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OPENSEQ.org
3lvk_A_C
Genes: A B A+B
Length: 393 81 446
Sequences: 18527 2108 238
Seq/Len: 47.14 26.02 0.53
MirrorTree (Pazo et al. 2001) 0.51
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 0.03 0.03 0.10
2 0.03 0.03 0.25
5 0.05 0.04 0.31
10 0.05 0.04 0.38
20 0.07 0.05 0.50
100 0.12 0.06 1.06
∞ 0.21 0.13 2.96
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
171_R 79_K 1.29 0.42 0.00
135_K 77_I 1.26 0.39 0.00
41_H 44_D 1.19 0.34 0.00
169_M 24_M 1.18 0.34 0.00
218_V 11_T 1.16 0.32 0.00
98_I 52_I 1.13 0.30 0.00
360_E 42_I 1.12 0.29 0.00
18_R 77_I 1.10 0.28 0.00
365_I 40_L 1.09 0.28 0.00
106_A 23_V 1.03 0.24 0.00
148_V 28_K 1.03 0.24 0.00
112_R 79_K 1.03 0.24 0.00
180_D 19_C 1.02 0.24 0.00
70_V 26_V 1.01 0.23 0.00
63_G 12_L 1.01 0.23 0.00
161_Q 48_T 1.00 0.23 0.00
169_M 26_V 1.00 0.22 0.00
351_S 68_T 1.00 0.22 0.00
177_Y 12_L 0.99 0.22 0.00
355_F 60_E 0.98 0.21 0.00
40_S 56_C 0.97 0.21 0.00
97_I 79_K 0.96 0.20 0.00
259_A 39_L 0.95 0.20 0.00
59_A 55_F 0.94 0.20 0.00
141_M 11_T 0.94 0.19 0.00
358_E 30_V 0.94 0.19 0.00
44_G 37_E 0.93 0.19 0.00
61_L 30_V 0.93 0.19 0.00
181_A 36_G 0.92 0.18 0.00
179_V 48_T 0.92 0.18 0.00
216_L 47_A 0.92 0.18 0.00
266_E 52_I 0.91 0.18 0.00
7_L 39_L 0.91 0.18 0.00
50_A 64_V 0.90 0.18 0.00
284_I 31_R 0.90 0.17 0.00
192_L 63_L 0.90 0.17 0.00
62_V 57_T 0.89 0.17 0.00
212_G 13_D 0.89 0.17 0.00
180_D 20_P 0.89 0.17 0.00
54_A 53_P 0.88 0.17 0.00
148_V 78_R 0.88 0.16 0.00
162_D 41_I 0.87 0.16 0.00
198_D 77_I 0.87 0.16 0.00
183_Q 51_D 0.87 0.16 0.00
74_G 55_F 0.87 0.16 0.00
282_K 41_I 0.86 0.16 0.00
246_V 77_I 0.86 0.16 0.00
26_F 79_K 0.86 0.16 0.00
52_D 25_M 0.85 0.15 0.00
239_M 25_M 0.85 0.15 0.00
238_G 56_C 0.84 0.15 0.00
189_P 11_T 0.84 0.15 0.00
360_E 70_G 0.84 0.15 0.00
271_R 30_V 0.84 0.15 0.00
268_E 32_N 0.83 0.14 0.00
56_N 53_P 0.83 0.14 0.00
313_L 24_M 0.83 0.14 0.00
59_A 41_I 0.83 0.14 0.00
15_V 10_H 0.82 0.14 0.00
17_P 31_R 0.82 0.14 0.00
83_I 68_T 0.81 0.14 0.00
34_G 26_V 0.81 0.14 0.00
25_Q 30_V 0.81 0.14 0.00
42_R 32_N 0.81 0.14 0.00
18_R 52_I 0.81 0.14 0.00
257_R 68_T 0.81 0.14 0.00
264_A 21_E 0.81 0.14 0.00
21_E 76_L 0.80 0.14 0.00
300_I 63_L 0.80 0.13 0.00
113_Q 39_L 0.80 0.13 0.00
226_I 56_C 0.80 0.13 0.00
371_S 12_L 0.80 0.13 0.00
281_I 57_T 0.79 0.13 0.00
259_A 75_Y 0.79 0.13 0.00
51_V 78_R 0.79 0.13 0.00
134_L 65_A 0.79 0.13 0.00
100_S 31_R 0.78 0.13 0.00
256_Y 51_D 0.78 0.13 0.00
349_R 19_C 0.78 0.13 0.00
99_T 12_L 0.78 0.13 0.00
219_R 34_Q 0.78 0.13 0.00
11_A 9_D 0.78 0.12 0.00
358_E 12_L 0.78 0.12 0.00
197_V 50_R 0.78 0.12 0.00
21_E 62_E 0.77 0.12 0.00
255_A 36_G 0.77 0.12 0.00
76_T 33_M 0.77 0.12 0.00
81_L 17_L 0.77 0.12 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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