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OPENSEQ.org
cIV_B_60_C_60_pn
Genes: A B A+B
Length: 252 273 494
Sequences: 2518 2410 2311
Seq/Len: 9.99 8.83 4.68
MirrorTree (Pazo et al. 2001) 0.90
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 0.20
2 0.00 0.00 0.44
5 0.00 0.00 3.99
10 0.00 0.00 4.23
20 0.00 0.00 4.30
100 0.00 0.00 4.37
∞ 0.00 0.00 4.40
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
53_L 265_F 1.31 0.95 0.52
92_I 6_H 1.12 0.87 0.34
203_W 8_Y 1.00 0.78 0.24
243_L 227_L 0.97 0.75 0.22
73_H 99_M 0.96 0.74 0.21
52_L 174_G 0.95 0.72 0.20
92_I 135_F 0.92 0.68 0.18
77_I 140_L 0.91 0.67 0.18
177_T 109_I 0.90 0.66 0.17
27_L 251_A 0.89 0.65 0.17
235_S 47_G 0.89 0.64 0.16
137_L 272_G 0.87 0.62 0.15
35_D 178_A 0.85 0.60 0.14
147_A 135_F 0.85 0.60 0.14
231_V 8_Y 0.84 0.59 0.14
15_N 240_T 0.83 0.57 0.13
36_H 16_W 0.82 0.56 0.13
57_I 70_V 0.81 0.54 0.12
92_I 191_Y 0.81 0.54 0.12
176_A 99_M 0.81 0.54 0.12
222_I 227_L 0.81 0.53 0.12
48_F 177_V 0.80 0.53 0.12
49_V 272_G 0.80 0.53 0.12
219_L 140_L 0.77 0.49 0.10
59_R 21_A 0.77 0.48 0.10
173_Q 90_F 0.76 0.48 0.10
90_V 32_V 0.76 0.47 0.10
243_L 22_I 0.76 0.47 0.10
20_F 18_F 0.76 0.47 0.10
154_Y 11_L 0.76 0.47 0.10
104_Q 134_T 0.76 0.47 0.10
184_T 32_V 0.76 0.46 0.10
50_C 83_R 0.75 0.46 0.10
40_Y 102_V 0.75 0.46 0.09
53_L 6_H 0.75 0.45 0.09
68_P 12_P 0.75 0.45 0.09
175_T 179_V 0.74 0.45 0.09
134_F 208_A 0.74 0.45 0.09
30_D 140_L 0.74 0.45 0.09
87_L 51_F 0.74 0.44 0.09
163_V 232_I 0.74 0.44 0.09
132_V 153_V 0.73 0.43 0.09
195_V 8_Y 0.73 0.43 0.09
223_N 71_N 0.73 0.43 0.09
185_I 158_A 0.73 0.43 0.09
90_V 21_A 0.73 0.43 0.09
194_A 24_A 0.73 0.43 0.09
168_K 200_L 0.72 0.42 0.08
23_A 251_A 0.72 0.42 0.08
180_I 218_A 0.72 0.41 0.08
116_A 53_I 0.72 0.41 0.08
105_E 110_K 0.71 0.41 0.08
238_K 229_V 0.71 0.41 0.08
23_A 176_I 0.71 0.40 0.08
230_V 247_F 0.70 0.39 0.08
115_K 152_G 0.70 0.39 0.07
168_K 183_V 0.70 0.39 0.07
56_C 162_F 0.69 0.38 0.07
94_A 164_L 0.69 0.38 0.07
25_S 195_H 0.69 0.38 0.07
205_S 177_V 0.69 0.38 0.07
167_G 158_A 0.69 0.38 0.07
204_F 210_Y 0.69 0.37 0.07
212_Y 242_K 0.69 0.37 0.07
42_I 140_L 0.69 0.37 0.07
44_A 150_L 0.69 0.37 0.07
70_R 180_I 0.68 0.37 0.07
105_E 115_P 0.68 0.37 0.07
95_F 124_D 0.68 0.36 0.07
166_V 228_F 0.68 0.36 0.07
230_V 54_G 0.67 0.35 0.07
248_E 46_E 0.67 0.35 0.07
158_T 244_H 0.67 0.35 0.07
53_L 51_F 0.67 0.35 0.07
52_L 169_K 0.67 0.34 0.06
75_T 184_C 0.66 0.34 0.06
158_T 21_A 0.66 0.34 0.06
48_F 227_L 0.66 0.34 0.06
158_T 238_Q 0.66 0.34 0.06
230_V 8_Y 0.66 0.33 0.06
143_A 131_G 0.66 0.33 0.06
226_Y 252_W 0.66 0.33 0.06
204_F 186_T 0.66 0.33 0.06
75_T 100_F 0.65 0.33 0.06
49_V 251_A 0.65 0.33 0.06
115_K 82_V 0.65 0.33 0.06
24_S 176_I 0.65 0.32 0.06
38_V 34_W 0.65 0.32 0.06
101_F 11_L 0.65 0.32 0.06
55_I 134_T 0.65 0.32 0.06
157_A 114_Y 0.65 0.32 0.06
41_I 75_T 0.65 0.32 0.06
192_Q 73_G 0.65 0.32 0.06
202_L 26_V 0.65 0.32 0.06
83_L 84_I 0.65 0.32 0.06
154_Y 198_F 0.64 0.32 0.06
101_F 67_A 0.64 0.32 0.06
92_I 77_E 0.64 0.31 0.06
30_D 194_S 0.64 0.31 0.06
96_S 106_W 0.64 0.31 0.06
92_I 5_N 0.64 0.31 0.06
56_C 13_P 0.64 0.31 0.06
154_Y 15_I 0.64 0.31 0.06
92_I 99_M 0.64 0.31 0.06
192_Q 146_L 0.64 0.31 0.06
17_G 5_N 0.64 0.31 0.06
200_A 11_L 0.64 0.31 0.06
29_H 135_F 0.64 0.31 0.06
170_V 117_G 0.63 0.31 0.06
91_A 103_A 0.63 0.31 0.06
91_A 158_A 0.63 0.30 0.05
172_V 191_Y 0.63 0.30 0.05
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
5103 4.09 cIV_B_80_C_80_pn Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.56 Done - Shared
5102 4.68 cIV_B_60_C_60_pn Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.52 Done - Shared
5005 5.58 cIV_B_4_C_4_pn Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
5004 5.13 cIV_B_20_C_20_pn Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
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