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OPENSEQ.org
cIp_6_40_cIV_C_40
Genes: A B A+B
Length: 175 274 429
Sequences: 1184 2529 265
Seq/Len: 6.77 9.23 0.62
MirrorTree (Pazo et al. 2001) 0.49
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.01
20 0.02 0.00 0.04
100 0.03 0.00 0.09
∞ 0.08 0.00 0.59
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
161_L 180_V 1.53 0.65 0.00
112_Y 8_D 1.44 0.58 0.00
112_Y 168_D 1.35 0.51 0.00
31_T 208_G 1.32 0.49 0.00
47_W 105_W 1.18 0.37 0.00
144_I 191_A 1.16 0.36 0.00
114_I 19_F 1.14 0.34 0.00
144_I 189_L 1.13 0.33 0.00
41_R 110_I 1.10 0.32 0.00
29_L 6_N 1.07 0.30 0.00
34_E 28_M 1.07 0.29 0.00
78_A 196_H 1.03 0.27 0.00
26_K 131_E 1.00 0.25 0.00
31_T 5_K 1.00 0.25 0.00
172_T 9_Y 1.00 0.25 0.00
31_T 6_N 0.99 0.24 0.00
38_N 144_I 0.98 0.24 0.00
23_L 35_W 0.98 0.24 0.00
102_K 184_V 0.97 0.23 0.00
131_S 56_L 0.96 0.23 0.00
157_L 188_G 0.96 0.23 0.00
111_R 153_G 0.95 0.22 0.00
26_K 92_I 0.95 0.22 0.00
76_P 89_Y 0.95 0.22 0.00
76_P 105_W 0.95 0.22 0.00
160_I 57_V 0.95 0.22 0.00
33_T 13_P 0.95 0.22 0.00
144_I 23_I 0.95 0.22 0.00
25_D 62_V 0.93 0.21 0.00
70_E 105_W 0.93 0.21 0.00
165_R 63_M 0.93 0.21 0.00
45_L 50_W 0.93 0.21 0.00
25_D 201_L 0.93 0.21 0.00
157_L 236_L 0.92 0.20 0.00
153_A 153_G 0.91 0.20 0.00
108_P 19_F 0.91 0.20 0.00
109_E 173_I 0.91 0.20 0.00
45_L 165_L 0.91 0.20 0.00
40_A 86_G 0.91 0.20 0.00
69_L 3_H 0.91 0.20 0.00
85_L 235_L 0.90 0.19 0.00
69_L 208_G 0.90 0.19 0.00
85_L 74_G 0.90 0.19 0.00
146_V 99_V 0.90 0.19 0.00
62_T 131_E 0.90 0.19 0.00
61_Q 154_V 0.90 0.19 0.00
46_H 105_W 0.89 0.19 0.00
61_Q 61_Y 0.89 0.19 0.00
146_V 205_V 0.89 0.18 0.00
93_T 7_H 0.88 0.18 0.00
168_R 28_M 0.88 0.18 0.00
36_I 148_I 0.88 0.18 0.00
111_R 175_G 0.87 0.18 0.00
64_M 81_P 0.87 0.18 0.00
142_V 205_V 0.86 0.17 0.00
102_K 238_G 0.86 0.17 0.00
78_A 78_E 0.86 0.17 0.00
63_S 211_Y 0.86 0.17 0.00
62_T 27_V 0.85 0.17 0.00
144_I 125_D 0.85 0.17 0.00
165_R 122_P 0.85 0.17 0.00
144_I 25_A 0.85 0.17 0.00
108_P 104_A 0.83 0.16 0.00
157_L 26_F 0.83 0.16 0.00
21_R 219_A 0.83 0.16 0.00
27_G 183_G 0.82 0.16 0.00
37_I 232_L 0.81 0.15 0.00
109_E 122_P 0.81 0.15 0.00
108_P 141_L 0.81 0.15 0.00
62_T 178_V 0.81 0.15 0.00
157_L 135_T 0.80 0.15 0.00
65_P 85_I 0.80 0.15 0.00
140_V 13_P 0.80 0.15 0.00
112_Y 239_Q 0.80 0.15 0.00
76_P 117_M 0.80 0.15 0.00
65_P 89_Y 0.80 0.15 0.00
37_I 177_I 0.80 0.15 0.00
32_T 121_S 0.80 0.14 0.00
65_P 141_L 0.79 0.14 0.00
139_I 28_M 0.79 0.14 0.00
146_V 90_G 0.79 0.14 0.00
114_I 58_G 0.78 0.14 0.00
157_L 59_V 0.78 0.14 0.00
69_L 204_T 0.78 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
3969 0.78 cIp_6_6_cIV_C_6 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3968 0.79 cIp_6_2_cIV_C_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3962 0.62 cIp_6_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3959 0.78 cIp_6_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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