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OPENSEQ.org
CC_scpA-scpB_complex
Genes: A B A+B
Length: 274 221 446
Sequences: 2182 1920 1597
Seq/Len: 7.96 8.69 3.58
MirrorTree (Pazo et al. 2001) 0.82
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 3.18
2 0.00 0.00 3.19
5 0.00 0.00 3.21
10 0.00 0.00 3.21
20 0.00 0.00 3.23
100 0.00 0.00 3.24
∞ 0.00 0.00 3.44
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
79_Y 65_R 1.88 1.00 0.97
143_F 73_S 1.72 0.99 0.95
139_K 153_E 1.53 0.97 0.90
79_Y 153_E 1.50 0.97 0.89
77_A 54_G 1.41 0.95 0.85
74_A 165_G 1.33 0.93 0.80
79_Y 23_P 1.32 0.93 0.79
125_M 100_H 1.27 0.90 0.76
239_S 145_F 1.26 0.90 0.75
128_A 165_G 1.23 0.89 0.72
135_R 157_L 1.23 0.89 0.72
62_L 111_V 1.23 0.88 0.72
80_L 109_E 1.14 0.83 0.64
169_A 95_A 1.14 0.83 0.64
145_R 18_F 1.11 0.81 0.61
77_A 117_S 1.10 0.80 0.60
78_D 87_S 1.10 0.80 0.60
123_D 160_L 1.09 0.79 0.59
144_T 67_Q 1.06 0.76 0.55
170_Y 100_H 1.04 0.74 0.53
139_K 23_P 1.02 0.73 0.51
125_M 103_V 1.01 0.71 0.50
76_A 61_A 1.00 0.70 0.48
84_A 146_G 0.99 0.68 0.47
248_G 50_Y 0.97 0.66 0.44
44_S 28_D 0.94 0.63 0.41
46_K 54_G 0.94 0.63 0.41
147_D 130_I 0.94 0.62 0.40
77_A 132_M 0.93 0.62 0.40
143_F 68_T 0.93 0.61 0.39
24_L 117_S 0.92 0.61 0.39
45_Q 23_P 0.92 0.61 0.39
239_S 65_R 0.92 0.60 0.39
87_A 117_S 0.92 0.60 0.39
78_D 121_I 0.92 0.60 0.38
78_D 103_V 0.92 0.60 0.38
129_V 157_L 0.91 0.60 0.38
72_R 22_E 0.91 0.60 0.38
81_V 61_A 0.91 0.59 0.37
54_I 117_S 0.91 0.59 0.37
123_D 117_S 0.91 0.59 0.37
216_A 42_G 0.90 0.58 0.36
144_T 18_F 0.90 0.57 0.36
255_L 97_V 0.90 0.57 0.36
138_L 70_A 0.89 0.57 0.35
54_I 126_E 0.89 0.57 0.35
203_L 108_I 0.89 0.57 0.35
29_D 20_A 0.89 0.56 0.35
128_A 166_I 0.89 0.56 0.35
62_L 176_E 0.88 0.56 0.34
28_I 95_A 0.88 0.56 0.34
78_D 91_Q 0.88 0.56 0.34
126_R 42_G 0.88 0.55 0.34
157_T 55_V 0.88 0.55 0.34
55_T 100_H 0.88 0.55 0.34
58_A 100_H 0.88 0.55 0.34
174_R 166_I 0.88 0.55 0.34
52_L 137_R 0.87 0.54 0.33
113_A 142_P 0.86 0.53 0.32
184_P 97_V 0.86 0.53 0.32
59_E 103_V 0.86 0.53 0.32
37_V 93_T 0.85 0.52 0.31
213_T 97_V 0.85 0.52 0.31
62_L 97_V 0.85 0.52 0.31
77_A 53_R 0.85 0.51 0.30
172_T 29_L 0.85 0.51 0.30
263_L 93_T 0.84 0.51 0.30
221_V 91_Q 0.84 0.51 0.30
78_D 68_T 0.84 0.51 0.30
170_Y 19_A 0.83 0.49 0.29
35_L 109_E 0.83 0.49 0.29
207_E 130_I 0.83 0.49 0.28
149_D 127_L 0.82 0.48 0.28
173_Q 95_A 0.82 0.47 0.27
190_Y 127_L 0.82 0.47 0.27
24_L 105_R 0.82 0.47 0.27
43_R 155_Y 0.81 0.47 0.27
62_L 170_K 0.81 0.46 0.26
244_L 123_V 0.81 0.46 0.26
202_L 125_L 0.81 0.46 0.26
47_V 171_A 0.81 0.46 0.26
26_I 166_I 0.81 0.46 0.26
181_H 29_L 0.80 0.45 0.26
142_V 56_E 0.80 0.45 0.25
71_V 107_E 0.80 0.44 0.25
174_R 133_R 0.79 0.43 0.24
60_Q 109_E 0.79 0.43 0.24
163_L 155_Y 0.79 0.43 0.24
168_S 59_C 0.79 0.43 0.24
61_Y 108_I 0.79 0.43 0.24
84_A 135_R 0.79 0.43 0.24
82_M 172_A 0.78 0.43 0.24
142_V 128_G 0.78 0.43 0.23
50_L 147_T 0.78 0.43 0.23
79_Y 129_L 0.78 0.43 0.23
154_V 57_L 0.78 0.42 0.23
46_K 80_R 0.78 0.42 0.23
216_A 111_V 0.77 0.42 0.23
35_L 23_P 0.77 0.42 0.23
245_V 125_L 0.77 0.41 0.23
163_L 126_E 0.77 0.41 0.23
72_R 71_D 0.77 0.41 0.23
258_F 96_I 0.77 0.41 0.22
23_A 116_A 0.76 0.40 0.22
91_S 131_R 0.76 0.40 0.22
53_S 120_T 0.76 0.40 0.21
204_P 162_D 0.76 0.40 0.21
189_A 145_F 0.76 0.40 0.21
126_R 145_F 0.76 0.40 0.21
208_D 25_S 0.76 0.39 0.21
245_V 96_I 0.76 0.39 0.21
81_V 115_Q 0.76 0.39 0.21
162_D 158_A 0.76 0.39 0.21
55_T 11_R 0.75 0.39 0.21
45_Q 142_P 0.75 0.39 0.21
91_S 141_R 0.75 0.39 0.21
89_L 66_F 0.75 0.39 0.21
39_L 105_R 0.75 0.39 0.21
199_L 89_A 0.75 0.39 0.21
29_D 70_A 0.75 0.39 0.20
28_I 166_I 0.75 0.39 0.20
78_D 162_D 0.75 0.38 0.20
248_G 55_V 0.75 0.38 0.20
125_M 143_V 0.75 0.38 0.20
175_K 93_T 0.74 0.38 0.20
74_A 169_M 0.74 0.38 0.20
250_L 62_G 0.74 0.37 0.20
241_S 121_I 0.74 0.37 0.20
129_V 73_S 0.74 0.37 0.20
206_M 16_L 0.73 0.37 0.19
58_A 122_D 0.73 0.36 0.19
256_E 52_G 0.73 0.36 0.19
96_P 95_A 0.73 0.36 0.18
106_P 57_L 0.73 0.36 0.18
84_A 33_L 0.72 0.35 0.18
248_G 24_L 0.72 0.35 0.18
235_A 108_I 0.72 0.35 0.18
135_R 9_V 0.72 0.35 0.18
174_R 146_G 0.71 0.34 0.17
94_L 105_R 0.71 0.34 0.17
209_W 25_S 0.71 0.34 0.17
264_R 130_I 0.71 0.34 0.17
24_L 136_R 0.71 0.34 0.17
128_A 9_V 0.71 0.34 0.17
248_G 93_T 0.71 0.34 0.17
140_R 130_I 0.71 0.34 0.17
210_T 44_D 0.71 0.34 0.17
170_Y 154_H 0.70 0.33 0.17
235_A 89_A 0.70 0.33 0.17
44_S 130_I 0.70 0.33 0.17
261_I 153_E 0.70 0.33 0.16
162_D 63_R 0.70 0.33 0.16
259_Q 54_G 0.70 0.33 0.16
97_K 33_L 0.70 0.33 0.16
107_P 95_A 0.70 0.32 0.16
39_L 99_Y 0.70 0.32 0.16
21_G 108_I 0.70 0.32 0.16
76_A 46_L 0.70 0.32 0.16
236_S 19_A 0.69 0.32 0.16
88_Y 154_H 0.69 0.32 0.16
143_F 103_V 0.69 0.32 0.16
204_P 97_V 0.69 0.32 0.16
85_W 100_H 0.69 0.32 0.16
263_L 29_L 0.69 0.32 0.16
164_Y 162_D 0.69 0.32 0.16
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
6885 2.04 t Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.71 Done - Shared
2846 3.58 CC_scpA-scpB_complex Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
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