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OPENSEQ.org
ssa1 and ydj1 (A, 379-508)
Genes: A B A+B
Length: 130 409 463
Sequences: 2335 3148 1092
Seq/Len: 17.96 7.7 2.36
MirrorTree (Pazo et al. 2001) 0.49
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 0.07 0.07 1.81
2 0.07 0.07 1.95
5 0.07 0.07 1.99
10 0.08 0.07 2.00
20 0.08 0.07 2.03
100 0.08 0.07 2.19
∞ 0.13 0.09 3.00
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
43_K 51_S 1.55 0.95 0.68
46_I 144_K 1.20 0.77 0.36
105_L 228_Q 1.15 0.73 0.32
101_S 30_A 1.11 0.69 0.28
102_N 27_R 1.02 0.60 0.22
108_S 193_D 1.01 0.59 0.21
19_S 276_T 1.00 0.58 0.20
42_K 205_N 1.00 0.57 0.20
79_E 37_K 1.00 0.57 0.20
113_G 317_P 0.95 0.51 0.17
56_G 334_K 0.92 0.48 0.15
42_K 295_V 0.90 0.46 0.14
35_R 329_I 0.89 0.45 0.13
51_A 139_K 0.88 0.44 0.13
105_L 31_L 0.88 0.44 0.13
58_L 37_K 0.88 0.43 0.13
60_Q 128_Y 0.88 0.43 0.13
117_S 235_E 0.86 0.41 0.12
25_A 102_G 0.86 0.41 0.12
90_V 13_V 0.84 0.39 0.11
59_I 297_I 0.83 0.38 0.11
46_I 149_R 0.83 0.38 0.10
82_G 251_V 0.82 0.37 0.10
113_G 27_R 0.82 0.36 0.10
67_A 42_E 0.82 0.36 0.10
34_P 319_P 0.80 0.35 0.09
32_L 330_K 0.80 0.35 0.09
46_I 310_V 0.80 0.34 0.09
29_M 225_K 0.80 0.34 0.09
105_L 138_N 0.79 0.34 0.09
62_F 7_F 0.79 0.34 0.09
67_A 50_A 0.79 0.34 0.09
108_S 42_E 0.79 0.33 0.09
60_Q 316_M 0.78 0.33 0.08
32_L 176_P 0.78 0.32 0.08
74_L 301_E 0.78 0.32 0.08
35_R 337_E 0.77 0.31 0.08
77_K 350_E 0.76 0.31 0.08
68_K 28_K 0.76 0.31 0.08
31_K 274_L 0.74 0.29 0.07
94_E 286_E 0.74 0.29 0.07
73_N 50_A 0.74 0.28 0.07
10_L 30_A 0.73 0.28 0.07
34_P 312_E 0.73 0.28 0.07
42_K 42_E 0.73 0.28 0.07
82_G 228_Q 0.73 0.28 0.07
106_N 354_P 0.73 0.28 0.07
68_K 302_V 0.73 0.28 0.07
112_K 249_F 0.73 0.27 0.07
44_S 126_E 0.72 0.27 0.06
102_N 169_F 0.72 0.27 0.06
59_I 5_T 0.72 0.26 0.06
79_E 92_D 0.71 0.26 0.06
112_K 120_I 0.71 0.26 0.06
56_G 73_G 0.71 0.26 0.06
77_K 274_L 0.71 0.26 0.06
32_L 56_I 0.70 0.25 0.06
82_G 295_V 0.70 0.25 0.06
113_G 273_D 0.70 0.25 0.06
46_I 135_L 0.69 0.24 0.06
42_K 120_I 0.69 0.24 0.05
43_K 134_K 0.69 0.24 0.05
41_T 32_K 0.68 0.23 0.05
48_S 72_D 0.68 0.23 0.05
62_F 68_Q 0.68 0.23 0.05
68_K 179_Q 0.68 0.23 0.05
13_L 30_A 0.68 0.23 0.05
34_P 187_V 0.68 0.23 0.05
62_F 269_E 0.68 0.23 0.05
32_L 267_V 0.67 0.22 0.05
114_T 52_A 0.67 0.22 0.05
77_K 139_K 0.67 0.22 0.05
59_I 68_Q 0.67 0.22 0.05
32_L 217_E 0.66 0.22 0.05
56_G 182_Q 0.66 0.22 0.05
81_S 21_E 0.66 0.21 0.05
85_P 257_K 0.66 0.21 0.05
25_A 119_E 0.66 0.21 0.05
105_L 37_K 0.65 0.21 0.04
102_N 242_V 0.65 0.21 0.04
25_A 68_Q 0.64 0.20 0.04
79_E 31_L 0.64 0.20 0.04
22_I 320_K 0.63 0.20 0.04
53_N 310_V 0.63 0.19 0.04
19_S 327_L 0.63 0.19 0.04
48_S 334_K 0.63 0.19 0.04
90_V 333_I 0.62 0.19 0.04
87_P 156_V 0.62 0.19 0.04
35_R 274_L 0.62 0.19 0.04
113_G 324_Y 0.62 0.18 0.04
112_K 273_D 0.62 0.18 0.04
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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