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OPENSEQ.org
cIV_B_40_cIII_cyt1_10_Pdenitr
Genes: A B A+B
Length: 252 263 490
Sequences: 4089 954 329
Seq/Len: 16.23 3.63 0.67
MirrorTree (Pazo et al. 2001) 0.35
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.01
10 0.00 0.01 0.01
20 0.01 0.01 0.02
100 0.01 0.01 0.08
∞ 0.03 0.01 0.64
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
183_W 194_Q 1.31 0.50 0.00
55_I 240_V 1.12 0.35 0.00
54_L 81_P 1.09 0.32 0.00
89_L 246_Y 1.04 0.29 0.00
187_A 74_D 0.99 0.26 0.00
239_Y 59_S 0.97 0.24 0.00
164_V 54_Y 0.93 0.22 0.00
226_Y 132_G 0.92 0.21 0.00
31_Q 105_R 0.91 0.21 0.00
22_P 220_A 0.90 0.20 0.00
129_N 230_V 0.89 0.20 0.00
188_F 251_K 0.88 0.19 0.00
117_I 38_P 0.88 0.19 0.00
116_A 207_Q 0.86 0.18 0.00
244_A 239_I 0.85 0.18 0.00
47_I 65_R 0.85 0.18 0.00
47_I 82_E 0.85 0.18 0.00
21_Q 244_L 0.84 0.17 0.00
29_H 119_M 0.84 0.17 0.00
118_G 141_L 0.83 0.17 0.00
130_D 240_V 0.83 0.17 0.00
70_R 215_F 0.83 0.17 0.00
23_A 76_G 0.82 0.16 0.00
50_C 90_A 0.82 0.16 0.00
239_Y 54_Y 0.82 0.16 0.00
109_D 42_F 0.82 0.16 0.00
162_V 185_Q 0.81 0.16 0.00
230_V 137_Y 0.81 0.16 0.00
109_D 243_A 0.81 0.16 0.00
170_V 213_A 0.81 0.16 0.00
187_A 252_L 0.81 0.16 0.00
188_F 64_L 0.81 0.16 0.00
170_V 108_T 0.80 0.15 0.00
72_T 219_T 0.80 0.15 0.00
53_L 156_A 0.80 0.15 0.00
245_G 213_A 0.80 0.15 0.00
76_P 216_L 0.80 0.15 0.00
205_S 94_I 0.79 0.15 0.00
94_A 36_E 0.79 0.15 0.00
246_A 101_E 0.78 0.14 0.00
45_V 65_R 0.78 0.14 0.00
208_Q 237_F 0.78 0.14 0.00
80_I 177_A 0.78 0.14 0.00
79_V 94_I 0.78 0.14 0.00
206_V 236_I 0.78 0.14 0.00
250_F 244_L 0.77 0.14 0.00
116_A 213_A 0.77 0.14 0.00
84_V 42_F 0.77 0.14 0.00
167_G 204_T 0.77 0.14 0.00
114_I 178_A 0.77 0.14 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
3119 0.35 cIV_B_60_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3118 0.46 cIV_B_20_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3116 0.41 cIV_B_40_cIII_cyt1_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3115 0.67 cIV_B_40_cIII_cyt1_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3114 0.32 cIV_B_40_cIII_cyt1_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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