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OPENSEQ.org
cI_5_10_cI_9_4_tt2
Genes: A B A+B
Length: 207 182 336
Sequences: 1025 1192 511
Seq/Len: 4.95 6.55 1.52
MirrorTree (Pazo et al. 2001) 0.87
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 0.01
2 0.00 0.05 0.03
5 0.01 0.05 0.12
10 0.01 0.06 0.93
20 0.01 0.06 1.03
100 0.02 0.06 1.08
∞ 0.06 0.09 1.31
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
154_E 85_E 1.56 0.89 0.30
109_G 22_V 1.51 0.87 0.27
47_N 10_L 1.31 0.75 0.16
171_R 48_N 1.29 0.72 0.15
110_S 145_P 1.23 0.67 0.12
124_I 134_E 1.22 0.67 0.12
174_L 5_A 1.22 0.66 0.12
154_E 96_L 1.21 0.65 0.12
94_V 22_V 1.20 0.65 0.11
77_L 6_L 1.18 0.63 0.11
135_I 15_K 1.18 0.62 0.10
49_L 33_L 1.14 0.59 0.09
77_L 85_E 1.13 0.58 0.09
172_A 100_F 1.13 0.58 0.09
29_L 74_E 1.10 0.55 0.08
101_L 142_G 1.07 0.52 0.07
64_R 25_P 1.07 0.52 0.07
31_R 7_A 1.07 0.52 0.07
49_L 22_V 1.06 0.51 0.07
72_Y 146_Q 1.04 0.49 0.07
52_I 6_L 1.03 0.48 0.06
157_T 14_L 1.02 0.47 0.06
8_E 142_G 1.02 0.47 0.06
31_R 103_L 1.00 0.44 0.06
127_E 47_P 0.99 0.43 0.06
93_Y 15_K 0.99 0.43 0.05
162_G 17_L 0.99 0.43 0.05
168_A 48_N 0.98 0.43 0.05
8_E 4_K 0.98 0.42 0.05
90_V 71_E 0.98 0.42 0.05
122_F 149_E 0.97 0.41 0.05
146_L 122_A 0.97 0.41 0.05
39_A 11_G 0.97 0.41 0.05
96_E 15_K 0.96 0.41 0.05
91_R 17_L 0.95 0.39 0.05
108_W 31_V 0.94 0.39 0.05
104_V 84_G 0.94 0.39 0.05
163_R 7_A 0.94 0.39 0.05
34_F 31_V 0.94 0.38 0.04
107_L 62_A 0.94 0.38 0.04
7_L 19_S 0.93 0.38 0.04
42_K 138_V 0.93 0.37 0.04
48_F 130_V 0.92 0.36 0.04
106_D 19_S 0.91 0.36 0.04
43_A 4_K 0.90 0.35 0.04
72_Y 131_Y 0.90 0.35 0.04
109_G 151_K 0.90 0.35 0.04
77_L 73_A 0.90 0.34 0.04
104_V 134_E 0.89 0.34 0.04
118_V 33_L 0.89 0.34 0.04
77_L 13_T 0.88 0.33 0.04
84_D 126_Y 0.88 0.33 0.04
92_V 149_E 0.88 0.33 0.04
96_E 74_E 0.87 0.31 0.03
59_T 19_S 0.86 0.31 0.03
34_F 33_L 0.86 0.31 0.03
162_G 103_L 0.85 0.30 0.03
172_A 123_D 0.85 0.30 0.03
9_E 96_L 0.85 0.30 0.03
108_W 14_L 0.84 0.30 0.03
172_A 139_D 0.84 0.29 0.03
42_K 7_A 0.84 0.29 0.03
102_P 30_P 0.84 0.29 0.03
37_E 72_P 0.83 0.29 0.03
119_Y 5_A 0.83 0.29 0.03
13_K 17_L 0.83 0.28 0.03
129_H 38_H 0.83 0.28 0.03
88_F 112_A 0.83 0.28 0.03
47_N 6_L 0.83 0.28 0.03
169_E 135_D 0.83 0.28 0.03
15_Y 19_S 0.83 0.28 0.03
49_L 43_L 0.82 0.28 0.03
70_V 119_F 0.82 0.28 0.03
94_V 74_E 0.82 0.28 0.03
34_F 131_Y 0.82 0.27 0.03
152_L 130_V 0.81 0.27 0.03
97_E 134_E 0.81 0.27 0.03
62_D 152_R 0.81 0.27 0.03
119_Y 132_G 0.81 0.27 0.03
152_L 66_Y 0.81 0.27 0.03
36_E 22_V 0.81 0.27 0.03
30_P 22_V 0.80 0.26 0.03
95_P 147_R 0.80 0.26 0.03
149_D 64_P 0.80 0.26 0.03
137_T 54_I 0.80 0.26 0.03
122_F 7_A 0.80 0.26 0.03
172_A 118_D 0.80 0.26 0.03
84_D 138_V 0.80 0.26 0.03
85_G 55_G 0.80 0.26 0.03
77_L 9_S 0.79 0.25 0.02
108_W 13_T 0.79 0.25 0.02
107_L 147_R 0.79 0.25 0.02
162_G 5_A 0.79 0.25 0.02
133_R 60_A 0.79 0.25 0.02
124_I 24_V 0.79 0.25 0.02
104_V 82_S 0.79 0.25 0.02
65_P 19_S 0.79 0.25 0.02
121_L 5_A 0.78 0.25 0.02
18_E 107_A 0.78 0.24 0.02
65_P 2_T 0.78 0.24 0.02
35_K 47_P 0.78 0.24 0.02
101_L 74_E 0.78 0.24 0.02
77_L 14_L 0.78 0.24 0.02
66_E 107_A 0.78 0.24 0.02
172_A 128_D 0.78 0.24 0.02
73_E 6_L 0.78 0.24 0.02
132_L 147_R 0.78 0.24 0.02
157_T 40_R 0.78 0.24 0.02
110_S 143_T 0.77 0.24 0.02
38_M 107_A 0.77 0.24 0.02
34_F 152_R 0.77 0.24 0.02
161_E 74_E 0.77 0.24 0.02
17_I 11_G 0.77 0.24 0.02
110_S 73_A 0.77 0.23 0.02
21_G 2_T 0.77 0.23 0.02
72_Y 135_D 0.77 0.23 0.02
155_T 13_T 0.77 0.23 0.02
96_E 8_Q 0.77 0.23 0.02
112_N 62_A 0.77 0.23 0.02
176_G 24_V 0.76 0.23 0.02
147_R 64_P 0.76 0.23 0.02
181_L 112_A 0.76 0.23 0.02
4_E 12_I 0.76 0.23 0.02
117_E 53_C 0.76 0.23 0.02
117_E 56_C 0.76 0.23 0.02
117_E 59_C 0.76 0.23 0.02
117_E 98_C 0.76 0.23 0.02
117_E 108_C 0.76 0.23 0.02
117_E 109_P 0.76 0.23 0.02
123_G 53_C 0.76 0.23 0.02
123_G 56_C 0.76 0.23 0.02
123_G 59_C 0.76 0.23 0.02
123_G 98_C 0.76 0.23 0.02
123_G 108_C 0.76 0.23 0.02
123_G 109_P 0.76 0.23 0.02
21_G 4_K 0.76 0.23 0.02
90_V 4_K 0.76 0.23 0.02
141_L 57_S 0.76 0.23 0.02
31_R 146_Q 0.76 0.23 0.02
50_A 19_S 0.76 0.23 0.02
110_S 100_F 0.76 0.22 0.02
38_M 26_Y 0.75 0.22 0.02
69_A 122_A 0.75 0.22 0.02
38_M 150_A 0.75 0.22 0.02
5_R 82_S 0.75 0.22 0.02
58_L 129_L 0.75 0.22 0.02
47_N 13_T 0.75 0.22 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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