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OPENSEQ.org
cIp_5_4_cIV_C_4
Genes: A B A+B
Length: 207 274 461
Sequences: 1036 2893 347
Seq/Len: 5 10.56 0.75
MirrorTree (Pazo et al. 2001) 0.35
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 0.20
∞ 0.01 0.01 0.72
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
21_R 11_I 1.35 0.57 0.00
17_I 191_A 1.34 0.56 0.00
17_I 26_F 1.31 0.53 0.00
38_A 219_A 1.29 0.51 0.00
123_L 22_A 1.24 0.47 0.00
103_V 219_A 1.23 0.46 0.00
111_P 77_G 1.22 0.46 0.00
40_L 61_Y 1.18 0.42 0.00
98_R 126_G 1.14 0.39 0.00
41_S 52_F 1.12 0.37 0.00
106_L 21_G 1.11 0.36 0.00
180_Y 269_I 1.09 0.35 0.00
155_T 14_P 1.04 0.31 0.00
124_F 59_V 1.03 0.30 0.00
47_I 188_G 1.03 0.30 0.00
34_L 64_F 1.02 0.30 0.00
107_I 200_G 1.01 0.29 0.00
32_G 242_Q 1.00 0.28 0.00
91_I 56_L 1.00 0.28 0.00
137_I 261_V 0.99 0.27 0.00
124_F 26_F 0.98 0.27 0.00
60_T 222_I 0.97 0.26 0.00
121_F 8_D 0.97 0.26 0.00
169_V 263_L 0.97 0.26 0.00
11_L 132_G 0.96 0.26 0.00
121_F 35_W 0.96 0.25 0.00
179_E 211_Y 0.96 0.25 0.00
21_R 229_F 0.94 0.24 0.00
31_V 229_F 0.94 0.24 0.00
107_I 53_L 0.93 0.24 0.00
107_I 189_L 0.93 0.23 0.00
106_L 156_V 0.92 0.23 0.00
26_I 21_G 0.90 0.22 0.00
93_V 211_Y 0.90 0.22 0.00
41_S 19_F 0.90 0.22 0.00
34_L 38_G 0.89 0.21 0.00
121_F 105_W 0.89 0.21 0.00
194_Y 105_W 0.88 0.21 0.00
126_I 3_H 0.88 0.21 0.00
17_I 195_S 0.88 0.20 0.00
144_R 148_I 0.88 0.20 0.00
107_I 71_V 0.87 0.20 0.00
109_V 50_W 0.86 0.20 0.00
51_R 205_V 0.86 0.20 0.00
107_I 20_F 0.86 0.20 0.00
129_S 56_L 0.86 0.19 0.00
17_I 177_I 0.85 0.19 0.00
131_H 104_A 0.85 0.19 0.00
91_I 23_I 0.85 0.19 0.00
109_V 225_T 0.85 0.19 0.00
79_V 150_L 0.84 0.19 0.00
51_R 50_W 0.84 0.18 0.00
76_F 110_I 0.84 0.18 0.00
129_S 20_F 0.83 0.18 0.00
131_H 154_V 0.83 0.18 0.00
87_Q 24_G 0.83 0.18 0.00
64_I 54_I 0.83 0.18 0.00
120_V 237_K 0.83 0.18 0.00
82_L 91_F 0.83 0.18 0.00
36_V 59_V 0.82 0.18 0.00
180_Y 16_I 0.82 0.18 0.00
120_V 64_F 0.82 0.17 0.00
71_A 269_I 0.82 0.17 0.00
108_G 170_K 0.82 0.17 0.00
137_I 189_L 0.81 0.17 0.00
116_Y 59_V 0.81 0.17 0.00
88_N 238_G 0.81 0.17 0.00
46_L 229_F 0.81 0.17 0.00
18_A 147_L 0.81 0.17 0.00
36_V 61_Y 0.80 0.17 0.00
91_I 222_I 0.80 0.17 0.00
114_N 22_A 0.80 0.17 0.00
157_Y 144_I 0.80 0.17 0.00
124_F 103_V 0.80 0.17 0.00
110_F 91_F 0.80 0.17 0.00
92_R 21_G 0.80 0.16 0.00
103_V 211_Y 0.80 0.16 0.00
191_G 238_G 0.80 0.16 0.00
109_V 196_H 0.80 0.16 0.00
158_V 91_F 0.80 0.16 0.00
58_F 135_T 0.79 0.16 0.00
137_I 53_L 0.79 0.16 0.00
110_F 179_A 0.79 0.16 0.00
101_E 209_A 0.79 0.16 0.00
64_I 205_V 0.79 0.16 0.00
36_V 20_F 0.79 0.16 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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