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OPENSEQ.org
cIp_6_2_cIV_C_2
Genes: A B A+B
Length: 175 274 428
Sequences: 1604 2881 337
Seq/Len: 9.17 10.51 0.79
MirrorTree (Pazo et al. 2001) 0.21
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 0.02 0.00 0.00
10 0.02 0.00 0.02
20 0.03 0.00 0.05
100 0.04 0.00 0.13
∞ 0.10 0.01 0.75
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
144_I 189_L 1.37 0.60 0.00
112_Y 8_D 1.18 0.43 0.00
31_T 208_G 1.14 0.40 0.00
112_Y 168_D 1.08 0.35 0.00
36_I 148_I 1.07 0.34 0.00
70_E 211_Y 1.05 0.33 0.00
60_M 175_G 1.00 0.29 0.00
47_W 105_W 1.00 0.29 0.00
31_T 5_K 0.98 0.28 0.00
160_I 225_T 0.94 0.25 0.00
29_L 223_I 0.91 0.23 0.00
31_T 6_N 0.90 0.22 0.00
69_L 30_T 0.88 0.21 0.00
65_P 105_W 0.88 0.21 0.00
38_N 144_I 0.87 0.20 0.00
28_F 226_I 0.86 0.20 0.00
160_I 223_I 0.85 0.20 0.00
144_I 191_A 0.84 0.19 0.00
85_L 114_L 0.83 0.19 0.00
46_H 105_W 0.83 0.18 0.00
108_P 162_A 0.83 0.18 0.00
62_T 28_M 0.83 0.18 0.00
114_I 177_I 0.82 0.18 0.00
26_K 92_I 0.81 0.18 0.00
157_L 29_L 0.81 0.17 0.00
65_P 141_L 0.80 0.17 0.00
88_V 109_F 0.79 0.17 0.00
157_L 188_G 0.78 0.16 0.00
32_T 221_V 0.78 0.16 0.00
108_P 19_F 0.78 0.16 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
3969 0.78 cIp_6_6_cIV_C_6 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3968 0.79 cIp_6_2_cIV_C_2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3962 0.62 cIp_6_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3959 0.78 cIp_6_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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