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OPENSEQ.org
cI_C_cIII_isp_Pdenitr
Genes: A B A+B
Length: 208 190 382
Sequences: 1081 1692 366
Seq/Len: 5.2 8.91 0.96
MirrorTree (Pazo et al. 2001) 0.55
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 0.01 0.01 0.01
10 0.01 0.01 0.01
20 0.01 0.01 0.01
100 0.02 0.01 0.12
∞ 0.05 0.05 0.92
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
96_V 87_Q 1.13 0.45 0.00
47_L 83_E 1.12 0.44 0.00
165_D 86_I 1.10 0.42 0.00
168_K 176_I 1.09 0.41 0.00
124_L 109_D 1.09 0.41 0.00
43_G 63_T 1.08 0.40 0.00
30_V 84_D 1.07 0.39 0.00
171_V 185_T 1.07 0.39 0.00
128_L 187_I 1.06 0.38 0.00
155_T 26_A 1.04 0.36 0.00
77_F 15_R 1.03 0.36 0.00
37_V 84_D 1.03 0.35 0.00
46_G 31_A 0.98 0.32 0.00
114_A 59_S 0.98 0.31 0.00
66_T 22_A 0.97 0.31 0.00
130_S 78_I 0.97 0.31 0.00
107_L 33_A 0.95 0.29 0.00
131_G 45_S 0.94 0.29 0.00
45_I 84_D 0.94 0.28 0.00
67_A 26_A 0.94 0.28 0.00
55_P 148_G 0.93 0.28 0.00
85_S 149_G 0.92 0.27 0.00
54_D 112_A 0.92 0.27 0.00
74_P 188_K 0.90 0.25 0.00
42_S 124_E 0.89 0.25 0.00
181_Y 98_I 0.89 0.25 0.00
62_L 19_L 0.89 0.25 0.00
86_M 45_S 0.88 0.24 0.00
111_F 184_D 0.88 0.24 0.00
62_L 16_R 0.88 0.24 0.00
159_V 129_I 0.88 0.24 0.00
168_K 31_A 0.87 0.24 0.00
182_R 85_E 0.87 0.23 0.00
93_R 148_G 0.87 0.23 0.00
113_G 67_L 0.86 0.23 0.00
171_V 28_T 0.85 0.22 0.00
159_V 72_L 0.85 0.22 0.00
64_D 81_R 0.84 0.22 0.00
171_V 143_G 0.84 0.22 0.00
27_S 175_H 0.83 0.21 0.00
33_G 112_A 0.83 0.21 0.00
204_P 93_D 0.83 0.21 0.00
147_H 176_I 0.83 0.21 0.00
59_F 73_G 0.83 0.21 0.00
130_S 180_E 0.83 0.21 0.00
60_S 121_E 0.83 0.21 0.00
121_V 48_V 0.82 0.21 0.00
65_I 174_L 0.82 0.20 0.00
176_N 15_R 0.82 0.20 0.00
92_I 25_G 0.81 0.20 0.00
158_Y 158_H 0.81 0.20 0.00
128_L 32_G 0.81 0.20 0.00
90_Q 59_S 0.81 0.20 0.00
42_S 32_G 0.80 0.19 0.00
104_V 167_R 0.80 0.19 0.00
163_W 126_L 0.80 0.19 0.00
164_S 81_R 0.80 0.19 0.00
37_V 54_I 0.80 0.19 0.00
127_I 186_T 0.80 0.19 0.00
142_Y 173_N 0.79 0.19 0.00
124_L 147_F 0.79 0.19 0.00
25_V 24_A 0.79 0.19 0.00
193_A 52_A 0.79 0.18 0.00
37_V 125_W 0.79 0.18 0.00
187_L 84_D 0.78 0.18 0.00
56_N 131_V 0.78 0.18 0.00
87_Y 181_F 0.78 0.18 0.00
108_I 112_A 0.78 0.18 0.00
115_N 28_T 0.78 0.18 0.00
21_R 158_H 0.78 0.18 0.00
179_Q 141_G 0.78 0.18 0.00
39_A 9_G 0.78 0.18 0.00
127_I 48_V 0.78 0.18 0.00
181_Y 78_I 0.78 0.18 0.00
23_N 61_V 0.78 0.18 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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