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OPENSEQ.org
spoIIIAC-AE
Genes: A B A+B
Length: 65 403 416
Sequences: 279 375 356
Seq/Len: 4.29 0.93 0.86
MirrorTree (Pazo et al. 2001) 0.42
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 0.00 0.01
2 0.01 0.00 0.75
5 0.01 0.00 0.76
10 0.01 0.00 0.76
20 0.01 0.00 0.76
100 0.01 0.00 0.76
∞ 0.01 0.00 0.76
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
15_L 133_L 1.55 0.76 0.01
30_D 62_N 1.50 0.72 0.01
30_D 209_G 1.33 0.59 0.01
28_R 229_A 1.29 0.55 0.01
30_D 340_I 1.27 0.54 0.01
48_I 235_I 1.26 0.53 0.01
16_I 203_L 1.25 0.53 0.01
41_I 238_L 1.23 0.50 0.01
41_I 253_Q 1.23 0.50 0.01
41_I 370_A 1.22 0.49 0.01
48_I 54_G 1.20 0.48 0.01
2_E 143_S 1.16 0.44 0.01
61_M 131_K 1.16 0.44 0.01
22_I 81_S 1.16 0.44 0.01
15_L 320_I 1.15 0.43 0.01
3_I 327_I 1.13 0.41 0.01
7_L 179_L 1.13 0.41 0.01
30_D 64_I 1.12 0.41 0.01
42_I 123_L 1.11 0.39 0.00
16_I 223_F 1.10 0.39 0.00
3_I 213_F 1.10 0.39 0.00
35_T 223_F 1.10 0.39 0.00
34_L 182_V 1.09 0.38 0.00
5_L 367_N 1.09 0.38 0.00
30_D 311_L 1.09 0.38 0.00
35_T 343_V 1.08 0.37 0.00
19_L 106_M 1.08 0.37 0.00
28_R 374_I 1.08 0.37 0.00
30_D 256_Y 1.07 0.36 0.00
11_G 296_I 1.06 0.36 0.00
41_I 247_F 1.06 0.36 0.00
48_I 76_D 1.05 0.35 0.00
22_I 117_V 1.05 0.34 0.00
51_I 121_L 1.01 0.32 0.00
6_I 398_S 1.01 0.32 0.00
11_G 303_V 1.00 0.31 0.00
40_V 357_V 1.00 0.31 0.00
16_I 200_S 1.00 0.31 0.00
43_V 196_F 1.00 0.31 0.00
38_A 73_V 0.99 0.30 0.00
22_I 347_Y 0.99 0.30 0.00
58_V 307_V 0.99 0.30 0.00
64_L 193_L 0.99 0.30 0.00
8_K 390_T 0.98 0.30 0.00
51_I 255_N 0.98 0.29 0.00
6_I 318_K 0.98 0.29 0.00
59_R 370_A 0.98 0.29 0.00
60_T 173_I 0.97 0.29 0.00
24_E 336_P 0.97 0.29 0.00
45_G 186_I 0.97 0.28 0.00
6_I 316_L 0.96 0.28 0.00
53_D 275_L 0.95 0.27 0.00
30_D 213_F 0.94 0.27 0.00
2_E 149_I 0.94 0.27 0.00
30_D 76_D 0.94 0.27 0.00
18_V 128_S 0.94 0.26 0.00
8_K 200_S 0.94 0.26 0.00
19_L 366_L 0.93 0.26 0.00
63_Q 391_V 0.93 0.26 0.00
35_T 257_V 0.92 0.25 0.00
4_S 394_L 0.92 0.25 0.00
41_I 393_I 0.92 0.25 0.00
13_G 362_I 0.92 0.25 0.00
6_I 268_G 0.91 0.24 0.00
2_E 270_V 0.91 0.24 0.00
6_I 334_L 0.90 0.24 0.00
24_E 370_A 0.89 0.23 0.00
22_I 183_I 0.89 0.23 0.00
2_E 127_S 0.89 0.23 0.00
47_V 192_L 0.89 0.23 0.00
51_I 200_S 0.88 0.23 0.00
5_L 61_I 0.88 0.23 0.00
56_N 149_I 0.88 0.23 0.00
1_M 322_G 0.88 0.23 0.00
47_V 351_A 0.88 0.22 0.00
29_K 337_V 0.88 0.22 0.00
22_I 217_F 0.88 0.22 0.00
6_I 389_V 0.88 0.22 0.00
11_G 387_F 0.88 0.22 0.00
16_I 332_I 0.88 0.22 0.00
54_L 264_T 0.88 0.22 0.00
59_R 173_I 0.87 0.22 0.00
31_W 156_S 0.87 0.22 0.00
59_R 74_I 0.87 0.22 0.00
47_V 55_Q 0.87 0.22 0.00
22_I 124_A 0.87 0.22 0.00
5_L 264_T 0.87 0.22 0.00
48_I 167_Q 0.87 0.22 0.00
22_I 304_S 0.87 0.22 0.00
47_V 282_K 0.86 0.21 0.00
4_S 157_L 0.86 0.21 0.00
15_L 145_I 0.86 0.21 0.00
17_S 257_V 0.86 0.21 0.00
22_I 109_E 0.86 0.21 0.00
31_W 169_C 0.86 0.21 0.00
4_S 370_A 0.86 0.21 0.00
53_D 108_D 0.86 0.21 0.00
15_L 208_I 0.86 0.21 0.00
42_I 316_L 0.86 0.21 0.00
2_E 145_I 0.85 0.21 0.00
42_I 130_L 0.85 0.21 0.00
48_I 373_M 0.85 0.21 0.00
22_I 263_F 0.85 0.21 0.00
8_K 348_K 0.85 0.21 0.00
53_D 381_I 0.85 0.21 0.00
47_V 268_G 0.85 0.20 0.00
42_I 77_V 0.84 0.20 0.00
43_V 121_L 0.84 0.20 0.00
56_N 351_A 0.84 0.20 0.00
43_V 296_I 0.84 0.20 0.00
20_N 275_L 0.84 0.20 0.00
37_L 247_F 0.84 0.20 0.00
5_L 348_K 0.84 0.20 0.00
64_L 156_S 0.84 0.20 0.00
15_L 249_S 0.84 0.20 0.00
22_I 82_F 0.83 0.20 0.00
24_E 387_F 0.83 0.20 0.00
41_I 167_Q 0.83 0.20 0.00
60_T 54_G 0.83 0.20 0.00
5_L 128_S 0.83 0.20 0.00
6_I 381_I 0.83 0.20 0.00
58_V 215_N 0.83 0.20 0.00
29_K 374_I 0.83 0.20 0.00
41_I 57_D 0.83 0.20 0.00
48_I 163_K 0.83 0.20 0.00
49_T 296_I 0.83 0.20 0.00
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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