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OPENSEQ.org
Kam_complex
Genes: A B A+B
Length: 157 223 360
Sequences: 6935 5162 213
Seq/Len: 44.17 23.15 0.59
MirrorTree (Pazo et al. 2001) 0.64
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 0.02 0.06 0.04
2 0.02 0.07 0.07
5 0.03 0.08 0.13
10 0.03 0.08 0.31
20 0.04 0.08 0.56
100 0.11 0.11 1.63
∞ 0.20 0.18 4.61
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
52_T 177_L 1.48 0.60 0.00
12_S 62_H 1.46 0.58 0.00
9_F 159_W 1.46 0.58 0.00
137_I 138_I 1.32 0.47 0.00
37_M 195_N 1.28 0.43 0.00
94_E 119_I 1.26 0.42 0.00
133_I 8_V 1.22 0.39 0.00
66_I 186_K 1.21 0.38 0.00
61_I 55_T 1.20 0.38 0.00
88_M 166_Q 1.17 0.36 0.00
117_V 186_K 1.17 0.35 0.00
99_A 37_E 1.17 0.35 0.00
127_I 150_V 1.13 0.33 0.00
128_I 142_F 1.12 0.32 0.00
106_M 52_G 1.11 0.31 0.00
33_A 157_K 1.10 0.30 0.00
50_V 206_A 1.07 0.29 0.00
65_D 201_G 1.07 0.28 0.00
115_L 94_V 1.07 0.28 0.00
49_P 114_G 1.07 0.28 0.00
62_S 136_N 1.05 0.27 0.00
27_F 198_L 1.05 0.27 0.00
109_I 24_N 1.04 0.27 0.00
18_L 7_G 1.04 0.27 0.00
122_N 8_V 1.04 0.27 0.00
17_Y 204_L 1.03 0.26 0.00
105_I 7_G 1.01 0.24 0.00
77_D 32_I 1.00 0.24 0.00
127_I 53_D 0.99 0.24 0.00
133_I 103_N 0.99 0.23 0.00
124_F 19_A 0.98 0.23 0.00
132_S 7_G 0.98 0.23 0.00
84_D 158_S 0.98 0.23 0.00
36_V 121_P 0.97 0.23 0.00
89_V 22_L 0.96 0.22 0.00
62_S 203_I 0.96 0.22 0.00
113_P 164_V 0.95 0.21 0.00
132_S 189_D 0.94 0.21 0.00
51_I 30_I 0.94 0.21 0.00
96_I 71_V 0.94 0.21 0.00
94_E 95_P 0.93 0.20 0.00
56_K 180_I 0.93 0.20 0.00
104_A 86_V 0.92 0.20 0.00
88_M 193_P 0.92 0.20 0.00
38_L 121_P 0.91 0.19 0.00
66_I 133_L 0.91 0.19 0.00
64_S 119_I 0.91 0.19 0.00
96_I 179_G 0.90 0.19 0.00
45_F 198_L 0.90 0.19 0.00
143_D 177_L 0.90 0.19 0.00
122_N 180_I 0.90 0.19 0.00
99_A 34_S 0.90 0.18 0.00
89_V 15_G 0.90 0.18 0.00
102_L 166_Q 0.90 0.18 0.00
29_D 23_S 0.89 0.18 0.00
61_I 157_K 0.89 0.18 0.00
27_F 59_F 0.89 0.18 0.00
120_D 103_N 0.89 0.18 0.00
109_I 207_I 0.89 0.18 0.00
121_Q 31_A 0.89 0.18 0.00
41_A 72_I 0.89 0.18 0.00
16_H 31_A 0.89 0.18 0.00
137_I 206_A 0.88 0.18 0.00
56_K 163_T 0.88 0.18 0.00
58_V 50_A 0.88 0.17 0.00
95_P 52_G 0.88 0.17 0.00
104_A 105_V 0.88 0.17 0.00
46_S 50_A 0.87 0.17 0.00
33_A 88_H 0.87 0.17 0.00
102_L 115_A 0.87 0.17 0.00
60_T 129_V 0.87 0.17 0.00
59_G 22_L 0.87 0.17 0.00
118_I 59_F 0.87 0.17 0.00
61_I 175_L 0.87 0.17 0.00
127_I 176_N 0.86 0.17 0.00
141_L 172_K 0.86 0.17 0.00
93_I 81_S 0.86 0.17 0.00
88_M 61_K 0.86 0.17 0.00
131_K 61_K 0.86 0.17 0.00
36_V 208_A 0.85 0.17 0.00
30_T 59_F 0.85 0.16 0.00
23_D 180_I 0.85 0.16 0.00
56_K 35_N 0.85 0.16 0.00
16_H 30_I 0.84 0.16 0.00
122_N 182_K 0.84 0.16 0.00
44_G 77_N 0.84 0.16 0.00
27_F 146_S 0.84 0.16 0.00
13_H 162_K 0.84 0.16 0.00
102_L 49_A 0.84 0.16 0.00
106_M 215_R 0.84 0.16 0.00
95_P 196_S 0.84 0.16 0.00
127_I 35_N 0.84 0.16 0.00
127_I 49_A 0.83 0.16 0.00
85_I 180_I 0.83 0.16 0.00
96_I 49_A 0.83 0.16 0.00
60_T 174_D 0.83 0.16 0.00
22_E 133_L 0.83 0.15 0.00
16_H 35_N 0.83 0.15 0.00
13_H 32_I 0.83 0.15 0.00
118_I 113_I 0.83 0.15 0.00
115_L 54_I 0.83 0.15 0.00
46_S 39_V 0.82 0.15 0.00
95_P 71_V 0.82 0.15 0.00
2_I 211_D 0.82 0.15 0.00
40_L 84_L 0.82 0.15 0.00
36_V 98_I 0.82 0.15 0.00
40_L 198_L 0.82 0.15 0.00
129_T 131_A 0.82 0.15 0.00
96_I 177_L 0.82 0.15 0.00
137_I 182_K 0.82 0.15 0.00
119_S 123_R 0.82 0.15 0.00
83_T 24_N 0.82 0.15 0.00
6_F 117_L 0.82 0.15 0.00
61_I 58_A 0.82 0.15 0.00
15_D 204_L 0.81 0.15 0.00
144_F 52_G 0.81 0.15 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)
ID Seq/Len Name Options I_Prob Status
10788 4.99 Kam_complex Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10758 0.59 Kam_complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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