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OPENSEQ.org
cI_5_6_cI_9_4_tt
Genes: A B A+B
Length: 207 182 337
Sequences: 1086 870 526
Seq/Len: 5.25 4.78 1.56
MirrorTree (Pazo et al. 2001) 0.89
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 0.22
10 0.01 0.01 1.08
20 0.01 0.01 1.19
100 0.01 0.01 1.23
∞ 0.02 0.02 1.35
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
124_I 7_A 1.54 0.89 0.28
109_G 22_V 1.50 0.87 0.26
178_D 129_L 1.33 0.77 0.17
135_I 15_K 1.24 0.69 0.12
183_F 112_A 1.20 0.66 0.11
103_T 19_S 1.20 0.65 0.11
178_D 96_L 1.16 0.61 0.10
178_D 123_D 1.12 0.58 0.09
154_E 85_E 1.11 0.57 0.08
31_R 7_A 1.10 0.56 0.08
30_P 15_K 1.10 0.56 0.08
92_V 149_E 1.09 0.55 0.08
168_A 48_N 1.09 0.55 0.08
180_G 112_A 1.08 0.54 0.07
106_D 19_S 1.07 0.53 0.07
48_F 130_V 1.06 0.51 0.07
186_G 123_D 1.06 0.51 0.07
178_D 131_Y 1.05 0.51 0.07
72_Y 150_A 1.04 0.49 0.06
171_R 103_L 1.04 0.49 0.06
21_G 2_T 1.03 0.49 0.06
47_N 10_L 1.03 0.49 0.06
96_E 134_E 1.03 0.48 0.06
64_R 25_P 0.99 0.45 0.05
171_R 9_S 0.99 0.44 0.05
186_G 135_D 0.98 0.43 0.05
92_V 17_L 0.97 0.42 0.05
101_L 74_E 0.97 0.42 0.05
128_G 84_G 0.97 0.42 0.05
36_E 16_Y 0.96 0.41 0.05
174_L 5_A 0.96 0.41 0.05
88_F 112_A 0.95 0.40 0.05
11_R 10_L 0.95 0.40 0.05
29_L 74_E 0.94 0.39 0.04
130_P 2_T 0.93 0.38 0.04
122_F 149_E 0.93 0.38 0.04
38_M 107_A 0.93 0.38 0.04
121_L 85_E 0.93 0.38 0.04
154_E 96_L 0.93 0.38 0.04
121_L 5_A 0.92 0.37 0.04
77_L 85_E 0.92 0.37 0.04
77_L 10_L 0.91 0.36 0.04
187_G 103_L 0.91 0.36 0.04
88_F 11_G 0.91 0.36 0.04
108_W 28_D 0.91 0.36 0.04
97_E 15_K 0.89 0.34 0.04
26_W 62_A 0.89 0.34 0.04
119_Y 132_G 0.89 0.34 0.04
132_L 147_R 0.89 0.34 0.04
178_D 130_V 0.89 0.34 0.04
121_L 43_L 0.88 0.34 0.04
103_T 103_L 0.88 0.33 0.04
110_S 145_P 0.88 0.33 0.04
99_P 71_E 0.88 0.33 0.03
96_E 74_E 0.88 0.33 0.03
49_L 33_L 0.87 0.33 0.03
16_P 15_K 0.87 0.32 0.03
178_D 116_G 0.87 0.32 0.03
72_Y 146_Q 0.87 0.32 0.03
49_L 43_L 0.86 0.31 0.03
77_L 73_A 0.86 0.31 0.03
94_V 74_E 0.86 0.31 0.03
138_P 60_A 0.85 0.31 0.03
22_L 30_P 0.85 0.31 0.03
36_E 8_Q 0.85 0.31 0.03
85_G 116_G 0.85 0.30 0.03
49_L 130_V 0.85 0.30 0.03
187_G 96_L 0.85 0.30 0.03
144_H 24_V 0.85 0.30 0.03
142_E 118_D 0.84 0.30 0.03
104_V 134_E 0.84 0.30 0.03
124_I 134_E 0.84 0.30 0.03
146_L 122_A 0.84 0.30 0.03
32_E 142_G 0.84 0.29 0.03
180_G 100_F 0.84 0.29 0.03
84_D 126_Y 0.83 0.29 0.03
35_K 47_P 0.83 0.29 0.03
29_L 33_L 0.83 0.29 0.03
59_T 142_G 0.83 0.29 0.03
104_V 150_A 0.83 0.29 0.03
34_F 2_T 0.83 0.29 0.03
138_P 44_T 0.83 0.28 0.03
45_G 19_S 0.82 0.28 0.03
84_D 138_V 0.82 0.28 0.03
98_D 74_E 0.82 0.28 0.03
97_E 149_E 0.82 0.28 0.03
35_K 8_Q 0.81 0.28 0.03
136_L 106_E 0.81 0.27 0.03
127_E 107_A 0.81 0.27 0.03
186_G 130_V 0.81 0.27 0.03
179_P 135_D 0.81 0.27 0.03
108_W 31_V 0.81 0.27 0.03
94_V 62_A 0.81 0.27 0.03
190_K 131_Y 0.81 0.27 0.03
58_L 129_L 0.81 0.27 0.03
36_E 4_K 0.81 0.27 0.03
108_W 13_T 0.81 0.27 0.03
60_Y 6_L 0.81 0.27 0.03
16_P 145_P 0.80 0.27 0.03
53_V 16_Y 0.80 0.26 0.03
91_R 17_L 0.80 0.26 0.03
131_D 67_A 0.80 0.26 0.03
34_F 119_F 0.80 0.26 0.03
50_A 17_L 0.80 0.26 0.03
50_A 135_D 0.80 0.26 0.03
175_T 118_D 0.79 0.26 0.02
21_G 4_K 0.79 0.26 0.02
104_V 14_L 0.79 0.26 0.02
31_R 103_L 0.79 0.26 0.02
72_Y 131_Y 0.79 0.25 0.02
72_Y 117_Y 0.79 0.25 0.02
8_E 119_F 0.79 0.25 0.02
174_L 40_R 0.79 0.25 0.02
101_L 142_G 0.79 0.25 0.02
59_T 19_S 0.79 0.25 0.02
179_P 143_T 0.79 0.25 0.02
10_A 153_T 0.79 0.25 0.02
37_E 134_E 0.78 0.25 0.02
77_L 13_T 0.78 0.24 0.02
180_G 130_V 0.77 0.24 0.02
76_S 49_G 0.77 0.24 0.02
90_V 85_E 0.77 0.24 0.02
167_P 118_D 0.77 0.24 0.02
91_R 18_F 0.77 0.24 0.02
179_P 25_P 0.77 0.24 0.02
137_T 91_Y 0.77 0.24 0.02
147_R 64_P 0.77 0.24 0.02
38_M 19_S 0.76 0.23 0.02
184_Y 121_M 0.76 0.23 0.02
65_P 16_Y 0.76 0.23 0.02
61_P 139_D 0.76 0.23 0.02
65_P 25_P 0.76 0.23 0.02
138_P 57_S 0.76 0.23 0.02
155_T 13_T 0.76 0.23 0.02
15_Y 17_L 0.76 0.23 0.02
99_P 13_T 0.76 0.23 0.02
67_R 67_A 0.76 0.23 0.02
179_P 131_Y 0.76 0.23 0.02
119_Y 5_A 0.76 0.23 0.02
151_P 102_G 0.75 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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