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OPENSEQ.org
cIV_B_20_C_20_pn
Genes: A B A+B
Length: 252 273 495
Sequences: 4606 2634 2540
Seq/Len: 18.28 9.65 5.13
MirrorTree (Pazo et al. 2001) 0.91
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 0.37
2 0.00 0.00 0.68
5 0.00 0.00 4.36
10 0.01 0.00 4.66
20 0.01 0.00 4.71
100 0.02 0.00 4.76
∞ 0.04 0.00 4.84
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
203_W 8_Y 1.02 0.81 0.03
53_L 265_F 1.01 0.81 0.03
92_I 6_H 0.99 0.79 0.03
73_H 99_M 0.99 0.78 0.03
147_A 135_F 0.94 0.73 0.02
49_V 272_G 0.92 0.71 0.02
52_L 174_G 0.88 0.66 0.02
27_L 251_A 0.87 0.65 0.02
17_G 5_N 0.85 0.62 0.02
116_A 53_I 0.84 0.62 0.02
77_I 140_L 0.83 0.59 0.02
172_V 191_Y 0.83 0.59 0.02
40_Y 102_V 0.81 0.58 0.02
105_E 115_P 0.80 0.55 0.02
175_T 179_V 0.80 0.55 0.02
50_C 83_R 0.79 0.53 0.01
192_Q 73_G 0.78 0.52 0.01
189_A 152_G 0.77 0.52 0.01
202_L 26_V 0.77 0.52 0.01
132_V 153_V 0.76 0.50 0.01
36_H 16_W 0.75 0.49 0.01
168_K 183_V 0.75 0.48 0.01
213_F 21_A 0.75 0.48 0.01
15_N 240_T 0.74 0.47 0.01
124_S 226_F 0.74 0.47 0.01
214_G 97_E 0.74 0.47 0.01
92_I 135_F 0.74 0.47 0.01
22_P 59_L 0.74 0.46 0.01
212_Y 242_K 0.73 0.46 0.01
209_E 60_Y 0.73 0.46 0.01
13_P 234_L 0.73 0.45 0.01
42_I 140_L 0.72 0.45 0.01
211_V 175_L 0.72 0.45 0.01
133_A 63_F 0.72 0.44 0.01
176_A 99_M 0.71 0.42 0.01
126_E 124_D 0.71 0.42 0.01
137_L 272_G 0.71 0.42 0.01
129_N 147_I 0.70 0.41 0.01
222_I 227_L 0.70 0.41 0.01
94_A 164_L 0.70 0.41 0.01
78_E 209_F 0.69 0.40 0.01
87_L 51_F 0.69 0.40 0.01
85_P 141_P 0.69 0.39 0.01
48_F 99_M 0.68 0.38 0.01
44_A 150_L 0.68 0.38 0.01
23_A 251_A 0.67 0.38 0.01
81_W 159_H 0.67 0.37 0.01
163_V 232_I 0.67 0.37 0.01
127_Y 147_I 0.67 0.37 0.01
71_F 10_I 0.67 0.37 0.01
222_I 262_L 0.67 0.37 0.01
57_I 70_V 0.67 0.37 0.01
176_A 37_G 0.67 0.36 0.01
172_V 183_V 0.67 0.36 0.01
172_V 51_F 0.67 0.36 0.01
233_A 169_K 0.66 0.36 0.01
75_T 184_C 0.66 0.36 0.01
20_F 18_F 0.66 0.36 0.01
205_S 177_V 0.66 0.36 0.01
175_T 54_G 0.66 0.35 0.01
68_P 12_P 0.66 0.35 0.01
39_L 99_M 0.65 0.35 0.01
194_A 24_A 0.65 0.35 0.01
171_L 90_F 0.65 0.35 0.01
83_L 204_V 0.65 0.35 0.01
88_I 146_L 0.65 0.34 0.01
55_I 134_T 0.65 0.34 0.01
195_V 102_V 0.65 0.34 0.01
15_N 13_P 0.65 0.34 0.01
152_D 102_V 0.65 0.34 0.01
35_D 178_A 0.65 0.34 0.01
74_N 121_P 0.64 0.34 0.01
172_V 236_K 0.64 0.34 0.01
212_Y 102_V 0.64 0.34 0.01
228_P 72_E 0.64 0.34 0.01
153_E 170_T 0.64 0.33 0.01
86_V 86_L 0.64 0.33 0.01
53_L 6_H 0.64 0.33 0.01
231_V 80_P 0.64 0.33 0.01
92_I 99_M 0.63 0.33 0.01
166_V 26_V 0.63 0.32 0.01
230_V 54_G 0.63 0.32 0.01
81_W 252_W 0.63 0.32 0.01
24_S 176_I 0.63 0.32 0.01
142_E 179_V 0.62 0.31 0.01
239_Y 270_I 0.62 0.31 0.01
137_L 158_A 0.62 0.31 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
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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