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OPENSEQ.org
3oaa_gh
Genes: A B A+B
Length: 284 138 417
Sequences: 3042 2587 1744
Seq/Len: 10.71 18.75 4.18
MirrorTree (Pazo et al. 2001) 0.76
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 0.09 0.08
2 0.09 0.09 3.97
5 0.09 0.09 4.07
10 0.09 0.09 4.08
20 0.09 0.09 4.13
100 0.09 0.09 4.20
∞ 0.10 0.09 4.41
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
206_L 39_A 1.29 0.93 0.42
55_L 42_L 1.17 0.88 0.31
220_R 68_I 1.16 0.88 0.31
167_L 81_D 1.14 0.86 0.29
64_H 40_P 1.12 0.84 0.28
214_L 29_E 1.11 0.84 0.27
259_E 41_L 1.04 0.79 0.22
47_T 70_E 1.01 0.76 0.20
221_R 81_D 1.00 0.74 0.19
208_E 29_E 0.99 0.73 0.19
5_E 11_A 0.98 0.72 0.18
51_V 42_L 0.96 0.71 0.17
30_K 48_G 0.96 0.70 0.17
4_K 48_G 0.95 0.68 0.16
80_V 57_G 0.94 0.68 0.16
214_L 8_V 0.92 0.65 0.15
222_Y 33_G 0.89 0.61 0.13
145_L 11_A 0.88 0.60 0.13
203_W 40_P 0.88 0.60 0.13
47_T 7_D 0.87 0.59 0.12
205_Y 70_E 0.86 0.58 0.12
243_M 70_E 0.85 0.56 0.11
45_A 4_Y 0.85 0.56 0.11
241_A 22_K 0.84 0.55 0.11
51_V 79_L 0.84 0.55 0.11
203_W 73_P 0.83 0.54 0.11
169_I 71_V 0.83 0.53 0.10
145_L 77_T 0.83 0.53 0.10
25_M 70_E 0.81 0.51 0.10
25_M 85_R 0.81 0.50 0.10
227_V 78_V 0.79 0.49 0.09
29_S 11_A 0.79 0.48 0.09
1_A 23_I 0.79 0.48 0.09
205_Y 42_L 0.78 0.47 0.09
171_S 130_V 0.78 0.46 0.09
89_G 51_R 0.78 0.46 0.08
219_L 78_V 0.78 0.46 0.08
52_I 68_I 0.78 0.46 0.08
54_H 72_Q 0.77 0.45 0.08
1_A 26_T 0.77 0.45 0.08
54_H 37_G 0.76 0.44 0.08
241_A 24_Q 0.75 0.43 0.08
38_M 69_L 0.75 0.43 0.08
188_L 94_A 0.75 0.43 0.07
34_S 76_V 0.75 0.42 0.07
271_S 65_S 0.74 0.42 0.07
281_S 25_V 0.73 0.40 0.07
214_L 44_A 0.73 0.40 0.07
143_P 83_A 0.72 0.39 0.07
51_V 83_A 0.72 0.39 0.07
263_V 78_V 0.71 0.38 0.06
178_M 64_L 0.71 0.38 0.06
284_A 8_V 0.71 0.38 0.06
51_V 80_A 0.71 0.37 0.06
99_L 128_L 0.71 0.37 0.06
243_M 83_A 0.71 0.37 0.06
208_E 27_G 0.70 0.36 0.06
92_I 128_L 0.70 0.36 0.06
104_T 21_E 0.70 0.36 0.06
87_C 103_E 0.70 0.36 0.06
24_E 52_I 0.69 0.35 0.06
236_A 38_H 0.69 0.35 0.06
102_M 21_E 0.69 0.35 0.06
205_Y 40_P 0.69 0.34 0.06
276_L 45_I 0.69 0.34 0.06
231_V 83_A 0.68 0.34 0.06
254_G 95_M 0.68 0.34 0.06
44_Y 66_G 0.68 0.33 0.05
247_K 64_L 0.68 0.33 0.05
79_V 134_T 0.67 0.33 0.05
244_V 32_L 0.67 0.33 0.05
276_L 82_T 0.67 0.32 0.05
146_S 128_L 0.67 0.32 0.05
259_E 95_M 0.66 0.32 0.05
27_A 134_T 0.66 0.32 0.05
276_L 95_M 0.66 0.31 0.05
281_S 24_Q 0.66 0.31 0.05
55_L 74_G 0.66 0.31 0.05
143_P 18_G 0.65 0.30 0.05
262_L 33_G 0.65 0.30 0.05
162_G 88_D 0.65 0.30 0.05
232_V 9_V 0.65 0.30 0.05
214_L 13_Q 0.65 0.30 0.05
133_V 23_I 0.64 0.29 0.05
264_Y 34_I 0.64 0.29 0.05
93_N 94_A 0.64 0.29 0.05
276_L 35_Y 0.64 0.29 0.05
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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