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OPENSEQ.org
4LW4
Genes: A B A+B
Length: 404 150 512
Sequences: 37507 1564 647
Seq/Len: 92.84 10.43 1.26
MirrorTree (Pazo et al. 2001) 0.50
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 0.02 0.80
2 0.03 0.02 0.90
5 0.05 0.02 1.02
10 0.06 0.02 1.08
20 0.09 0.02 1.17
100 0.18 0.02 1.59
∞ 0.24 0.07 2.28
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
191_S 48_P 1.14 0.53 0.00
357_A 65_E 1.13 0.52 0.00
124_A 119_F 1.11 0.51 0.00
289_L 79_K 1.10 0.50 0.00
116_I 36_K 1.10 0.49 0.00
76_A 57_Q 1.09 0.48 0.00
31_T 84_G 1.06 0.46 0.00
117_V 40_L 1.06 0.45 0.00
284_G 22_T 1.03 0.42 0.00
209_A 58_A 1.01 0.41 0.00
341_H 129_S 1.01 0.40 0.00
172_M 88_G 1.00 0.40 0.00
362_A 82_F 0.97 0.37 0.00
282_V 41_I 0.96 0.36 0.00
198_V 50_L 0.96 0.36 0.00
345_V 141_E 0.95 0.35 0.00
278_N 61_I 0.95 0.35 0.00
205_V 36_K 0.94 0.34 0.00
255_V 92_R 0.93 0.33 0.00
114_E 123_G 0.93 0.33 0.00
164_S 34_E 0.92 0.32 0.00
131_M 61_I 0.92 0.32 0.00
380_A 36_K 0.92 0.32 0.00
199_D 64_C 0.91 0.32 0.00
41_A 40_L 0.91 0.32 0.00
77_Q 104_G 0.90 0.31 0.00
285_L 88_G 0.90 0.31 0.00
131_M 139_L 0.90 0.30 0.00
230_T 43_L 0.89 0.30 0.00
89_W 133_S 0.88 0.29 0.00
223_G 143_I 0.87 0.28 0.00
132_V 27_F 0.86 0.28 0.00
89_W 15_G 0.86 0.27 0.00
204_A 109_E 0.85 0.27 0.00
79_L 143_I 0.85 0.27 0.00
284_G 72_Y 0.85 0.27 0.00
39_V 102_V 0.85 0.26 0.00
385_K 121_E 0.84 0.26 0.00
260_F 129_S 0.84 0.26 0.00
199_D 132_R 0.84 0.26 0.00
93_T 61_I 0.83 0.25 0.00
369_L 39_Q 0.83 0.25 0.00
73_E 108_A 0.83 0.25 0.00
75_V 51_P 0.83 0.25 0.00
323_S 129_S 0.83 0.25 0.00
84_D 109_E 0.83 0.25 0.00
124_A 122_L 0.83 0.25 0.00
139_K 28_A 0.82 0.25 0.00
95_E 91_V 0.82 0.25 0.00
203_G 109_E 0.82 0.24 0.00
376_R 135_G 0.82 0.24 0.00
311_A 90_I 0.82 0.24 0.00
320_G 48_P 0.81 0.24 0.00
266_Q 61_I 0.81 0.23 0.00
166_I 114_S 0.81 0.23 0.00
330_S 98_L 0.81 0.23 0.00
221_F 136_L 0.80 0.23 0.00
259_S 50_L 0.80 0.23 0.00
170_G 129_S 0.80 0.23 0.00
333_A 23_L 0.80 0.23 0.00
255_V 91_V 0.79 0.22 0.00
212_Q 126_A 0.79 0.22 0.00
253_K 23_L 0.79 0.22 0.00
53_V 119_F 0.78 0.22 0.00
26_L 111_Q 0.78 0.22 0.00
225_K 64_C 0.78 0.22 0.00
61_A 70_L 0.78 0.21 0.00
180_P 118_L 0.78 0.21 0.00
402_L 33_W 0.78 0.21 0.00
240_E 53_E 0.78 0.21 0.00
213_Q 76_E 0.78 0.21 0.00
199_D 135_G 0.77 0.21 0.00
353_I 31_T 0.77 0.21 0.00
179_C 110_L 0.77 0.21 0.00
376_R 64_C 0.77 0.21 0.00
216_I 143_I 0.77 0.21 0.00
87_I 79_K 0.77 0.21 0.00
96_S 92_R 0.77 0.21 0.00
184_R 58_A 0.77 0.21 0.00
145_L 23_L 0.77 0.20 0.00
248_W 55_K 0.76 0.20 0.00
145_L 92_R 0.76 0.20 0.00
256_H 104_G 0.76 0.20 0.00
39_V 54_L 0.76 0.20 0.00
111_P 56_A 0.76 0.20 0.00
199_D 93_G 0.76 0.20 0.00
259_S 74_V 0.75 0.20 0.00
53_V 98_L 0.75 0.20 0.00
319_P 49_A 0.75 0.20 0.00
287_A 36_K 0.75 0.20 0.00
292_L 36_K 0.75 0.19 0.00
399_L 55_K 0.75 0.19 0.00
204_A 40_L 0.74 0.19 0.00
158_E 121_E 0.74 0.19 0.00
89_W 98_L 0.74 0.19 0.00
271_K 127_Q 0.73 0.19 0.00
44_Q 73_T 0.73 0.19 0.00
80_N 44_G 0.73 0.18 0.00
182_L 95_L 0.73 0.18 0.00
47_S 115_P 0.73 0.18 0.00
80_N 49_A 0.73 0.18 0.00
268_A 88_G 0.73 0.18 0.00
200_G 43_L 0.73 0.18 0.00
257_E 62_A 0.73 0.18 0.00
191_S 114_S 0.73 0.18 0.00
270_W 96_A 0.73 0.18 0.00
93_T 96_A 0.73 0.18 0.00
109_L 48_P 0.73 0.18 0.00
51_G 79_K 0.73 0.18 0.00
392_V 36_K 0.72 0.18 0.00
29_A 129_S 0.72 0.18 0.00
41_A 48_P 0.72 0.18 0.00
337_A 92_R 0.72 0.18 0.00
127_V 44_G 0.72 0.18 0.00
111_P 138_A 0.72 0.18 0.00
255_V 139_L 0.72 0.18 0.00
183_A 52_D 0.72 0.18 0.00
114_E 55_K 0.72 0.18 0.00
394_A 33_W 0.72 0.18 0.00
96_S 62_A 0.72 0.18 0.00
320_G 144_I 0.72 0.18 0.00
213_Q 53_E 0.72 0.18 0.00
164_S 139_L 0.72 0.17 0.00
319_P 41_I 0.71 0.17 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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