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OPENSEQ.org
cIV_B_4_C_4_pn
Genes: A B A+B
Length: 252 273 492
Sequences: 4637 2888 2747
Seq/Len: 18.4 10.58 5.58
MirrorTree (Pazo et al. 2001) 0.92
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 0.68
2 0.00 0.00 1.05
5 0.00 0.00 4.69
10 0.01 0.00 5.02
20 0.01 0.00 5.09
100 0.02 0.00 5.14
∞ 0.04 0.01 5.23
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
73_H 99_M 0.92 0.74 0.01
203_W 8_Y 0.92 0.74 0.01
92_I 6_H 0.90 0.71 0.01
17_G 5_N 0.89 0.70 0.01
147_A 135_F 0.89 0.70 0.01
114_I 126_V 0.81 0.59 0.01
49_V 272_G 0.81 0.59 0.01
116_A 53_I 0.79 0.57 0.01
53_L 265_F 0.79 0.56 0.01
15_N 240_T 0.78 0.56 0.01
202_L 26_V 0.77 0.53 0.01
212_Y 242_K 0.77 0.53 0.01
92_I 135_F 0.76 0.53 0.01
170_V 236_K 0.74 0.49 0.01
52_L 174_G 0.74 0.49 0.01
137_L 272_G 0.74 0.49 0.01
133_A 63_F 0.74 0.49 0.01
129_N 147_I 0.73 0.48 0.01
105_E 115_P 0.73 0.48 0.01
172_V 191_Y 0.73 0.48 0.01
13_P 234_L 0.73 0.48 0.01
23_A 176_I 0.73 0.47 0.01
124_S 226_F 0.72 0.47 0.01
94_A 164_L 0.72 0.47 0.01
22_P 59_L 0.72 0.46 0.01
176_A 99_M 0.71 0.46 0.01
78_E 209_F 0.71 0.45 0.01
50_C 83_R 0.71 0.45 0.01
23_A 251_A 0.71 0.44 0.01
172_V 173_N 0.69 0.43 0.01
189_A 152_G 0.69 0.43 0.01
48_F 99_M 0.69 0.43 0.01
172_V 51_F 0.69 0.43 0.01
172_V 49_W 0.69 0.42 0.01
15_N 6_H 0.69 0.42 0.01
77_I 140_L 0.69 0.42 0.01
142_E 169_K 0.68 0.41 0.01
81_W 252_W 0.68 0.41 0.01
137_L 158_A 0.68 0.40 0.01
223_N 104_W 0.68 0.40 0.01
40_Y 102_V 0.68 0.40 0.01
228_P 189_Q 0.68 0.40 0.01
243_L 227_L 0.68 0.40 0.01
76_P 5_N 0.67 0.40 0.01
43_T 3_V 0.67 0.40 0.01
14_V 25_F 0.67 0.39 0.01
14_V 5_N 0.67 0.39 0.01
244_A 180_I 0.67 0.39 0.01
143_A 121_P 0.67 0.39 0.00
13_P 153_V 0.67 0.39 0.00
147_A 4_K 0.67 0.39 0.00
82_T 209_F 0.67 0.39 0.00
213_F 21_A 0.67 0.39 0.00
27_L 251_A 0.66 0.38 0.00
78_E 185_F 0.66 0.38 0.00
15_N 13_P 0.66 0.38 0.00
86_V 86_L 0.66 0.38 0.00
53_L 6_H 0.66 0.37 0.00
142_E 187_G 0.66 0.37 0.00
166_V 228_F 0.66 0.37 0.00
167_G 225_I 0.65 0.37 0.00
133_A 121_P 0.65 0.37 0.00
132_V 153_V 0.65 0.36 0.00
126_E 124_D 0.65 0.36 0.00
142_E 22_I 0.65 0.36 0.00
177_T 98_V 0.64 0.36 0.00
168_K 183_V 0.64 0.35 0.00
192_Q 73_G 0.64 0.35 0.00
139_L 81_V 0.64 0.35 0.00
180_I 218_A 0.64 0.35 0.00
163_V 232_I 0.64 0.35 0.00
87_L 51_F 0.64 0.35 0.00
39_L 99_M 0.64 0.35 0.00
82_T 159_H 0.64 0.35 0.00
237_E 39_T 0.64 0.34 0.00
55_I 134_T 0.63 0.34 0.00
233_A 169_K 0.63 0.34 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
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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