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OPENSEQ.org
cIp_5_4_cIV_D_4
Genes: A B A+B
Length: 207 50 246
Sequences: 1036 202 68
Seq/Len: 5 4.04 0.28
MirrorTree (Pazo et al. 2001) 0.32
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.00
100 0.00 0.01 0.02
∞ 0.01 0.01 0.26
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
52_N 34_V 1.64 0.49 0.00
38_A 3_S 1.38 0.33 0.00
51_R 34_V 1.34 0.30 0.00
185_F 16_D 1.33 0.29 0.00
36_V 28_I 1.32 0.29 0.00
137_I 22_A 1.26 0.26 0.00
85_M 17_I 1.25 0.25 0.00
114_N 10_H 1.23 0.24 0.00
31_V 19_H 1.21 0.24 0.00
43_V 29_K 1.21 0.23 0.00
16_H 19_H 1.20 0.23 0.00
107_I 40_A 1.12 0.20 0.00
64_I 26_G 1.10 0.19 0.00
85_M 9_D 1.09 0.18 0.00
180_Y 20_Q 1.08 0.18 0.00
133_D 15_M 1.06 0.17 0.00
25_V 5_H 1.05 0.17 0.00
65_T 29_K 1.03 0.16 0.00
69_N 33_W 1.02 0.16 0.00
157_Y 12_H 1.01 0.15 0.00
36_V 26_G 1.01 0.15 0.00
127_L 42_L 1.00 0.15 0.00
47_I 43_V 1.00 0.15 0.00
203_P 9_D 1.00 0.15 0.00
32_G 35_S 0.99 0.15 0.00
165_I 32_T 0.99 0.15 0.00
108_G 40_A 0.98 0.14 0.00
121_F 17_I 0.97 0.14 0.00
82_L 37_L 0.96 0.14 0.00
114_N 35_S 0.94 0.13 0.00
112_G 4_H 0.94 0.13 0.00
95_V 39_I 0.93 0.13 0.00
157_Y 20_Q 0.93 0.13 0.00
137_I 28_I 0.93 0.13 0.00
126_I 44_F 0.92 0.12 0.00
183_F 27_F 0.92 0.12 0.00
192_A 44_F 0.90 0.12 0.00
30_A 39_I 0.90 0.12 0.00
100_D 43_V 0.90 0.12 0.00
66_A 29_K 0.88 0.11 0.00
22_E 5_H 0.88 0.11 0.00
129_S 45_L 0.87 0.11 0.00
193_K 47_L 0.87 0.11 0.00
176_L 27_F 0.86 0.11 0.00
129_S 25_A 0.86 0.11 0.00
49_F 45_L 0.85 0.11 0.00
94_K 34_V 0.85 0.11 0.00
69_N 18_R 0.85 0.11 0.00
185_F 13_G 0.85 0.10 0.00
17_I 33_W 0.84 0.10 0.00
146_H 34_V 0.84 0.10 0.00
52_N 35_S 0.84 0.10 0.00
67_V 6_E 0.84 0.10 0.00
49_F 22_A 0.84 0.10 0.00
82_L 2_A 0.84 0.10 0.00
65_T 44_F 0.83 0.10 0.00
102_L 7_I 0.82 0.10 0.00
157_Y 14_E 0.82 0.10 0.00
165_I 31_A 0.82 0.10 0.00
23_N 39_I 0.82 0.10 0.00
129_S 12_H 0.82 0.10 0.00
104_P 32_T 0.81 0.10 0.00
89_Q 40_A 0.81 0.10 0.00
137_I 30_G 0.81 0.10 0.00
46_L 45_L 0.81 0.10 0.00
87_Q 40_A 0.80 0.10 0.00
77_D 22_A 0.80 0.10 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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