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OPENSEQ.org
cIV_C_4_cI_H_4_Pdenitr
Genes: A B A+B
Length: 273 345 577
Sequences: 2888 4768 2511
Seq/Len: 10.58 13.82 4.35
MirrorTree (Pazo et al. 2001) 0.76
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 0.08
2 0.00 0.00 0.28
5 0.00 0.00 0.60
10 0.00 0.01 3.42
20 0.00 0.01 3.52
100 0.00 0.02 3.63
∞ 0.01 0.05 4.06
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
62_M 325_V 1.06 0.81 0.04
267_V 301_Y 1.03 0.79 0.04
138_W 141_K 0.95 0.70 0.03
108_F 233_T 0.90 0.64 0.03
150_L 91_S 0.90 0.64 0.03
18_F 143_P 0.90 0.63 0.03
225_I 17_L 0.90 0.63 0.03
146_L 207_V 0.89 0.63 0.03
184_C 220_L 0.89 0.62 0.03
224_T 95_A 0.89 0.62 0.03
153_V 291_F 0.87 0.60 0.02
111_N 258_L 0.85 0.58 0.02
211_M 46_M 0.85 0.57 0.02
139_H 46_M 0.84 0.56 0.02
83_R 120_I 0.83 0.55 0.02
201_A 63_A 0.83 0.55 0.02
52_L 203_V 0.82 0.53 0.02
215_F 307_M 0.82 0.53 0.02
123_K 166_I 0.81 0.52 0.02
229_V 197_P 0.81 0.52 0.02
48_P 326_A 0.81 0.51 0.02
55_L 266_W 0.80 0.51 0.02
60_Y 121_F 0.80 0.50 0.02
35_M 42_A 0.80 0.50 0.02
252_W 48_R 0.79 0.50 0.02
221_I 286_F 0.79 0.50 0.02
5_N 141_K 0.79 0.48 0.02
100_F 307_M 0.78 0.48 0.02
221_I 309_I 0.78 0.48 0.02
123_K 73_I 0.78 0.48 0.02
161_A 117_I 0.78 0.47 0.02
161_A 150_S 0.77 0.47 0.02
27_M 122_A 0.77 0.47 0.02
95_M 111_A 0.77 0.47 0.02
229_V 85_F 0.77 0.47 0.02
228_F 21_A 0.77 0.47 0.02
180_I 117_I 0.77 0.46 0.02
50_M 26_V 0.77 0.46 0.02
84_I 102_I 0.77 0.46 0.02
231_L 324_L 0.76 0.45 0.02
133_V 257_L 0.75 0.44 0.02
90_F 58_L 0.75 0.44 0.02
108_F 97_F 0.75 0.44 0.02
225_I 102_I 0.75 0.44 0.02
140_L 298_V 0.75 0.44 0.02
191_Y 104_F 0.73 0.42 0.01
140_L 223_A 0.73 0.42 0.01
130_E 169_I 0.73 0.41 0.01
211_M 252_Y 0.73 0.41 0.01
126_V 16_L 0.73 0.41 0.01
98_V 23_I 0.73 0.41 0.01
236_K 266_W 0.73 0.41 0.01
6_H 62_F 0.73 0.41 0.01
265_F 92_M 0.73 0.41 0.01
126_V 20_L 0.73 0.41 0.01
224_T 22_V 0.73 0.41 0.01
25_F 183_A 0.72 0.40 0.01
34_W 238_T 0.72 0.40 0.01
12_P 65_A 0.72 0.40 0.01
21_A 162_G 0.72 0.40 0.01
138_W 198_H 0.72 0.40 0.01
131_G 301_Y 0.72 0.40 0.01
6_H 59_L 0.71 0.39 0.01
125_G 167_G 0.71 0.39 0.01
166_G 284_M 0.71 0.39 0.01
150_L 134_G 0.71 0.39 0.01
22_I 65_A 0.71 0.39 0.01
225_I 70_V 0.71 0.38 0.01
21_A 164_I 0.71 0.38 0.01
21_A 249_I 0.71 0.38 0.01
183_V 17_L 0.71 0.38 0.01
103_A 216_P 0.70 0.38 0.01
170_T 258_L 0.70 0.38 0.01
70_V 328_L 0.70 0.37 0.01
51_F 327_I 0.70 0.37 0.01
205_Y 170_I 0.70 0.37 0.01
18_F 178_T 0.70 0.37 0.01
171_T 42_A 0.70 0.37 0.01
18_F 46_M 0.70 0.37 0.01
238_Q 56_W 0.70 0.37 0.01
38_I 233_T 0.70 0.37 0.01
23_G 76_P 0.69 0.36 0.01
75_T 33_M 0.69 0.36 0.01
28_L 258_L 0.69 0.36 0.01
162_F 148_L 0.69 0.36 0.01
243_Q 72_E 0.69 0.36 0.01
232_I 324_L 0.69 0.36 0.01
87_Q 151_A 0.69 0.36 0.01
153_V 260_L 0.69 0.35 0.01
180_I 175_M 0.69 0.35 0.01
229_V 86_L 0.69 0.35 0.01
37_G 130_G 0.68 0.35 0.01
60_Y 185_R 0.68 0.35 0.01
102_V 282_I 0.68 0.35 0.01
34_W 55_P 0.68 0.35 0.01
244_H 129_Y 0.68 0.35 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
3186 4.31 cIV_C_2_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3185 4.33 cIV_C_6_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3184 4.3 cIV_C_4_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3183 4.35 cIV_C_4_cI_H_40_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3182 4.25 cIV_C_20_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3181 4.35 cIV_C_4_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3180 4.35 cIV_C_4_cI_H_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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