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OPENSEQ.org
TmEncFlp
Genes: A B A+B
Length: 265 114 376
Sequences: 542 142 53
Seq/Len: 2.05 1.25 0.14
MirrorTree (Pazo et al. 2001) 0.61
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.14
2 0.00 0.00 0.14
5 0.00 0.00 0.14
10 0.00 0.00 0.14
20 0.00 0.00 0.14
100 0.00 0.00 0.14
∞ 0.02 0.01 0.15
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
60_D 23_L 1.45 0.23 0.00
173_N 30_I 1.41 0.22 0.00
69_L 89_K 1.40 0.21 0.00
237_R 111_I 1.36 0.20 0.00
188_Y 50_K 1.33 0.19 0.00
33_G 3_D 1.32 0.18 0.00
212_A 21_R 1.31 0.18 0.00
32_Y 60_M 1.31 0.18 0.00
224_L 34_A 1.31 0.18 0.00
51_P 40_V 1.30 0.18 0.00
159_F 48_V 1.30 0.18 0.00
169_T 113_K 1.23 0.16 0.00
80_A 23_L 1.22 0.15 0.00
211_D 47_T 1.21 0.15 0.00
64_V 57_D 1.19 0.15 0.00
111_V 52_L 1.19 0.15 0.00
49_A 35_W 1.19 0.15 0.00
245_F 106_G 1.18 0.14 0.00
232_I 91_I 1.17 0.14 0.00
252_F 109_L 1.16 0.14 0.00
169_T 51_I 1.15 0.14 0.00
264_K 108_D 1.15 0.14 0.00
232_I 67_L 1.12 0.13 0.00
237_R 112_R 1.12 0.13 0.00
38_D 17_R 1.12 0.13 0.00
46_E 81_L 1.11 0.13 0.00
109_R 90_P 1.11 0.12 0.00
215_V 82_R 1.10 0.12 0.00
230_L 111_I 1.10 0.12 0.00
46_E 90_P 1.10 0.12 0.00
230_L 48_V 1.10 0.12 0.00
40_E 43_T 1.09 0.12 0.00
228_Q 96_E 1.09 0.12 0.00
253_Q 111_I 1.08 0.12 0.00
19_I 33_V 1.08 0.12 0.00
67_W 23_L 1.08 0.12 0.00
202_K 113_K 1.08 0.12 0.00
149_L 111_I 1.06 0.12 0.00
103_S 12_L 1.06 0.11 0.00
119_I 64_A 1.05 0.11 0.00
6_R 38_Q 1.05 0.11 0.00
211_D 34_A 1.05 0.11 0.00
65_V 111_I 1.05 0.11 0.00
54_E 23_L 1.04 0.11 0.00
39_V 23_L 1.04 0.11 0.00
52_L 20_V 1.03 0.11 0.00
203_I 8_P 1.02 0.11 0.00
41_G 68_E 1.02 0.11 0.00
4_L 10_S 1.02 0.10 0.00
59_S 33_V 1.02 0.10 0.00
201_G 35_W 1.01 0.10 0.00
14_K 96_E 1.01 0.10 0.00
243_R 30_I 1.01 0.10 0.00
194_V 73_N 1.01 0.10 0.00
52_L 40_V 1.01 0.10 0.00
256_N 77_W 1.00 0.10 0.00
109_R 84_Y 0.99 0.10 0.00
90_D 22_A 0.99 0.10 0.00
82_F 56_R 0.99 0.10 0.00
39_V 20_V 0.99 0.10 0.00
230_L 75_P 0.99 0.10 0.00
19_I 94_I 0.98 0.10 0.00
37_V 91_I 0.97 0.10 0.00
100_D 99_S 0.97 0.10 0.00
13_E 89_K 0.97 0.10 0.00
187_H 21_R 0.97 0.10 0.00
1_M 95_E 0.96 0.10 0.00
152_I 81_L 0.96 0.09 0.00
87_W 22_A 0.95 0.09 0.00
117_E 81_L 0.95 0.09 0.00
194_V 13_T 0.95 0.09 0.00
36_F 96_E 0.94 0.09 0.00
18_E 74_M 0.94 0.09 0.00
176_R 17_R 0.94 0.09 0.00
85_D 18_D 0.94 0.09 0.00
162_D 12_L 0.94 0.09 0.00
253_Q 3_D 0.94 0.09 0.00
197_C 21_R 0.94 0.09 0.00
149_L 42_T 0.94 0.09 0.00
131_L 17_R 0.93 0.09 0.00
154_R 82_R 0.93 0.09 0.00
247_T 76_G 0.93 0.09 0.00
125_K 43_T 0.93 0.09 0.00
59_S 10_S 0.93 0.09 0.00
100_D 53_E 0.93 0.09 0.00
82_F 55_N 0.93 0.09 0.00
214_V 14_G 0.93 0.09 0.00
161_K 104_N 0.93 0.09 0.00
174_T 67_L 0.92 0.09 0.00
226_L 16_D 0.92 0.09 0.00
19_I 91_I 0.92 0.09 0.00
177_W 74_M 0.92 0.09 0.00
148_L 108_D 0.92 0.09 0.00
36_F 53_E 0.92 0.09 0.00
187_H 33_V 0.91 0.09 0.00
212_A 7_E 0.91 0.09 0.00
220_G 46_E 0.91 0.09 0.00
22_R 27_K 0.91 0.09 0.00
210_E 51_I 0.91 0.09 0.00
25_E 27_K 0.91 0.08 0.00
41_G 85_L 0.91 0.08 0.00
152_I 91_I 0.91 0.08 0.00
96_K 48_V 0.90 0.08 0.00
31_L 70_L 0.90 0.08 0.00
229_D 70_L 0.90 0.08 0.00
233_G 70_L 0.90 0.08 0.00
186_G 30_I 0.90 0.08 0.00
97_P 83_T 0.90 0.08 0.00
213_L 100_G 0.90 0.08 0.00
195_E 97_E 0.90 0.08 0.00
66_K 91_I 0.90 0.08 0.00
63_E 90_P 0.89 0.08 0.00
149_L 60_M 0.89 0.08 0.00
239_K 40_V 0.89 0.08 0.00
91_N 45_D 0.89 0.08 0.00
89_L 84_Y 0.89 0.08 0.00
4_L 75_P 0.88 0.08 0.00
86_L 16_D 0.88 0.08 0.00
73_L 77_W 0.88 0.08 0.00
92_L 67_L 0.88 0.08 0.00
236_D 23_L 0.88 0.08 0.00
48_A 19_F 0.88 0.08 0.00
204_I 7_E 0.88 0.08 0.00
90_D 26_L 0.88 0.08 0.00
41_G 71_R 0.88 0.08 0.00
203_I 87_T 0.87 0.08 0.00
253_Q 48_V 0.87 0.08 0.00
46_E 13_T 0.87 0.08 0.00
154_R 89_K 0.87 0.08 0.00
174_T 75_P 0.87 0.08 0.00
168_Y 30_I 0.87 0.08 0.00
154_R 92_T 0.87 0.08 0.00
132_L 96_E 0.87 0.08 0.00
194_V 92_T 0.87 0.08 0.00
169_T 44_K 0.87 0.08 0.00
116_D 22_A 0.87 0.08 0.00
246_I 16_D 0.87 0.08 0.00
104_L 78_D 0.87 0.08 0.00
156_L 51_I 0.86 0.08 0.00
17_Q 30_I 0.86 0.08 0.00
166_G 20_V 0.86 0.08 0.00
161_K 4_Q 0.86 0.08 0.00
174_T 43_T 0.85 0.08 0.00
31_L 86_F 0.85 0.08 0.00
229_D 86_F 0.85 0.08 0.00
233_G 86_F 0.85 0.08 0.00
204_I 30_I 0.85 0.08 0.00
37_V 21_R 0.85 0.08 0.00
120_F 108_D 0.85 0.07 0.00
91_N 20_V 0.85 0.07 0.00
212_A 111_I 0.85 0.07 0.00
214_V 3_D 0.85 0.07 0.00
203_I 92_T 0.85 0.07 0.00
112_A 25_S 0.84 0.07 0.00
90_D 74_M 0.84 0.07 0.00
243_R 16_D 0.84 0.07 0.00
256_N 91_I 0.84 0.07 0.00
36_F 40_V 0.84 0.07 0.00
219_G 110_G 0.84 0.07 0.00
214_V 51_I 0.84 0.07 0.00
256_N 53_E 0.84 0.07 0.00
1_M 54_H 0.84 0.07 0.00
1_M 61_E 0.84 0.07 0.00
1_M 69_W 0.84 0.07 0.00
114_F 80_A 0.84 0.07 0.00
253_Q 38_Q 0.84 0.07 0.00
206_T 112_R 0.84 0.07 0.00
94_R 109_L 0.83 0.07 0.00
28_K 43_T 0.83 0.07 0.00
20_D 38_Q 0.83 0.07 0.00
218_R 107_G 0.83 0.07 0.00
11_L 93_E 0.83 0.07 0.00
76_I 105_T 0.83 0.07 0.00
20_D 33_V 0.82 0.07 0.00
42_P 26_L 0.82 0.07 0.00
232_I 106_G 0.82 0.07 0.00
108_V 50_K 0.82 0.07 0.00
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)
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