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OPENSEQ.org
TTDA_TTDB
Genes: A B A+B
Length: 303 201 476
Sequences: 1104 1088 557
Seq/Len: 3.64 5.41 1.17
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 1.08
2 0.00 0.00 1.10
5 0.00 0.00 1.10
10 0.00 0.00 1.11
20 0.00 0.00 1.11
100 0.01 0.01 1.13
∞ 0.03 0.03 1.19
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 1.97 0.96 0.82
55_T 124_P 1.81 0.93 0.73
66_L 133_T 1.68 0.89 0.63
68_R 132_A 1.44 0.77 0.42
246_Q 124_P 1.22 0.58 0.23
154_G 167_I 1.19 0.56 0.21
183_S 179_K 1.14 0.51 0.18
248_L 124_P 1.13 0.50 0.17
47_S 182_F 1.11 0.48 0.16
49_G 164_I 1.09 0.46 0.15
264_R 167_I 1.08 0.45 0.14
101_V 145_E 1.08 0.45 0.14
189_A 85_S 1.07 0.44 0.14
236_E 12_E 1.05 0.42 0.13
221_R 130_L 1.04 0.42 0.13
16_E 52_N 1.04 0.41 0.12
76_E 167_I 1.02 0.40 0.12
258_H 173_N 1.02 0.40 0.12
58_D 134_Q 1.02 0.40 0.12
123_T 128_A 1.02 0.39 0.11
276_G 59_A 1.01 0.38 0.11
97_L 29_L 1.00 0.38 0.10
211_R 125_A 0.98 0.36 0.10
194_L 91_I 0.97 0.35 0.09
72_Q 76_G 0.96 0.34 0.09
222_H 5_L 0.96 0.34 0.09
219_G 138_I 0.95 0.33 0.09
62_K 129_V 0.94 0.33 0.08
191_P 83_M 0.94 0.32 0.08
116_E 5_L 0.93 0.32 0.08
232_L 18_R 0.93 0.31 0.08
147_I 154_V 0.93 0.31 0.08
49_G 183_A 0.93 0.31 0.08
179_F 182_F 0.92 0.30 0.07
60_M 59_A 0.91 0.30 0.07
225_P 15_Q 0.91 0.30 0.07
69_P 147_G 0.91 0.30 0.07
264_R 173_N 0.89 0.28 0.06
177_F 59_A 0.88 0.27 0.06
49_G 170_H 0.88 0.27 0.06
187_V 173_N 0.87 0.27 0.06
225_P 50_D 0.87 0.27 0.06
162_S 62_I 0.87 0.27 0.06
246_Q 59_A 0.87 0.26 0.06
154_G 113_C 0.87 0.26 0.06
113_N 105_M 0.86 0.26 0.06
30_P 24_Y 0.86 0.26 0.06
168_S 86_F 0.86 0.26 0.06
224_N 135_V 0.86 0.26 0.06
229_E 117_K 0.85 0.26 0.06
187_V 104_G 0.85 0.25 0.06
238_L 170_H 0.85 0.25 0.06
153_G 33_R 0.85 0.25 0.06
152_A 120_H 0.85 0.25 0.05
279_A 131_A 0.85 0.25 0.05
268_T 167_I 0.84 0.25 0.05
189_A 124_P 0.83 0.24 0.05
122_N 19_V 0.83 0.24 0.05
257_V 160_F 0.83 0.24 0.05
210_S 149_P 0.83 0.24 0.05
47_S 21_D 0.83 0.24 0.05
232_L 12_E 0.82 0.23 0.05
24_M 51_L 0.82 0.23 0.05
70_A 128_A 0.82 0.23 0.05
49_G 181_L 0.82 0.23 0.05
182_I 57_F 0.82 0.23 0.05
51_I 22_V 0.82 0.23 0.05
41_K 3_K 0.81 0.23 0.05
269_I 32_C 0.81 0.22 0.04
95_S 144_T 0.80 0.22 0.04
279_A 125_A 0.80 0.22 0.04
189_A 81_M 0.79 0.21 0.04
168_S 97_K 0.79 0.21 0.04
228_A 107_P 0.79 0.21 0.04
203_V 39_R 0.79 0.21 0.04
113_N 84_E 0.78 0.21 0.04
20_N 111_E 0.78 0.21 0.04
62_K 133_T 0.78 0.21 0.04
115_V 167_I 0.78 0.20 0.04
43_A 42_E 0.77 0.20 0.04
213_A 13_D 0.77 0.20 0.04
267_S 60_G 0.77 0.20 0.04
258_H 167_I 0.76 0.19 0.04
145_A 113_C 0.76 0.19 0.04
217_P 137_E 0.75 0.19 0.04
15_T 107_P 0.75 0.19 0.04
156_C 125_A 0.75 0.19 0.03
254_V 167_I 0.75 0.19 0.03
52_I 164_I 0.74 0.18 0.03
68_R 65_K 0.74 0.18 0.03
204_E 99_V 0.74 0.18 0.03
32_D 173_N 0.74 0.18 0.03
266_P 84_E 0.74 0.18 0.03
45_T 181_L 0.74 0.18 0.03
87_F 143_W 0.74 0.18 0.03
267_S 96_V 0.74 0.18 0.03
103_E 3_K 0.74 0.18 0.03
105_T 105_M 0.73 0.18 0.03
224_N 100_V 0.73 0.17 0.03
169_E 91_I 0.73 0.17 0.03
126_N 150_E 0.73 0.17 0.03
29_M 79_T 0.73 0.17 0.03
68_R 68_D 0.72 0.17 0.03
248_L 183_A 0.72 0.17 0.03
180_E 12_E 0.72 0.17 0.03
35_D 184_E 0.72 0.17 0.03
261_S 153_W 0.72 0.17 0.03
12_N 6_T 0.72 0.17 0.03
77_I 112_G 0.72 0.17 0.03
46_S 183_A 0.72 0.17 0.03
188_N 81_M 0.72 0.17 0.03
187_V 166_S 0.71 0.17 0.03
207_A 55_A 0.71 0.17 0.03
260_E 74_S 0.71 0.17 0.03
72_Q 120_H 0.71 0.17 0.03
194_L 14_L 0.71 0.17 0.03
189_A 122_I 0.71 0.16 0.03
138_I 46_P 0.71 0.16 0.03
259_I 12_E 0.71 0.16 0.03
199_I 44_K 0.71 0.16 0.03
153_G 61_P 0.70 0.16 0.03
113_N 123_F 0.70 0.16 0.03
45_T 170_H 0.70 0.16 0.03
167_P 83_M 0.70 0.16 0.03
139_I 130_L 0.70 0.16 0.03
193_V 62_I 0.70 0.16 0.03
204_E 96_V 0.70 0.16 0.03
256_G 25_L 0.70 0.16 0.03
102_E 43_L 0.70 0.16 0.03
111_R 33_R 0.70 0.16 0.03
189_A 9_I 0.69 0.16 0.03
89_L 106_G 0.69 0.16 0.03
166_M 118_A 0.69 0.16 0.03
13_K 107_P 0.69 0.16 0.03
33_V 128_A 0.69 0.15 0.03
165_L 39_R 0.69 0.15 0.03
204_E 163_L 0.69 0.15 0.03
105_T 58_H 0.69 0.15 0.03
267_S 75_V 0.69 0.15 0.03
278_W 123_F 0.69 0.15 0.03
276_G 135_V 0.69 0.15 0.03
70_A 132_A 0.69 0.15 0.02
61_Q 16_D 0.69 0.15 0.02
167_P 61_P 0.68 0.15 0.02
264_R 169_T 0.68 0.15 0.02
65_D 46_P 0.68 0.15 0.02
107_K 158_K 0.68 0.15 0.02
210_S 141_V 0.68 0.15 0.02
161_R 104_G 0.68 0.15 0.02
243_I 49_Y 0.68 0.15 0.02
255_M 85_S 0.68 0.15 0.02
59_N 129_V 0.68 0.15 0.02
93_L 107_P 0.68 0.15 0.02
92_E 137_E 0.67 0.15 0.02
55_T 160_F 0.67 0.15 0.02
113_N 58_H 0.67 0.14 0.02
105_T 140_E 0.67 0.14 0.02
30_P 5_L 0.67 0.14 0.02
55_T 75_V 0.67 0.14 0.02
37_L 87_E 0.67 0.14 0.02
33_V 41_I 0.67 0.14 0.02
37_L 156_R 0.67 0.14 0.02
248_L 178_N 0.67 0.14 0.02
72_Q 61_P 0.67 0.14 0.02
248_L 85_S 0.67 0.14 0.02
209_L 130_L 0.67 0.14 0.02
265_H 82_R 0.67 0.14 0.02
76_E 113_C 0.67 0.14 0.02
168_S 35_V 0.67 0.14 0.02
109_P 66_N 0.67 0.14 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
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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