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OPENSEQ.org
cIp_5_40_cIV_C_40
Genes: A B A+B
Length: 207 274 465
Sequences: 946 2529 325
Seq/Len: 4.57 9.23 0.7
MirrorTree (Pazo et al. 2001) 0.66
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 0.01
2 0.00 0.00 0.02
5 0.00 0.00 0.05
10 0.00 0.00 0.08
20 0.00 0.00 0.13
100 0.00 0.00 0.19
∞ 0.00 0.00 0.68
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
103_V 219_A 1.54 0.70 0.00
123_L 22_A 1.42 0.60 0.00
40_L 61_Y 1.35 0.55 0.00
34_L 64_F 1.29 0.50 0.00
38_A 219_A 1.27 0.48 0.00
171_Y 183_G 1.23 0.45 0.00
109_V 196_H 1.21 0.43 0.00
111_P 77_G 1.21 0.43 0.00
121_F 35_W 1.19 0.41 0.00
17_I 26_F 1.19 0.41 0.00
60_T 222_I 1.19 0.41 0.00
17_I 191_A 1.16 0.39 0.00
15_E 156_V 1.13 0.36 0.00
109_V 50_W 1.13 0.36 0.00
172_E 225_T 1.11 0.35 0.00
79_V 150_L 1.11 0.35 0.00
107_I 200_G 1.11 0.34 0.00
155_T 14_P 1.10 0.34 0.00
126_I 3_H 1.09 0.33 0.00
60_T 57_V 1.08 0.33 0.00
22_E 246_V 1.08 0.33 0.00
180_Y 269_I 1.04 0.30 0.00
46_L 155_A 1.03 0.29 0.00
124_F 26_F 1.03 0.29 0.00
107_I 189_L 1.03 0.29 0.00
124_F 59_V 1.03 0.29 0.00
124_F 22_A 1.02 0.28 0.00
121_F 8_D 1.01 0.28 0.00
76_F 110_I 1.01 0.28 0.00
170_V 52_F 1.01 0.28 0.00
82_L 91_F 1.01 0.27 0.00
43_V 71_V 0.99 0.26 0.00
121_F 203_D 0.99 0.26 0.00
120_V 64_F 0.99 0.26 0.00
26_I 21_G 0.99 0.26 0.00
121_F 105_W 0.98 0.26 0.00
17_I 195_S 0.98 0.26 0.00
106_L 156_V 0.97 0.25 0.00
15_E 211_Y 0.96 0.25 0.00
110_F 112_N 0.95 0.24 0.00
40_L 135_T 0.95 0.24 0.00
167_K 241_T 0.93 0.23 0.00
36_V 26_F 0.93 0.23 0.00
32_G 242_Q 0.93 0.22 0.00
67_V 161_H 0.92 0.22 0.00
36_V 244_Q 0.92 0.22 0.00
93_V 19_F 0.92 0.22 0.00
78_V 192_Y 0.92 0.22 0.00
164_D 269_I 0.92 0.22 0.00
126_I 173_I 0.92 0.22 0.00
174_V 211_Y 0.91 0.21 0.00
168_R 92_I 0.91 0.21 0.00
154_T 199_F 0.91 0.21 0.00
179_E 211_Y 0.90 0.21 0.00
111_P 82_V 0.90 0.21 0.00
25_V 205_V 0.90 0.21 0.00
21_R 11_I 0.89 0.20 0.00
29_Q 60_L 0.89 0.20 0.00
56_C 26_F 0.88 0.20 0.00
21_R 155_A 0.88 0.20 0.00
70_P 231_C 0.88 0.20 0.00
123_L 267_V 0.88 0.20 0.00
146_H 54_I 0.87 0.19 0.00
144_R 250_A 0.87 0.19 0.00
108_G 167_G 0.87 0.19 0.00
48_E 229_F 0.87 0.19 0.00
17_I 229_F 0.86 0.19 0.00
95_V 211_Y 0.86 0.19 0.00
73_P 139_W 0.86 0.19 0.00
175_N 113_A 0.86 0.18 0.00
111_P 247_G 0.85 0.18 0.00
106_L 21_G 0.85 0.18 0.00
38_A 240_M 0.85 0.18 0.00
174_V 212_M 0.85 0.18 0.00
91_I 23_I 0.85 0.18 0.00
131_H 3_H 0.85 0.18 0.00
92_R 150_L 0.85 0.18 0.00
184_D 89_Y 0.85 0.18 0.00
177_V 144_I 0.85 0.18 0.00
74_A 223_I 0.85 0.18 0.00
179_E 36_M 0.85 0.18 0.00
149_R 84_R 0.84 0.18 0.00
103_V 211_Y 0.84 0.18 0.00
36_V 59_V 0.84 0.18 0.00
70_P 92_I 0.84 0.18 0.00
184_D 213_A 0.84 0.17 0.00
93_V 211_Y 0.84 0.17 0.00
83_L 249_E 0.84 0.17 0.00
81_H 28_M 0.83 0.17 0.00
94_K 26_F 0.83 0.17 0.00
120_V 237_K 0.83 0.17 0.00
64_I 205_V 0.83 0.17 0.00
160_V 136_F 0.83 0.17 0.00
168_R 219_A 0.83 0.17 0.00
194_Y 105_W 0.83 0.17 0.00
149_R 94_F 0.83 0.17 0.00
22_E 154_V 0.83 0.17 0.00
15_E 52_F 0.83 0.17 0.00
17_I 267_V 0.82 0.17 0.00
116_Y 59_V 0.82 0.17 0.00
62_I 71_V 0.82 0.17 0.00
154_T 52_F 0.82 0.17 0.00
46_L 246_V 0.82 0.17 0.00
191_G 183_G 0.82 0.17 0.00
132_S 24_G 0.82 0.17 0.00
78_V 134_V 0.82 0.17 0.00
121_F 32_A 0.82 0.17 0.00
25_V 33_V 0.82 0.17 0.00
137_I 261_V 0.81 0.16 0.00
36_V 61_Y 0.81 0.16 0.00
158_V 91_F 0.81 0.16 0.00
120_V 273_G 0.81 0.16 0.00
109_V 225_T 0.81 0.16 0.00
67_V 162_A 0.81 0.16 0.00
46_L 11_I 0.81 0.16 0.00
79_V 263_L 0.81 0.16 0.00
174_V 238_G 0.81 0.16 0.00
97_V 155_A 0.80 0.16 0.00
109_V 33_V 0.80 0.16 0.00
149_R 250_A 0.80 0.16 0.00
44_I 237_K 0.80 0.16 0.00
18_A 247_G 0.80 0.16 0.00
11_L 68_A 0.80 0.16 0.00
95_V 135_T 0.80 0.16 0.00
186_L 124_K 0.80 0.16 0.00
53_D 183_G 0.80 0.16 0.00
34_L 38_G 0.79 0.15 0.00
88_N 88_Q 0.79 0.15 0.00
129_S 61_Y 0.79 0.15 0.00
31_V 192_Y 0.79 0.15 0.00
93_V 219_A 0.79 0.15 0.00
109_V 241_T 0.79 0.15 0.00
177_V 93_L 0.79 0.15 0.00
177_V 84_R 0.78 0.15 0.00
92_R 21_G 0.78 0.15 0.00
93_V 181_I 0.78 0.15 0.00
139_T 157_T 0.78 0.15 0.00
71_A 267_V 0.78 0.15 0.00
112_G 61_Y 0.78 0.15 0.00
175_N 63_M 0.78 0.15 0.00
21_R 108_A 0.78 0.15 0.00
57_R 74_G 0.78 0.15 0.00
154_T 179_A 0.77 0.15 0.00
86_Y 177_I 0.77 0.14 0.00
201_K 105_W 0.77 0.14 0.00
166_E 238_G 0.77 0.14 0.00
182_Q 181_I 0.77 0.14 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
3972 0.7 cIp_5_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3970 0.75 cIp_5_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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