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OPENSEQ.org
TTDA_TTDB
Genes: A B A+B
Length: 303 201 478
Sequences: 1104 1088 991
Seq/Len: 3.64 5.41 2.07
MirrorTree (Pazo et al. 2001) 0.93
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 1.97
2 0.00 0.00 2.00
5 0.00 0.00 2.00
10 0.00 0.00 2.00
20 0.00 0.00 2.00
100 0.01 0.01 2.03
∞ 0.03 0.03 2.09
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
168_S 85_S 1.93 0.99 0.94
55_T 124_P 1.89 0.98 0.94
66_L 133_T 1.62 0.95 0.85
68_R 132_A 1.56 0.94 0.82
55_T 130_L 1.22 0.76 0.54
248_L 124_P 1.19 0.72 0.50
51_I 22_V 1.09 0.63 0.39
183_S 179_K 1.09 0.63 0.39
62_K 129_V 1.08 0.62 0.38
276_G 59_A 1.05 0.59 0.35
246_Q 124_P 1.04 0.57 0.34
211_R 125_A 1.03 0.57 0.34
191_P 83_M 1.00 0.53 0.30
221_R 130_L 0.99 0.53 0.30
154_G 167_I 0.99 0.52 0.29
168_S 86_F 0.97 0.50 0.28
47_S 182_F 0.97 0.50 0.27
72_Q 76_G 0.96 0.49 0.27
248_L 85_S 0.95 0.47 0.25
123_T 128_A 0.94 0.47 0.25
279_A 125_A 0.92 0.45 0.23
69_P 147_G 0.92 0.44 0.23
76_E 167_I 0.91 0.43 0.22
87_F 143_W 0.90 0.42 0.21
154_G 113_C 0.90 0.42 0.21
116_E 5_L 0.89 0.41 0.21
246_Q 59_A 0.89 0.41 0.21
258_H 173_N 0.89 0.41 0.20
113_N 105_M 0.88 0.40 0.20
60_M 59_A 0.88 0.40 0.19
279_A 131_A 0.87 0.39 0.19
264_R 167_I 0.87 0.39 0.19
58_D 134_Q 0.86 0.38 0.18
153_G 33_R 0.86 0.38 0.18
113_N 84_E 0.86 0.38 0.18
256_G 25_L 0.86 0.38 0.18
269_I 32_C 0.85 0.37 0.17
187_V 104_G 0.85 0.37 0.17
188_N 81_M 0.85 0.36 0.17
101_V 145_E 0.83 0.35 0.16
231_E 103_G 0.82 0.34 0.15
210_S 149_P 0.81 0.33 0.14
152_A 120_H 0.80 0.32 0.14
35_D 184_E 0.80 0.32 0.14
105_T 140_E 0.79 0.31 0.13
177_F 59_A 0.79 0.30 0.13
229_E 117_K 0.78 0.30 0.13
148_E 145_E 0.78 0.30 0.13
189_A 124_P 0.78 0.30 0.13
189_A 85_S 0.78 0.30 0.13
68_R 68_D 0.78 0.30 0.13
174_V 18_R 0.78 0.30 0.13
179_F 182_F 0.78 0.29 0.12
93_L 107_P 0.77 0.29 0.12
122_N 19_V 0.77 0.29 0.12
243_I 143_W 0.77 0.29 0.12
16_E 52_N 0.77 0.29 0.12
224_N 135_V 0.77 0.29 0.12
231_E 8_P 0.76 0.28 0.12
246_Q 24_Y 0.76 0.28 0.12
60_M 81_M 0.76 0.28 0.12
266_P 148_M 0.76 0.28 0.11
62_K 133_T 0.76 0.28 0.11
156_C 125_A 0.76 0.28 0.11
68_R 65_K 0.76 0.28 0.11
55_T 75_V 0.75 0.27 0.11
42_D 92_E 0.75 0.27 0.11
81_V 140_E 0.75 0.27 0.11
49_G 183_A 0.75 0.27 0.11
105_T 105_M 0.75 0.27 0.11
224_N 100_V 0.75 0.27 0.11
24_M 51_L 0.74 0.27 0.11
47_S 21_D 0.74 0.27 0.11
41_K 3_K 0.74 0.27 0.11
160_G 23_I 0.74 0.27 0.11
188_N 175_I 0.74 0.27 0.11
264_R 173_N 0.74 0.26 0.10
130_G 58_H 0.74 0.26 0.10
193_V 62_I 0.74 0.26 0.10
273_V 136_E 0.74 0.26 0.10
162_S 62_I 0.74 0.26 0.10
85_S 143_W 0.74 0.26 0.10
169_E 160_F 0.74 0.26 0.10
82_K 156_R 0.74 0.26 0.10
50_K 115_K 0.73 0.26 0.10
130_G 73_V 0.73 0.26 0.10
187_V 166_S 0.73 0.25 0.10
50_K 136_E 0.72 0.25 0.10
169_E 91_I 0.72 0.25 0.10
204_E 96_V 0.72 0.24 0.10
147_I 154_V 0.72 0.24 0.10
267_S 60_G 0.72 0.24 0.09
203_V 39_R 0.72 0.24 0.09
222_H 5_L 0.72 0.24 0.09
49_G 181_L 0.71 0.24 0.09
41_K 132_A 0.71 0.24 0.09
257_V 160_F 0.71 0.24 0.09
260_E 74_S 0.71 0.24 0.09
49_G 170_H 0.71 0.24 0.09
97_L 90_F 0.71 0.24 0.09
248_L 183_A 0.71 0.24 0.09
248_L 122_I 0.71 0.24 0.09
77_I 135_V 0.71 0.24 0.09
207_A 55_A 0.71 0.24 0.09
126_N 150_E 0.71 0.23 0.09
105_T 58_H 0.71 0.23 0.09
50_K 145_E 0.71 0.23 0.09
56_M 166_S 0.71 0.23 0.09
279_A 37_H 0.70 0.23 0.09
189_A 81_M 0.70 0.23 0.09
42_D 140_E 0.70 0.23 0.09
49_G 164_I 0.70 0.23 0.09
72_Q 34_D 0.70 0.23 0.09
30_P 24_Y 0.70 0.23 0.09
219_G 138_I 0.70 0.23 0.09
246_Q 22_V 0.70 0.23 0.08
153_G 61_P 0.70 0.23 0.08
189_A 9_I 0.69 0.22 0.08
72_Q 61_P 0.69 0.22 0.08
113_N 58_H 0.69 0.22 0.08
50_K 139_E 0.69 0.22 0.08
204_E 163_L 0.69 0.22 0.08
138_I 46_P 0.69 0.22 0.08
29_M 134_Q 0.69 0.22 0.08
130_G 105_M 0.69 0.22 0.08
273_V 46_P 0.69 0.22 0.08
239_N 20_G 0.69 0.22 0.08
186_A 83_M 0.68 0.22 0.08
109_P 66_N 0.68 0.21 0.08
265_H 83_M 0.68 0.21 0.08
52_I 164_I 0.68 0.21 0.08
69_P 77_P 0.68 0.21 0.08
158_L 125_A 0.68 0.21 0.07
187_V 173_N 0.68 0.21 0.07
180_E 12_E 0.68 0.21 0.07
199_I 111_E 0.67 0.21 0.07
61_Q 166_S 0.67 0.21 0.07
145_A 14_L 0.67 0.21 0.07
31_D 108_L 0.67 0.20 0.07
178_V 177_E 0.67 0.20 0.07
236_E 156_R 0.67 0.20 0.07
15_T 111_E 0.67 0.20 0.07
169_E 87_E 0.67 0.20 0.07
89_L 106_G 0.67 0.20 0.07
273_V 174_L 0.67 0.20 0.07
113_N 59_A 0.67 0.20 0.07
70_A 130_L 0.66 0.20 0.07
115_V 167_I 0.66 0.20 0.07
178_V 12_E 0.66 0.20 0.07
111_R 33_R 0.66 0.20 0.07
217_P 158_K 0.66 0.20 0.07
72_Q 83_M 0.66 0.20 0.07
180_E 42_E 0.66 0.20 0.07
61_Q 44_K 0.66 0.20 0.07
107_K 158_K 0.66 0.20 0.07
261_S 153_W 0.66 0.20 0.07
124_G 105_M 0.66 0.20 0.07
95_S 52_N 0.66 0.19 0.07
259_I 12_E 0.66 0.19 0.07
50_K 52_N 0.66 0.19 0.07
45_T 181_L 0.66 0.19 0.07
168_S 144_T 0.65 0.19 0.07
115_V 130_L 0.65 0.19 0.07
199_I 44_K 0.65 0.19 0.07
220_S 167_I 0.65 0.19 0.07
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
7294 3.17 EcoliTtd-JAck Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.99 Done - Shared
7293 1.31 EcoliTtd Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.93 Done
0882 2.07 TTDA_TTDB Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.94 Done
0881 1.17 TTDA_TTDB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.82 Done
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