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OPENSEQ.org
SMC_NTH_SCPA_GREM
Genes: A B A+B
Length: 166 251 398
Sequences: 4671 2308 1208
Seq/Len: 28.14 9.2 3.04
MirrorTree (Pazo et al. 2001) 0.34
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 0.01 0.02 0.24
2 0.01 0.02 0.25
5 0.02 0.02 0.29
10 0.02 0.02 0.34
20 0.02 0.02 0.43
100 0.05 0.02 0.82
∞ 0.14 0.02 2.90
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
157_R 127_K 1.45 0.95 0.64
29_V 188_I 1.35 0.91 0.55
146_V 57_S 1.27 0.88 0.48
6_L 91_E 1.20 0.84 0.42
150_L 57_S 1.19 0.83 0.40
124_I 205_F 1.18 0.82 0.40
161_F 110_A 1.13 0.78 0.34
20_V 181_I 1.12 0.77 0.34
119_C 210_K 1.05 0.71 0.28
22_F 181_I 1.02 0.68 0.25
159_S 29_I 1.02 0.67 0.25
143_Q 21_L 1.01 0.67 0.25
83_T 187_E 1.01 0.67 0.25
149_I 45_V 1.00 0.65 0.23
142_S 57_S 0.97 0.61 0.21
80_V 98_I 0.92 0.56 0.18
161_F 132_L 0.92 0.56 0.18
6_L 201_F 0.92 0.56 0.18
40_I 129_P 0.92 0.55 0.18
6_L 4_Y 0.90 0.53 0.17
81_T 8_I 0.90 0.53 0.17
27_T 26_E 0.90 0.53 0.16
63_D 21_L 0.89 0.52 0.16
159_S 183_A 0.89 0.52 0.16
43_A 216_T 0.89 0.52 0.16
83_T 192_L 0.88 0.51 0.15
19_S 231_I 0.88 0.50 0.15
157_R 65_T 0.88 0.50 0.15
124_I 112_K 0.88 0.50 0.15
63_D 27_I 0.88 0.50 0.15
55_S 178_D 0.87 0.50 0.15
67_A 23_N 0.87 0.49 0.15
125_I 184_R 0.87 0.49 0.15
43_A 236_N 0.87 0.49 0.15
40_I 213_L 0.87 0.49 0.15
1_M 63_A 0.86 0.48 0.14
153_K 113_D 0.85 0.47 0.14
76_N 67_L 0.85 0.47 0.14
29_V 111_A 0.85 0.47 0.14
62_E 57_S 0.84 0.46 0.13
104_V 90_E 0.84 0.45 0.13
26_V 150_V 0.82 0.44 0.12
150_L 237_F 0.82 0.43 0.12
8_V 203_D 0.82 0.43 0.12
67_A 190_H 0.82 0.43 0.12
156_D 149_T 0.82 0.43 0.12
53_A 28_D 0.82 0.43 0.12
6_L 240_I 0.81 0.42 0.12
28_A 11_F 0.81 0.42 0.12
81_T 191_S 0.81 0.41 0.11
22_F 150_V 0.80 0.41 0.11
17_R 71_S 0.80 0.41 0.11
47_V 64_A 0.80 0.41 0.11
142_S 59_Y 0.80 0.40 0.11
20_V 210_K 0.79 0.40 0.11
147_E 27_I 0.79 0.40 0.11
64_I 181_I 0.79 0.39 0.11
104_V 149_T 0.79 0.39 0.10
26_V 237_F 0.79 0.39 0.10
126_D 212_H 0.78 0.39 0.10
28_A 41_Y 0.78 0.39 0.10
133_L 56_A 0.78 0.38 0.10
116_N 63_A 0.78 0.38 0.10
48_L 67_L 0.78 0.38 0.10
40_I 68_S 0.78 0.38 0.10
64_I 174_I 0.78 0.38 0.10
28_A 226_N 0.78 0.38 0.10
149_I 32_I 0.77 0.37 0.10
119_C 37_I 0.77 0.37 0.10
1_M 21_L 0.77 0.37 0.10
8_V 158_Q 0.77 0.37 0.10
142_S 67_L 0.77 0.37 0.10
6_L 26_E 0.77 0.37 0.10
8_V 162_K 0.77 0.36 0.10
138_F 59_Y 0.76 0.36 0.10
161_F 53_L 0.76 0.36 0.09
132_G 204_L 0.76 0.36 0.09
117_Q 100_K 0.76 0.36 0.09
145_K 215_V 0.76 0.36 0.09
78_A 42_L 0.76 0.36 0.09
38_S 160_V 0.76 0.36 0.09
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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