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OPENSEQ.org
3IP4_BC
Genes: A B A+B
Length: 482 92 555
Sequences: 2613 1894 1164
Seq/Len: 5.42 20.59 2.1
MirrorTree (Pazo et al. 2001) 0.73
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 0.09 0.07 0.04
2 0.09 0.07 1.66
5 0.09 0.07 1.93
10 0.09 0.07 1.99
20 0.09 0.07 2.03
100 0.10 0.08 2.11
∞ 0.11 0.08 2.58
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
53_K 63_E 4.27 1.00 1.00
18_D 65_K 1.65 0.96 0.91
42_L 75_A 1.53 0.93 0.86
35_S 72_Q 1.47 0.91 0.83
19_S 66_A 1.44 0.89 0.81
25_S 69_G 1.30 0.82 0.71
82_F 14_A 1.22 0.76 0.63
24_P 69_G 1.20 0.74 0.62
24_P 67_I 1.18 0.72 0.59
137_S 92_I 1.14 0.69 0.55
276_V 59_N 1.11 0.65 0.51
26_P 69_G 1.08 0.62 0.47
19_S 3_T 1.04 0.59 0.44
32_E 72_Q 1.00 0.54 0.39
281_D 29_T 1.00 0.53 0.38
130_S 92_I 0.97 0.50 0.35
18_D 66_A 0.96 0.49 0.33
131_T 86_Q 0.94 0.47 0.32
24_P 62_R 0.93 0.46 0.30
42_L 87_F 0.93 0.46 0.30
80_N 18_I 0.90 0.43 0.28
270_F 13_L 0.90 0.42 0.27
241_I 82_T 0.89 0.42 0.27
268_R 13_L 0.89 0.41 0.26
318_T 23_T 0.85 0.37 0.22
93_S 87_F 0.84 0.36 0.22
11_V 14_A 0.83 0.35 0.20
25_S 75_A 0.83 0.35 0.20
23_S 69_G 0.82 0.34 0.20
38_N 69_G 0.82 0.34 0.20
344_L 7_V 0.79 0.30 0.17
138_L 86_Q 0.78 0.30 0.16
166_Y 30_L 0.77 0.29 0.16
120_R 38_K 0.76 0.28 0.15
279_Y 58_Q 0.76 0.28 0.15
42_L 70_I 0.76 0.28 0.15
278_L 61_L 0.76 0.28 0.15
41_D 69_G 0.75 0.28 0.15
123_M 72_Q 0.74 0.27 0.14
317_L 20_P 0.74 0.27 0.14
350_E 85_G 0.73 0.26 0.13
37_T 76_L 0.73 0.26 0.13
37_T 69_G 0.73 0.25 0.13
263_G 26_M 0.72 0.24 0.12
434_E 5_E 0.72 0.24 0.12
195_I 77_K 0.71 0.24 0.12
269_Y 13_L 0.71 0.24 0.12
153_S 86_Q 0.71 0.24 0.12
272_E 5_E 0.71 0.24 0.12
262_E 16_L 0.71 0.24 0.12
271_P 13_L 0.70 0.23 0.12
105_I 48_V 0.69 0.23 0.11
131_T 14_A 0.69 0.22 0.11
82_F 12_N 0.69 0.22 0.11
129_K 89_V 0.68 0.21 0.10
26_P 66_A 0.68 0.21 0.10
255_T 7_V 0.68 0.21 0.10
67_N 47_G 0.67 0.21 0.10
136_Y 81_E 0.67 0.21 0.10
75_K 53_H 0.67 0.21 0.10
348_V 28_N 0.67 0.21 0.10
228_E 51_T 0.66 0.20 0.09
25_S 67_I 0.66 0.20 0.09
80_N 13_L 0.66 0.20 0.09
106_D 19_S 0.66 0.20 0.09
51_V 61_L 0.66 0.20 0.09
262_E 13_L 0.66 0.20 0.09
351_Y 43_A 0.65 0.20 0.09
220_V 6_E 0.65 0.19 0.09
418_L 91_T 0.65 0.19 0.09
87_P 13_L 0.64 0.19 0.08
262_E 90_P 0.64 0.19 0.08
157_I 45_T 0.64 0.18 0.08
24_P 66_A 0.64 0.18 0.08
263_G 40_N 0.64 0.18 0.08
39_V 75_A 0.64 0.18 0.08
35_S 85_G 0.63 0.18 0.08
185_E 37_A 0.63 0.18 0.08
179_V 75_A 0.63 0.18 0.07
390_F 50_P 0.62 0.18 0.07
448_V 2_V 0.62 0.17 0.07
428_N 35_D 0.62 0.17 0.07
263_G 9_H 0.62 0.17 0.07
156_D 14_A 0.62 0.17 0.07
48_L 13_L 0.61 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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