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OPENSEQ.org
4HR7_A_B
Genes: A B A+B
Length: 449 176 591
Sequences: 12797 2268 1485
Seq/Len: 28.5 12.89 2.51
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 1.91
2 0.03 0.01 2.35
5 0.04 0.01 2.36
10 0.10 0.01 2.36
20 0.12 0.01 2.38
100 0.17 0.02 2.44
∞ 0.25 0.03 2.59
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
34_S 169_D 2.50 1.00 0.99
72_I 165_P 1.25 0.82 0.70
34_S 168_F 1.11 0.71 0.56
69_A 165_P 0.98 0.57 0.41
386_G 43_I 0.98 0.56 0.41
377_V 152_S 0.93 0.51 0.35
214_V 103_V 0.91 0.49 0.33
267_I 154_T 0.89 0.47 0.31
167_R 43_I 0.89 0.47 0.31
293_I 110_T 0.89 0.47 0.31
130_C 144_M 0.88 0.45 0.30
171_V 119_A 0.84 0.41 0.26
71_E 165_P 0.83 0.39 0.24
67_I 169_D 0.83 0.39 0.24
198_V 163_G 0.83 0.39 0.24
192_A 144_M 0.80 0.36 0.22
287_I 143_M 0.80 0.35 0.21
49_V 165_P 0.79 0.35 0.21
364_G 40_E 0.79 0.34 0.20
186_R 37_G 0.75 0.31 0.17
369_S 168_F 0.75 0.30 0.17
384_M 121_A 0.75 0.30 0.17
152_I 38_I 0.74 0.29 0.16
57_V 164_Q 0.73 0.29 0.16
369_S 54_R 0.73 0.29 0.16
117_V 143_M 0.73 0.28 0.15
227_E 174_V 0.72 0.28 0.15
161_S 152_S 0.72 0.28 0.15
18_L 146_Q 0.72 0.28 0.15
105_P 108_V 0.72 0.27 0.15
204_L 138_V 0.71 0.27 0.14
437_I 117_P 0.71 0.27 0.14
359_A 107_M 0.71 0.27 0.14
278_L 42_E 0.71 0.26 0.14
351_P 110_T 0.70 0.26 0.13
251_E 158_I 0.69 0.25 0.13
384_M 26_I 0.69 0.25 0.13
161_S 130_N 0.69 0.25 0.13
318_G 134_T 0.69 0.25 0.13
187_A 144_M 0.69 0.25 0.13
255_Y 95_A 0.68 0.24 0.12
78_I 147_I 0.68 0.24 0.12
350_S 164_Q 0.67 0.23 0.12
130_C 26_I 0.67 0.23 0.12
197_M 136_C 0.67 0.23 0.11
313_L 124_E 0.67 0.23 0.11
65_A 114_T 0.67 0.23 0.11
354_I 67_A 0.66 0.22 0.11
109_T 150_D 0.66 0.22 0.11
219_Q 103_V 0.65 0.22 0.10
432_H 50_V 0.65 0.22 0.10
359_A 168_F 0.65 0.21 0.10
172_V 169_D 0.65 0.21 0.10
124_K 28_K 0.64 0.21 0.10
68_S 108_V 0.64 0.21 0.10
334_A 115_P 0.64 0.21 0.10
43_L 41_L 0.64 0.21 0.10
198_V 105_S 0.64 0.21 0.10
67_I 134_T 0.64 0.21 0.10
232_M 53_S 0.64 0.21 0.10
386_G 120_K 0.63 0.20 0.10
401_R 119_A 0.63 0.20 0.09
245_A 136_C 0.63 0.20 0.09
275_F 22_D 0.63 0.20 0.09
208_R 122_F 0.63 0.20 0.09
268_G 133_D 0.63 0.20 0.09
315_I 43_I 0.63 0.20 0.09
88_N 155_V 0.62 0.20 0.09
34_S 104_R 0.62 0.20 0.09
223_I 157_A 0.62 0.20 0.09
363_F 138_V 0.62 0.19 0.09
54_A 163_G 0.62 0.19 0.09
402_M 136_C 0.62 0.19 0.09
25_G 163_G 0.62 0.19 0.09
326_E 96_A 0.62 0.19 0.09
157_I 148_E 0.62 0.19 0.09
225_L 51_R 0.62 0.19 0.09
7_I 92_A 0.61 0.19 0.09
299_V 125_V 0.61 0.19 0.09
421_Q 144_M 0.61 0.19 0.08
390_C 164_Q 0.61 0.18 0.08
310_K 161_E 0.61 0.18 0.08
243_A 171_P 0.61 0.18 0.08
424_I 164_Q 0.60 0.18 0.08
439_Y 146_Q 0.60 0.18 0.08
258_E 122_F 0.60 0.18 0.08
232_M 113_R 0.60 0.18 0.08
178_L 115_P 0.60 0.18 0.08
386_G 121_A 0.60 0.18 0.08
440_L 32_L 0.60 0.18 0.08
367_W 103_V 0.60 0.18 0.08
156_V 61_F 0.59 0.17 0.08
49_V 144_M 0.59 0.17 0.08
417_N 163_G 0.59 0.17 0.08
62_N 133_D 0.59 0.17 0.08
113_M 29_L 0.59 0.17 0.08
113_M 34_E 0.59 0.17 0.08
100_F 168_F 0.59 0.17 0.08
409_L 143_M 0.59 0.17 0.07
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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