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OPENSEQ.org
cIp_5_2_cIV_B_6
Genes: A B A+B
Length: 207 298 464
Sequences: 998 2942 468
Seq/Len: 4.82 9.87 1.01
MirrorTree (Pazo et al. 2001) 0.31
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 0.02
5 0.00 0.01 0.04
10 0.00 0.01 0.08
20 0.00 0.02 0.12
100 0.00 0.03 0.20
∞ 0.01 0.08 0.93
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
110_F 205_A 1.81 0.91 0.42
137_I 241_Y 1.44 0.73 0.18
91_I 145_A 1.40 0.70 0.16
124_F 99_R 1.31 0.62 0.12
162_W 119_V 1.24 0.56 0.10
100_D 146_I 1.12 0.45 0.07
124_F 273_A 1.08 0.41 0.06
126_I 274_G 1.06 0.40 0.05
48_E 195_V 1.06 0.39 0.05
36_V 104_T 1.01 0.35 0.04
63_D 218_A 1.00 0.34 0.04
123_L 109_I 0.99 0.33 0.04
129_S 116_L 0.96 0.31 0.04
17_I 170_K 0.96 0.31 0.04
97_V 238_E 0.94 0.29 0.03
114_N 108_V 0.93 0.29 0.03
46_L 146_I 0.91 0.27 0.03
166_E 267_K 0.88 0.25 0.03
53_D 118_L 0.88 0.25 0.03
114_N 112_L 0.85 0.23 0.02
137_I 163_F 0.85 0.23 0.02
124_F 88_R 0.85 0.23 0.02
95_V 223_A 0.84 0.23 0.02
109_V 191_V 0.84 0.22 0.02
126_I 191_V 0.83 0.22 0.02
44_I 264_S 0.83 0.21 0.02
93_V 155_E 0.83 0.21 0.02
110_F 242_F 0.83 0.21 0.02
124_F 105_P 0.82 0.21 0.02
41_S 35_D 0.81 0.20 0.02
170_V 74_V 0.80 0.20 0.02
106_L 272_L 0.80 0.20 0.02
64_I 202_Q 0.80 0.20 0.02
43_V 171_E 0.80 0.20 0.02
111_P 158_N 0.80 0.20 0.02
36_V 67_V 0.79 0.19 0.02
21_R 160_G 0.79 0.19 0.02
115_W 152_W 0.79 0.19 0.02
99_E 203_V 0.78 0.19 0.02
32_G 237_Q 0.78 0.19 0.02
123_L 69_Y 0.78 0.19 0.02
82_L 141_L 0.78 0.18 0.01
85_M 145_A 0.78 0.18 0.01
126_I 182_E 0.76 0.18 0.01
14_A 106_I 0.76 0.18 0.01
109_V 108_V 0.76 0.17 0.01
49_F 54_S 0.76 0.17 0.01
47_I 163_F 0.76 0.17 0.01
108_G 113_V 0.76 0.17 0.01
25_V 266_E 0.75 0.17 0.01
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
3990 1.01 cIp_5_2_cIV_B_6 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.42 Done - Shared
3989 1.02 cIp_5_6_cIV_B_6 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.73 Done - Shared
3988 1.01 cIp_5_4_cIV_B_10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
3983 1.01 cIp_5_4_cIV_B_6 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.77 Done - Shared
3981 1.02 cIp_5_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.60 Done - Shared
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