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OPENSEQ.org
cIV_C_4_cI_J_20_Pdenitr
Genes: A B A+B
Length: 273 200 460
Sequences: 2888 2148 569
Seq/Len: 10.58 10.74 1.24
MirrorTree (Pazo et al. 2001) 0.32
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 0.09
2 0.00 0.00 0.15
5 0.00 0.01 0.35
10 0.00 0.01 0.46
20 0.00 0.01 0.54
100 0.00 0.02 0.61
∞ 0.01 0.03 1.20
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
136_D 151_G 1.28 0.66 0.00
25_F 153_V 1.22 0.60 0.00
225_I 94_L 1.16 0.55 0.00
174_G 53_A 1.15 0.54 0.00
69_V 92_L 1.12 0.51 0.00
30_G 90_L 1.12 0.50 0.00
210_Y 77_V 1.11 0.49 0.00
175_L 147_F 1.10 0.48 0.00
99_M 72_V 1.09 0.48 0.00
182_G 56_L 1.04 0.43 0.00
83_R 31_L 1.03 0.41 0.00
158_A 150_A 1.02 0.41 0.00
69_V 27_V 1.02 0.41 0.00
125_G 17_G 1.01 0.40 0.00
115_P 65_A 1.00 0.39 0.00
143_I 132_T 1.00 0.39 0.00
96_S 135_L 1.00 0.39 0.00
210_Y 189_M 0.99 0.38 0.00
6_H 160_G 0.98 0.37 0.00
10_I 20_V 0.97 0.36 0.00
29_T 8_L 0.97 0.36 0.00
37_G 54_M 0.96 0.36 0.00
210_Y 98_V 0.96 0.35 0.00
210_Y 116_Q 0.96 0.35 0.00
222_I 181_M 0.95 0.34 0.00
70_V 102_A 0.94 0.34 0.00
241_Q 27_V 0.94 0.33 0.00
201_A 121_R 0.94 0.33 0.00
205_Y 107_A 0.93 0.33 0.00
29_T 13_A 0.93 0.33 0.00
140_L 34_I 0.92 0.32 0.00
25_F 13_A 0.91 0.31 0.00
138_W 32_W 0.91 0.31 0.00
31_A 94_L 0.90 0.30 0.00
18_F 72_V 0.90 0.30 0.00
22_I 31_L 0.90 0.30 0.00
100_F 55_L 0.90 0.30 0.00
109_I 159_I 0.90 0.30 0.00
21_A 99_V 0.90 0.30 0.00
134_T 135_L 0.89 0.29 0.00
70_V 8_L 0.88 0.29 0.00
164_L 53_A 0.88 0.29 0.00
205_Y 93_A 0.88 0.29 0.00
52_L 53_A 0.88 0.29 0.00
25_F 95_V 0.88 0.28 0.00
166_G 171_D 0.88 0.28 0.00
232_I 45_V 0.87 0.28 0.00
200_L 57_V 0.87 0.28 0.00
178_A 141_D 0.87 0.28 0.00
27_M 53_A 0.86 0.27 0.00
190_A 6_F 0.86 0.27 0.00
26_V 172_V 0.86 0.27 0.00
150_L 17_G 0.86 0.27 0.00
187_G 145_L 0.86 0.27 0.00
147_I 12_S 0.86 0.27 0.00
128_P 81_E 0.86 0.27 0.00
183_V 118_E 0.86 0.27 0.00
230_C 55_L 0.85 0.27 0.00
54_G 156_V 0.85 0.27 0.00
250_A 164_L 0.84 0.26 0.00
146_L 140_Y 0.84 0.26 0.00
265_F 78_D 0.84 0.25 0.00
237_G 144_V 0.84 0.25 0.00
50_M 133_L 0.84 0.25 0.00
266_V 5_A 0.83 0.25 0.00
114_Y 17_G 0.83 0.25 0.00
83_R 122_A 0.83 0.25 0.00
205_Y 147_F 0.83 0.25 0.00
67_A 32_W 0.83 0.25 0.00
250_A 157_A 0.83 0.25 0.00
183_V 133_L 0.83 0.25 0.00
208_A 54_M 0.83 0.25 0.00
179_V 96_I 0.83 0.25 0.00
73_G 125_V 0.83 0.24 0.00
251_A 56_L 0.82 0.24 0.00
96_S 10_A 0.82 0.24 0.00
57_G 18_F 0.82 0.24 0.00
58_V 76_D 0.82 0.24 0.00
37_G 10_A 0.82 0.24 0.00
134_T 29_S 0.82 0.24 0.00
19_F 45_V 0.82 0.24 0.00
157_W 39_S 0.81 0.23 0.00
139_H 151_G 0.81 0.23 0.00
170_T 158_M 0.81 0.23 0.00
251_A 6_F 0.81 0.23 0.00
160_H 161_A 0.81 0.23 0.00
98_V 103_Q 0.81 0.23 0.00
245_V 6_F 0.81 0.23 0.00
73_G 53_A 0.81 0.23 0.00
210_Y 122_A 0.80 0.23 0.00
23_G 125_V 0.80 0.23 0.00
243_Q 20_V 0.80 0.23 0.00
21_A 18_F 0.80 0.23 0.00
204_V 140_Y 0.80 0.23 0.00
36_K 77_V 0.80 0.22 0.00
179_V 19_M 0.80 0.22 0.00
158_A 27_V 0.80 0.22 0.00
136_D 158_M 0.79 0.22 0.00
74_E 132_T 0.79 0.22 0.00
270_I 48_G 0.79 0.22 0.00
83_R 32_W 0.79 0.22 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
3179 5.65 cIV_C_10_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
3178 5.68 cIV_C_6_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3177 5.65 cIV_C_2_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
3176 5.68 cIV_C_4_cI_J_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.86 Done - Shared
3175 1.26 cIV_C_4_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3174 1.24 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3173 6.66 cIV_C_4_cI_J_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
3172 6.66 cIV_C_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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