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OPENSEQ.org
cIp_6_2_cIV_2_4
Genes: A B A+B
Length: 213 227 396
Sequences: 424 5082 204
Seq/Len: 1.99 22.39 0.52
MirrorTree (Pazo et al. 2001) 0.48
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.01 0.01 0.00
20 0.01 0.01 0.02
100 0.01 0.02 0.07
∞ 0.01 0.04 0.46
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
194_I 144_L 1.25 0.38 0.00
191_L 101_G 1.20 0.34 0.00
120_M 162_S 1.19 0.34 0.00
190_L 20_L 1.06 0.26 0.00
191_L 211_L 1.05 0.25 0.00
180_I 77_A 1.04 0.24 0.00
201_I 212_E 1.03 0.24 0.00
66_K 144_L 1.02 0.23 0.00
178_I 154_I 1.00 0.22 0.00
143_E 154_I 0.99 0.22 0.00
95_H 35_C 0.98 0.21 0.00
47_P 219_F 0.98 0.21 0.00
72_N 156_S 0.98 0.21 0.00
178_I 223_P 0.95 0.20 0.00
203_R 63_T 0.95 0.20 0.00
104_D 61_M 0.95 0.19 0.00
194_I 220_E 0.94 0.19 0.00
99_P 63_T 0.93 0.19 0.00
121_I 39_L 0.93 0.19 0.00
131_A 95_L 0.92 0.18 0.00
201_I 148_A 0.92 0.18 0.00
94_M 156_S 0.91 0.18 0.00
194_I 178_R 0.90 0.17 0.00
64_V 192_Y 0.89 0.17 0.00
180_I 154_I 0.89 0.17 0.00
178_I 142_V 0.89 0.17 0.00
74_A 150_I 0.89 0.17 0.00
108_V 165_V 0.88 0.16 0.00
74_A 77_A 0.86 0.16 0.00
68_D 114_G 0.86 0.16 0.00
98_A 156_S 0.86 0.16 0.00
194_I 156_S 0.86 0.15 0.00
180_I 100_I 0.86 0.15 0.00
193_G 38_V 0.85 0.15 0.00
113_S 29_M 0.85 0.15 0.00
109_V 14_S 0.84 0.15 0.00
62_Y 215_P 0.84 0.15 0.00
131_A 143_V 0.83 0.14 0.00
87_A 89_E 0.82 0.14 0.00
94_M 151_R 0.82 0.14 0.00
191_L 78_L 0.81 0.14 0.00
108_V 169_G 0.81 0.14 0.00
139_D 197_S 0.81 0.14 0.00
64_V 212_E 0.81 0.13 0.00
201_I 99_S 0.80 0.13 0.00
152_S 56_S 0.80 0.13 0.00
120_M 72_I 0.80 0.13 0.00
194_I 216_L 0.80 0.13 0.00
193_G 68_L 0.80 0.13 0.00
122_V 215_P 0.79 0.13 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
4321 0.48 cIp_6_20_cIV_2_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4320 0.32 cIp_6_40_cIV_2_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4319 0.52 cIp_6_2_cIV_2_4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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