
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 0.01 0.12
2 0.01 0.01 0.16
5 0.01 0.01 0.61
10 0.02 0.02 1.64
20 0.02 0.02 1.67
100 0.03 0.03 1.73
∞ 0.08 0.07 1.88
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
149_Y 122_A 1.49 0.91 0.45
135_V 124_Y 1.47 0.91 0.44
149_Y 120_E 1.47 0.91 0.43
63_F 28_D 1.37 0.86 0.35
58_N 31_V 1.29 0.81 0.29
86_K 70_V 1.22 0.75 0.24
117_M 99_I 1.20 0.74 0.23
113_S 35_P 1.16 0.71 0.20
130_V 54_I 1.15 0.69 0.20
125_Q 97_R 1.15 0.69 0.19
92_M 29_A 1.14 0.69 0.19
58_N 24_V 1.13 0.68 0.18
152_M 30_P 1.12 0.67 0.18
18_G 102_G 1.10 0.65 0.17
151_V 65_A 1.09 0.63 0.16
39_A 91_Y 1.09 0.63 0.16
159_R 100_F 1.08 0.62 0.16
19_I 119_F 1.06 0.60 0.15
57_R 24_V 1.06 0.60 0.15
107_S 21_P 1.06 0.60 0.14
122_A 133_K 1.05 0.59 0.14
103_K 122_A 1.04 0.58 0.14
88_M 129_L 1.03 0.57 0.13
143_R 37_F 1.02 0.56 0.13
85_S 10_L 1.01 0.54 0.12
150_A 31_V 1.00 0.53 0.12
159_R 103_L 0.99 0.53 0.11
130_V 103_L 0.98 0.51 0.11
51_M 9_S 0.97 0.50 0.11
113_S 96_L 0.96 0.49 0.10
60_L 25_P 0.95 0.48 0.10
104_W 37_F 0.95 0.47 0.10
103_K 12_I 0.94 0.47 0.10
119_N 67_A 0.93 0.46 0.09
147_L 76_D 0.93 0.46 0.09
151_V 76_D 0.92 0.45 0.09
18_G 67_A 0.92 0.45 0.09
153_Q 124_Y 0.92 0.44 0.09
137_V 20_K 0.91 0.44 0.09
117_M 97_R 0.90 0.43 0.08
61_A 54_I 0.90 0.42 0.08
150_A 123_D 0.90 0.42 0.08
117_M 65_A 0.89 0.42 0.08
44_A 9_S 0.89 0.41 0.08
152_M 62_A 0.89 0.41 0.08
74_Q 103_L 0.89 0.41 0.08
137_V 16_Y 0.89 0.41 0.08
61_A 28_D 0.89 0.41 0.08
107_S 44_T 0.89 0.41 0.08
154_L 62_A 0.88 0.40 0.07
75_A 137_L 0.88 0.40 0.07
123_I 123_D 0.88 0.40 0.07
154_L 7_A 0.88 0.40 0.07
77_V 34_K 0.87 0.39 0.07
128_D 126_Y 0.87 0.39 0.07
151_V 128_D 0.87 0.39 0.07
92_M 18_F 0.86 0.38 0.07
21_F 125_E 0.86 0.38 0.07
145_E 119_F 0.86 0.38 0.07
137_V 102_G 0.85 0.37 0.07
125_Q 107_A 0.85 0.37 0.07
118_F 37_F 0.85 0.37 0.07
61_A 5_A 0.84 0.36 0.06
71_S 128_D 0.84 0.36 0.06
141_P 64_P 0.84 0.35 0.06
145_E 124_Y 0.84 0.35 0.06
138_P 120_E 0.84 0.35 0.06
13_E 18_F 0.83 0.35 0.06
113_S 85_E 0.83 0.35 0.06
71_S 62_A 0.83 0.35 0.06
56_A 22_V 0.82 0.34 0.06
94_R 66_Y 0.82 0.34 0.06
119_N 97_R 0.82 0.34 0.06
131_V 90_V 0.82 0.34 0.06
154_L 120_E 0.82 0.34 0.06
138_P 100_F 0.81 0.33 0.06
92_M 11_G 0.81 0.33 0.06
41_F 68_I 0.81 0.33 0.05
152_M 32_A 0.81 0.32 0.05
88_M 37_F 0.81 0.32 0.05
34_N 134_E 0.81 0.32 0.05
147_L 122_A 0.80 0.32 0.05
131_V 49_G 0.80 0.32 0.05
126_N 106_E 0.80 0.32 0.05
18_G 71_E 0.80 0.32 0.05
103_K 4_K 0.80 0.32 0.05
86_K 105_E 0.80 0.32 0.05
155_Q 91_Y 0.80 0.31 0.05
24_L 62_A 0.79 0.31 0.05
103_K 105_E 0.78 0.30 0.05
21_F 76_D 0.78 0.30 0.05
67_V 54_I 0.78 0.30 0.05
107_S 113_I 0.78 0.29 0.05
78_M 121_M 0.77 0.29 0.05
130_V 71_E 0.77 0.29 0.05
58_N 68_I 0.77 0.29 0.05
43_L 55_G 0.77 0.28 0.04
107_S 51_E 0.76 0.28 0.04
47_A 86_R 0.76 0.28 0.04
36_L 12_I 0.76 0.28 0.04
28_V 48_N 0.76 0.28 0.04
106_I 116_G 0.76 0.28 0.04
101_D 31_V 0.76 0.28 0.04
19_I 11_G 0.76 0.28 0.04
107_S 65_A 0.76 0.28 0.04
93_R 51_E 0.75 0.28 0.04
138_P 122_A 0.75 0.27 0.04
145_E 105_E 0.75 0.27 0.04
20_L 7_A 0.75 0.27 0.04
30_W 93_I 0.75 0.27 0.04
34_N 94_N 0.75 0.27 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)
ID Seq/Len Name Options I_Prob Status
4979 0.57 cI_6_20_cI_9_60_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
4978 0.56 cI_6_60_cI_9_60_tt Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
4977 0.56 cI_6_40_cI_9_60_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.90 Done - Shared
4976 2.08 cI_6_40_cI_9_20_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.45 Done - Shared
4975 1.47 cI_6_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.64 Done - Shared
4974 1.46 cI_6_20_cI_9_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.63 Done - Shared
4972 1.85 cI_6_20_cI_9_10_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
4971 2.05 cI_6_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.59 Done - Shared
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