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OPENSEQ.org
3ip B vs C
Genes: A B A+B
Length: 483 100 556
Sequences: 2608 1891 1167
Seq/Len: 5.4 18.91 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 1.64
5 0.09 0.07 1.90
10 0.09 0.07 1.97
20 0.09 0.07 2.00
100 0.10 0.08 2.08
∞ 0.11 0.08 2.54
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 65_E 4.37 1.00 1.00
18_D 67_K 1.72 0.97 0.93
35_S 74_Q 1.52 0.93 0.86
42_L 77_A 1.50 0.92 0.85
19_S 68_A 1.45 0.90 0.82
25_S 71_G 1.28 0.81 0.70
82_F 16_A 1.20 0.74 0.62
137_S 94_I 1.20 0.74 0.61
24_P 69_I 1.19 0.73 0.60
24_P 71_G 1.18 0.72 0.59
19_S 5_T 1.16 0.71 0.57
26_P 71_G 1.07 0.62 0.47
276_V 61_N 1.07 0.62 0.47
281_D 31_T 1.03 0.57 0.41
32_E 74_Q 0.97 0.51 0.35
130_S 94_I 0.95 0.48 0.33
24_P 64_R 0.94 0.47 0.32
131_T 88_Q 0.94 0.47 0.32
18_D 68_A 0.93 0.46 0.31
42_L 89_F 0.91 0.44 0.28
80_N 20_I 0.89 0.42 0.27
270_F 15_L 0.88 0.41 0.26
318_T 25_T 0.87 0.39 0.24
241_I 84_T 0.86 0.39 0.24
268_R 15_L 0.86 0.38 0.24
197_L 95_M 0.85 0.37 0.22
23_S 71_G 0.84 0.36 0.21
25_S 77_A 0.83 0.35 0.20
11_V 16_A 0.80 0.32 0.18
344_L 9_V 0.80 0.32 0.18
138_L 88_Q 0.79 0.31 0.17
93_S 89_F 0.79 0.31 0.17
123_M 74_Q 0.78 0.30 0.16
38_N 71_G 0.77 0.29 0.16
120_R 40_K 0.77 0.29 0.16
41_D 71_G 0.75 0.28 0.15
42_L 72_I 0.75 0.28 0.15
279_Y 60_Q 0.75 0.27 0.14
166_Y 32_L 0.75 0.27 0.14
37_T 78_L 0.75 0.27 0.14
350_E 87_G 0.74 0.27 0.14
406_D 22_P 0.74 0.27 0.14
272_E 7_E 0.72 0.25 0.12
136_Y 83_E 0.72 0.24 0.12
263_G 28_M 0.72 0.24 0.12
317_L 22_P 0.71 0.24 0.12
153_S 88_Q 0.71 0.24 0.12
271_P 15_L 0.70 0.23 0.12
262_E 18_L 0.70 0.23 0.11
278_L 63_L 0.70 0.23 0.11
35_S 87_G 0.69 0.23 0.11
37_T 71_G 0.69 0.22 0.11
228_E 53_T 0.69 0.22 0.11
82_F 14_N 0.69 0.22 0.11
269_Y 15_L 0.68 0.21 0.10
131_T 16_A 0.68 0.21 0.10
205_F 28_M 0.67 0.21 0.10
390_F 52_P 0.67 0.21 0.10
348_V 30_N 0.67 0.21 0.10
195_I 79_K 0.67 0.21 0.10
39_V 77_A 0.67 0.21 0.10
75_K 55_H 0.67 0.20 0.09
263_G 42_N 0.66 0.20 0.09
232_E 95_M 0.66 0.20 0.09
262_E 15_L 0.66 0.20 0.09
434_E 7_E 0.66 0.20 0.09
351_Y 45_A 0.65 0.20 0.09
129_K 91_V 0.65 0.19 0.09
80_N 15_L 0.65 0.19 0.09
448_V 4_V 0.65 0.19 0.09
399_N 60_Q 0.65 0.19 0.09
105_I 50_V 0.65 0.19 0.08
418_L 93_T 0.65 0.19 0.08
402_Q 28_M 0.64 0.19 0.08
24_P 68_A 0.64 0.18 0.08
26_P 68_A 0.64 0.18 0.08
19_S 86_D 0.64 0.18 0.08
67_N 49_G 0.63 0.18 0.08
262_E 92_P 0.63 0.18 0.07
25_S 69_I 0.63 0.18 0.07
276_V 58_D 0.62 0.17 0.07
185_E 39_A 0.62 0.17 0.07
406_D 45_A 0.62 0.17 0.07
157_I 47_T 0.62 0.17 0.07
365_T 65_E 0.62 0.17 0.07
157_I 75_E 0.62 0.17 0.07
305_N 37_D 0.61 0.17 0.07
87_P 15_L 0.61 0.17 0.07
56_V 68_A 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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