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OPENSEQ.org
cIp_2_4_cIV_D_4
Genes: A B A+B
Length: 239 50 280
Sequences: 755 202 74
Seq/Len: 3.16 4.04 0.26
MirrorTree (Pazo et al. 2001) 0.20
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 0.01 0.00 0.00
20 0.01 0.00 0.00
100 0.01 0.01 0.00
∞ 0.04 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
77_T 19_H 1.49 0.37 0.00
153_F 20_Q 1.40 0.32 0.00
26_Q 36_I 1.30 0.27 0.00
89_S 45_L 1.28 0.26 0.00
110_I 38_S 1.22 0.23 0.00
22_W 36_I 1.21 0.22 0.00
11_D 32_T 1.16 0.20 0.00
125_S 28_I 1.13 0.19 0.00
147_A 20_Q 1.11 0.18 0.00
162_L 44_F 1.10 0.18 0.00
116_K 13_G 1.04 0.16 0.00
95_I 43_V 1.04 0.15 0.00
121_P 46_A 1.03 0.15 0.00
93_I 3_S 1.03 0.15 0.00
166_I 37_L 1.02 0.15 0.00
93_I 24_F 1.02 0.15 0.00
160_E 5_H 1.01 0.15 0.00
81_M 44_F 1.00 0.14 0.00
190_G 34_V 0.99 0.14 0.00
55_R 39_I 0.98 0.14 0.00
166_I 13_G 0.98 0.14 0.00
185_S 25_A 0.95 0.13 0.00
146_M 20_Q 0.95 0.13 0.00
61_C 35_S 0.94 0.13 0.00
23_A 42_L 0.92 0.12 0.00
171_A 13_G 0.91 0.12 0.00
130_F 47_L 0.91 0.12 0.00
3_R 20_Q 0.90 0.12 0.00
194_A 43_V 0.90 0.12 0.00
165_L 44_F 0.90 0.11 0.00
116_K 40_A 0.90 0.11 0.00
189_L 37_L 0.90 0.11 0.00
45_R 36_I 0.89 0.11 0.00
129_R 20_Q 0.89 0.11 0.00
102_M 12_H 0.89 0.11 0.00
75_V 15_M 0.88 0.11 0.00
102_M 11_K 0.87 0.11 0.00
100_T 20_Q 0.87 0.11 0.00
16_T 48_A 0.87 0.11 0.00
194_A 22_A 0.87 0.11 0.00
19_N 36_I 0.86 0.10 0.00
17_P 26_G 0.85 0.10 0.00
61_C 36_I 0.85 0.10 0.00
77_T 30_G 0.84 0.10 0.00
17_P 21_Q 0.84 0.10 0.00
72_A 18_R 0.84 0.10 0.00
72_A 36_I 0.83 0.10 0.00
12_S 18_R 0.83 0.10 0.00
75_V 14_E 0.83 0.10 0.00
48_E 46_A 0.82 0.10 0.00
55_R 14_E 0.82 0.10 0.00
121_P 43_V 0.82 0.09 0.00
164_A 26_G 0.81 0.09 0.00
36_Q 14_E 0.81 0.09 0.00
26_Q 35_S 0.81 0.09 0.00
77_T 45_L 0.81 0.09 0.00
28_T 34_V 0.81 0.09 0.00
66_G 16_D 0.81 0.09 0.00
160_E 3_S 0.81 0.09 0.00
162_L 36_I 0.81 0.09 0.00
76_A 23_T 0.80 0.09 0.00
173_E 8_T 0.80 0.09 0.00
193_T 15_M 0.79 0.09 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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