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OPENSEQ.org
cI_5_6_cI_9_6_tt
Genes: A B A+B
Length: 207 182 339
Sequences: 1086 855 572
Seq/Len: 5.25 4.7 1.69
MirrorTree (Pazo et al. 2001) 0.92
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 0.00 0.01
2 0.00 0.00 0.05
5 0.01 0.01 0.33
10 0.01 0.01 1.23
20 0.01 0.01 1.33
100 0.01 0.01 1.38
∞ 0.02 0.03 1.47
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
109_G 22_V 1.48 0.87 0.22
154_E 85_E 1.33 0.79 0.15
23_G 153_T 1.27 0.74 0.12
124_I 134_E 1.23 0.70 0.11
178_D 129_L 1.22 0.70 0.11
187_G 103_L 1.21 0.69 0.10
36_E 16_Y 1.20 0.68 0.10
30_P 15_K 1.19 0.67 0.10
11_R 10_L 1.19 0.67 0.10
183_F 112_A 1.17 0.65 0.09
178_D 96_L 1.14 0.62 0.08
108_W 13_T 1.11 0.59 0.08
92_V 149_E 1.10 0.58 0.07
178_D 131_Y 1.08 0.56 0.07
121_L 24_V 1.07 0.55 0.07
31_R 7_A 1.07 0.55 0.07
48_F 130_V 1.06 0.54 0.06
38_M 19_S 1.05 0.52 0.06
178_D 123_D 1.05 0.52 0.06
36_E 8_Q 1.05 0.52 0.06
180_G 112_A 1.03 0.51 0.06
168_A 48_N 1.03 0.51 0.06
49_L 43_L 1.03 0.51 0.06
68_F 29_A 1.03 0.51 0.06
92_V 17_L 1.02 0.49 0.06
105_T 73_A 1.01 0.49 0.05
96_E 134_E 1.01 0.48 0.05
121_L 5_A 1.01 0.48 0.05
102_P 30_P 1.00 0.47 0.05
186_G 123_D 0.99 0.47 0.05
124_I 7_A 0.99 0.47 0.05
85_G 116_G 0.99 0.46 0.05
174_L 5_A 0.99 0.46 0.05
138_P 97_R 0.98 0.45 0.05
49_L 33_L 0.98 0.45 0.05
107_L 2_T 0.97 0.45 0.05
154_E 96_L 0.97 0.45 0.05
171_R 9_S 0.96 0.44 0.04
121_L 85_E 0.96 0.43 0.04
77_L 85_E 0.95 0.42 0.04
108_W 22_V 0.95 0.42 0.04
16_P 15_K 0.94 0.41 0.04
37_E 134_E 0.93 0.40 0.04
135_I 15_K 0.92 0.39 0.04
78_P 71_E 0.91 0.38 0.04
35_K 7_A 0.91 0.38 0.04
178_D 130_V 0.91 0.38 0.04
11_R 4_K 0.90 0.37 0.04
108_W 31_V 0.90 0.37 0.04
38_M 107_A 0.89 0.36 0.03
186_G 135_D 0.89 0.36 0.03
29_L 74_E 0.89 0.36 0.03
103_T 19_S 0.89 0.35 0.03
104_V 117_Y 0.88 0.35 0.03
161_E 74_E 0.87 0.34 0.03
106_D 19_S 0.87 0.34 0.03
96_E 74_E 0.87 0.34 0.03
72_Y 150_A 0.86 0.33 0.03
84_D 126_Y 0.85 0.33 0.03
40_H 119_F 0.85 0.32 0.03
94_V 74_E 0.85 0.32 0.03
127_E 47_P 0.85 0.32 0.03
121_L 149_E 0.85 0.32 0.03
90_V 135_D 0.85 0.32 0.03
72_Y 117_Y 0.85 0.32 0.03
191_G 129_L 0.84 0.31 0.03
15_Y 7_A 0.84 0.31 0.03
108_W 28_D 0.84 0.31 0.03
86_S 7_A 0.83 0.30 0.03
138_P 94_N 0.83 0.30 0.03
8_E 17_L 0.83 0.30 0.03
187_G 96_L 0.82 0.30 0.03
190_K 131_Y 0.82 0.29 0.03
141_L 92_E 0.82 0.29 0.03
50_A 135_D 0.82 0.29 0.03
26_W 24_V 0.81 0.29 0.03
153_G 91_Y 0.81 0.28 0.02
119_Y 5_A 0.81 0.28 0.02
64_R 25_P 0.81 0.28 0.02
153_G 114_V 0.81 0.28 0.02
98_D 72_P 0.81 0.28 0.02
125_V 103_L 0.81 0.28 0.02
138_P 60_A 0.80 0.28 0.02
160_R 144_K 0.80 0.28 0.02
58_L 131_Y 0.80 0.28 0.02
8_E 4_K 0.80 0.28 0.02
84_D 138_V 0.80 0.28 0.02
59_T 142_G 0.80 0.28 0.02
49_L 130_V 0.80 0.28 0.02
119_Y 147_R 0.80 0.28 0.02
101_L 16_Y 0.80 0.27 0.02
141_L 97_R 0.79 0.27 0.02
55_L 10_L 0.79 0.27 0.02
90_V 10_L 0.79 0.27 0.02
97_E 149_E 0.79 0.27 0.02
174_L 40_R 0.79 0.27 0.02
121_L 82_S 0.79 0.27 0.02
72_Y 131_Y 0.79 0.27 0.02
146_L 122_A 0.79 0.27 0.02
179_P 143_T 0.79 0.27 0.02
74_L 13_T 0.78 0.26 0.02
88_F 112_A 0.78 0.26 0.02
186_G 130_V 0.78 0.26 0.02
8_E 119_F 0.78 0.26 0.02
29_L 7_A 0.78 0.26 0.02
108_W 20_K 0.78 0.26 0.02
21_G 4_K 0.78 0.26 0.02
33_R 8_Q 0.78 0.26 0.02
142_E 118_D 0.77 0.26 0.02
140_D 70_V 0.77 0.26 0.02
110_S 145_P 0.77 0.25 0.02
135_I 133_K 0.77 0.25 0.02
21_G 2_T 0.77 0.25 0.02
54_G 17_L 0.77 0.25 0.02
179_P 96_L 0.77 0.25 0.02
34_F 119_F 0.77 0.25 0.02
38_M 152_R 0.77 0.25 0.02
45_G 19_S 0.76 0.25 0.02
96_E 72_P 0.76 0.25 0.02
53_V 16_Y 0.76 0.25 0.02
21_G 72_P 0.76 0.25 0.02
179_P 131_Y 0.76 0.24 0.02
118_V 24_V 0.76 0.24 0.02
10_A 153_T 0.76 0.24 0.02
48_F 10_L 0.76 0.24 0.02
119_Y 8_Q 0.76 0.24 0.02
99_P 10_L 0.76 0.24 0.02
23_G 4_K 0.75 0.24 0.02
175_T 118_D 0.75 0.24 0.02
37_E 11_G 0.75 0.24 0.02
59_T 19_S 0.75 0.24 0.02
178_D 121_M 0.75 0.24 0.02
187_G 128_D 0.75 0.24 0.02
43_A 4_K 0.75 0.24 0.02
37_E 138_V 0.75 0.24 0.02
184_Y 121_M 0.75 0.24 0.02
71_V 100_F 0.75 0.24 0.02
6_V 126_Y 0.75 0.23 0.02
71_V 133_K 0.75 0.23 0.02
95_P 147_R 0.74 0.23 0.02
156_P 113_I 0.74 0.23 0.02
122_F 149_E 0.74 0.23 0.02
179_P 135_D 0.74 0.23 0.02
97_E 15_K 0.74 0.23 0.02
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
4911 1.52 cI_5_10_cI_9_4_tt2 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4910 1.59 cI_5_6_cI_2_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4909 1.52 cI_5_10_cI_9_4_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4908 1.56 cI_5_6_cI_9_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4907 1.7 cI_5_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4906 1.69 cI_5_6_cI_9_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4905 1.52 cI_5_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4904 0.04 cI_5_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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