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OPENSEQ.org
cI_5_6_cI_6_6_tt
Genes: A B A+B
Length: 207 181 348
Sequences: 1086 1588 686
Seq/Len: 5.25 8.77 1.97
MirrorTree (Pazo et al. 2001) 0.83
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 1.60
2 0.00 0.01 1.66
5 0.01 0.02 1.66
10 0.01 0.02 1.68
20 0.01 0.03 1.68
100 0.01 0.04 1.71
∞ 0.02 0.10 1.77
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
52_I 151_V 1.21 0.73 0.02
119_Y 81_A 1.20 0.73 0.02
111_A 62_R 1.20 0.72 0.02
109_G 56_A 1.15 0.67 0.02
109_G 61_A 1.11 0.64 0.01
89_F 103_K 1.10 0.63 0.01
32_E 20_L 1.09 0.62 0.01
122_F 104_W 1.07 0.60 0.01
179_P 31_G 1.03 0.56 0.01
173_A 14_L 1.02 0.55 0.01
146_L 85_S 1.01 0.53 0.01
138_P 117_M 1.01 0.53 0.01
97_E 103_K 1.01 0.53 0.01
151_P 93_R 1.00 0.52 0.01
159_F 114_S 0.99 0.51 0.01
53_V 103_K 0.97 0.49 0.01
72_Y 106_I 0.97 0.48 0.01
138_P 127_V 0.97 0.48 0.01
108_W 152_M 0.96 0.47 0.01
32_E 23_T 0.96 0.47 0.01
134_K 126_N 0.95 0.47 0.01
92_V 16_R 0.95 0.47 0.01
85_G 123_I 0.95 0.46 0.01
108_W 101_D 0.95 0.46 0.01
92_V 24_L 0.94 0.46 0.01
185_K 104_W 0.94 0.45 0.01
163_R 103_K 0.94 0.45 0.01
59_T 159_R 0.94 0.45 0.01
150_Y 118_F 0.94 0.45 0.01
124_I 135_V 0.93 0.44 0.01
121_L 161_Q 0.92 0.43 0.01
147_R 161_Q 0.91 0.42 0.01
54_G 137_V 0.91 0.42 0.01
161_E 152_M 0.91 0.42 0.01
171_R 148_I 0.91 0.42 0.01
180_G 85_S 0.91 0.41 0.01
104_V 62_R 0.90 0.41 0.01
105_T 101_D 0.90 0.41 0.01
187_G 31_G 0.90 0.41 0.01
165_I 150_A 0.90 0.41 0.01
49_L 56_A 0.90 0.41 0.01
103_T 150_A 0.90 0.40 0.01
125_V 135_V 0.89 0.40 0.01
143_G 101_D 0.89 0.40 0.01
138_P 125_Q 0.89 0.40 0.01
108_W 60_L 0.89 0.39 0.01
138_P 119_N 0.88 0.39 0.01
141_L 117_M 0.88 0.39 0.01
34_F 28_V 0.88 0.39 0.01
88_F 60_L 0.88 0.39 0.01
138_P 144_P 0.88 0.39 0.01
154_E 106_I 0.88 0.38 0.01
168_A 18_G 0.87 0.38 0.01
35_K 20_L 0.87 0.38 0.01
150_Y 86_K 0.87 0.38 0.01
25_L 58_N 0.87 0.37 0.01
92_V 122_A 0.86 0.37 0.01
125_V 148_I 0.85 0.36 0.01
27_V 135_V 0.85 0.36 0.01
141_L 125_Q 0.85 0.36 0.01
76_S 18_G 0.85 0.36 0.01
36_E 151_V 0.85 0.35 0.01
121_L 23_T 0.85 0.35 0.01
75_V 110_A 0.84 0.34 0.01
85_G 58_N 0.84 0.34 0.01
153_G 93_R 0.84 0.34 0.01
138_P 114_S 0.83 0.34 0.01
29_L 56_A 0.83 0.34 0.01
107_L 159_R 0.83 0.34 0.01
140_D 118_F 0.83 0.34 0.01
110_S 53_S 0.83 0.34 0.01
137_T 125_Q 0.83 0.34 0.01
124_I 162_A 0.83 0.33 0.01
156_P 113_S 0.82 0.33 0.01
128_G 70_A 0.82 0.33 0.01
106_D 19_I 0.81 0.32 0.01
141_L 91_V 0.81 0.32 0.01
99_P 93_R 0.81 0.32 0.01
156_P 146_A 0.80 0.31 0.01
150_Y 91_V 0.80 0.31 0.01
166_I 48_I 0.80 0.30 0.01
15_Y 21_F 0.80 0.30 0.01
52_I 53_S 0.79 0.30 0.01
146_L 53_S 0.79 0.30 0.01
150_Y 120_N 0.79 0.30 0.01
163_R 94_R 0.79 0.30 0.01
178_D 85_S 0.79 0.30 0.01
138_P 143_R 0.79 0.29 0.01
15_Y 67_V 0.78 0.29 0.01
22_L 22_T 0.78 0.29 0.01
154_E 153_Q 0.78 0.28 0.01
159_F 122_A 0.77 0.28 0.01
156_P 88_M 0.77 0.28 0.01
152_L 44_A 0.77 0.28 0.01
38_M 36_L 0.77 0.28 0.01
162_G 100_P 0.77 0.28 0.01
90_V 36_L 0.77 0.28 0.01
9_E 56_A 0.77 0.28 0.01
154_E 95_V 0.77 0.28 0.01
31_R 15_E 0.76 0.27 0.01
50_A 106_I 0.76 0.27 0.01
119_Y 21_F 0.76 0.27 0.01
97_E 56_A 0.76 0.27 0.01
140_D 119_N 0.76 0.27 0.01
110_S 100_P 0.76 0.27 0.01
50_A 100_P 0.76 0.27 0.01
63_P 148_I 0.75 0.27 0.01
143_G 113_S 0.75 0.26 0.01
91_R 148_I 0.75 0.26 0.01
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
4920 1.81 cI_5_20_cI_6_60_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4919 1.84 cI_5_10_cI_6_40_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
4918 1.94 cI_5_20_cI_6_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4917 0.03 cI_5_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
4916 1.9 cI_5_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4914 1.82 cI_5_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4913 1.97 cI_5_6_cI_6_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4912 1.86 cI_5_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
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