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OPENSEQ.org
3N39
Genes: A B A+B
Length: 319 153 444
Sequences: 1954 661 421
Seq/Len: 6.13 4.32 0.95
MirrorTree (Pazo et al. 2001) 0.84
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 0.02 0.05 0.18
2 0.02 0.05 0.73
5 0.02 0.05 0.85
10 0.02 0.05 0.86
20 0.02 0.05 0.89
100 0.02 0.05 0.92
∞ 0.07 0.07 1.00
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
194_V 111_G 1.66 0.85 0.10
152_I 104_R 1.42 0.70 0.05
222_A 104_R 1.29 0.59 0.04
87_E 106_F 1.25 0.55 0.03
266_G 130_E 1.18 0.49 0.03
279_N 25_V 1.12 0.43 0.02
220_S 145_V 1.10 0.41 0.02
189_I 126_L 1.06 0.38 0.02
44_A 138_I 1.06 0.38 0.02
202_K 67_P 1.06 0.38 0.02
201_Y 106_F 1.05 0.37 0.02
136_Q 145_V 1.05 0.37 0.02
211_S 101_S 1.05 0.37 0.02
207_M 31_S 1.03 0.35 0.01
152_I 145_V 1.02 0.35 0.01
55_L 31_S 1.02 0.34 0.01
38_L 97_G 1.01 0.34 0.01
151_K 67_P 1.00 0.33 0.01
183_D 26_Y 0.99 0.32 0.01
176_G 107_G 0.98 0.31 0.01
279_N 29_S 0.96 0.30 0.01
232_N 70_G 0.96 0.30 0.01
209_K 110_Y 0.96 0.30 0.01
180_N 106_F 0.96 0.30 0.01
190_R 97_G 0.95 0.29 0.01
187_L 97_G 0.95 0.29 0.01
54_Q 63_I 0.95 0.29 0.01
96_F 34_T 0.94 0.29 0.01
272_P 41_L 0.93 0.27 0.01
103_R 114_G 0.93 0.27 0.01
315_E 50_L 0.92 0.27 0.01
315_E 62_Y 0.92 0.27 0.01
232_N 27_F 0.91 0.26 0.01
138_I 125_W 0.91 0.26 0.01
215_R 110_Y 0.91 0.26 0.01
145_D 119_R 0.91 0.26 0.01
246_W 74_T 0.90 0.25 0.01
33_P 114_G 0.90 0.25 0.01
242_A 38_I 0.90 0.25 0.01
9_I 97_G 0.89 0.25 0.01
282_I 148_F 0.89 0.24 0.01
194_V 100_A 0.88 0.24 0.01
118_V 40_R 0.88 0.24 0.01
203_Y 32_E 0.88 0.24 0.01
37_P 97_G 0.88 0.24 0.01
30_F 129_F 0.87 0.23 0.01
184_L 31_S 0.87 0.23 0.01
65_L 129_F 0.87 0.23 0.01
202_K 34_T 0.86 0.23 0.01
202_K 106_F 0.86 0.23 0.01
107_S 111_G 0.86 0.23 0.01
122_Y 32_E 0.85 0.22 0.01
207_M 96_R 0.85 0.22 0.01
107_S 95_L 0.85 0.22 0.01
310_V 35_Q 0.85 0.22 0.01
136_Q 110_Y 0.85 0.22 0.01
17_D 143_K 0.84 0.22 0.01
294_H 131_L 0.84 0.21 0.01
215_R 139_E 0.84 0.21 0.01
246_W 73_G 0.84 0.21 0.01
96_F 67_P 0.84 0.21 0.01
225_L 40_R 0.83 0.21 0.01
122_Y 132_M 0.83 0.21 0.01
202_K 69_Y 0.83 0.21 0.01
255_C 68_S 0.83 0.21 0.01
271_F 113_A 0.83 0.21 0.01
312_T 106_F 0.83 0.21 0.01
247_A 135_Q 0.83 0.21 0.01
263_M 132_M 0.83 0.21 0.01
176_G 79_P 0.82 0.20 0.01
99_A 149_W 0.82 0.20 0.01
228_E 147_E 0.82 0.20 0.01
116_K 108_E 0.82 0.20 0.01
303_S 99_I 0.82 0.20 0.01
85_P 36_R 0.82 0.20 0.01
198_Y 141_V 0.82 0.20 0.01
194_V 123_V 0.82 0.20 0.01
93_N 106_F 0.81 0.20 0.01
26_L 71_G 0.81 0.20 0.01
180_N 82_V 0.81 0.20 0.01
273_A 110_Y 0.81 0.19 0.01
76_P 111_G 0.80 0.19 0.01
52_E 62_Y 0.80 0.19 0.01
216_E 147_E 0.80 0.19 0.01
123_A 65_I 0.80 0.19 0.01
203_Y 71_G 0.80 0.19 0.01
172_F 101_S 0.79 0.19 0.01
286_L 120_K 0.79 0.19 0.01
205_K 106_F 0.79 0.19 0.01
315_E 146_T 0.79 0.18 0.01
51_V 122_G 0.79 0.18 0.01
208_E 139_E 0.79 0.18 0.01
306_M 38_I 0.78 0.18 0.01
224_D 59_D 0.78 0.18 0.01
240_L 134_T 0.78 0.18 0.01
216_E 136_S 0.78 0.18 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)
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