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OPENSEQ.org
cIV_B_40_cI_J_20_Pdenitr
Genes: A B A+B
Length: 252 200 441
Sequences: 4089 2148 881
Seq/Len: 16.23 10.74 2
MirrorTree (Pazo et al. 2001) 0.50
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 0.06
2 0.00 0.00 0.12
5 0.00 0.01 0.23
10 0.00 0.01 0.41
20 0.01 0.01 0.50
100 0.01 0.02 0.62
∞ 0.03 0.03 1.95
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
239_Y 64_V 1.36 0.84 0.14
82_T 21_V 1.15 0.68 0.07
57_I 59_V 1.14 0.67 0.07
77_I 151_G 1.12 0.66 0.07
114_I 147_F 1.07 0.60 0.06
188_F 151_G 1.07 0.60 0.06
119_H 55_L 1.04 0.57 0.05
51_L 10_A 1.03 0.56 0.05
79_V 28_H 1.00 0.52 0.04
112_L 88_R 0.99 0.52 0.04
170_V 159_I 0.99 0.51 0.04
212_Y 142_R 0.98 0.50 0.04
233_A 166_M 0.94 0.46 0.04
237_E 40_A 0.94 0.45 0.04
243_L 156_V 0.93 0.44 0.04
143_A 12_S 0.90 0.42 0.03
187_A 12_S 0.90 0.41 0.03
24_S 76_D 0.90 0.41 0.03
119_H 151_G 0.89 0.40 0.03
57_I 147_F 0.88 0.39 0.03
176_A 34_I 0.88 0.39 0.03
97_L 32_W 0.87 0.38 0.03
80_I 135_L 0.86 0.37 0.03
68_P 41_A 0.85 0.36 0.03
21_Q 30_V 0.85 0.36 0.03
47_I 59_V 0.85 0.36 0.03
212_Y 9_F 0.85 0.36 0.03
246_A 92_L 0.84 0.35 0.03
231_V 128_A 0.83 0.34 0.03
138_M 74_M 0.83 0.34 0.02
44_A 108_F 0.82 0.33 0.02
174_V 28_H 0.82 0.33 0.02
225_A 99_V 0.82 0.33 0.02
162_V 161_A 0.81 0.32 0.02
34_L 176_N 0.81 0.32 0.02
29_H 45_V 0.81 0.32 0.02
25_S 79_F 0.81 0.31 0.02
111_D 9_F 0.79 0.30 0.02
19_N 27_V 0.79 0.30 0.02
93_G 149_L 0.79 0.30 0.02
185_I 108_F 0.78 0.29 0.02
182_A 167_R 0.78 0.29 0.02
34_L 76_D 0.78 0.29 0.02
243_L 45_V 0.78 0.29 0.02
170_V 145_L 0.77 0.28 0.02
237_E 92_L 0.77 0.28 0.02
114_I 149_L 0.77 0.28 0.02
47_I 95_V 0.77 0.28 0.02
83_L 41_A 0.77 0.28 0.02
239_Y 13_A 0.76 0.27 0.02
204_F 64_V 0.74 0.26 0.02
30_D 44_F 0.74 0.26 0.02
120_Q 67_L 0.74 0.26 0.02
88_I 18_F 0.74 0.25 0.02
175_T 136_G 0.74 0.25 0.02
186_P 62_G 0.73 0.25 0.02
240_E 148_Q 0.73 0.25 0.02
129_N 94_L 0.73 0.24 0.02
32_Q 45_V 0.73 0.24 0.02
25_S 64_V 0.72 0.24 0.02
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
3238 0.58 cIV_B_40_cI_J_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3237 0.92 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3236 0.99 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
3235 2.02 cIV_B_40_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.13 Done - Shared
3234 2 cIV_B_40_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3233 1.1 cIV_B_20_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3232 2.3 cIV_B_20_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3231 2.3 cIV_B_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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