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OPENSEQ.org
cIp_1_40_cIV_B_40
Genes: A B A+B
Length: 455 227 653
Sequences: 2247 4148 616
Seq/Len: 4.94 18.27 0.94
MirrorTree (Pazo et al. 2001) 0.19
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 0.02 0.00 0.01
20 0.02 0.00 0.01
100 0.04 0.01 0.08
∞ 0.12 0.02 0.90
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
435_P 224_V 1.00 0.33 0.00
400_I 36_F 0.97 0.30 0.00
186_V 165_V 0.90 0.25 0.00
69_G 72_I 0.85 0.22 0.00
64_P 220_E 0.84 0.21 0.00
410_I 27_A 0.84 0.21 0.00
345_V 148_A 0.83 0.20 0.00
134_L 46_L 0.82 0.20 0.00
433_F 152_M 0.81 0.20 0.00
331_D 98_K 0.81 0.19 0.00
67_I 68_L 0.80 0.19 0.00
362_I 43_F 0.79 0.18 0.00
49_S 150_I 0.78 0.18 0.00
108_A 224_V 0.77 0.17 0.00
345_V 191_V 0.77 0.17 0.00
158_S 218_I 0.77 0.17 0.00
349_D 37_L 0.77 0.17 0.00
401_D 225_F 0.76 0.17 0.00
176_N 46_L 0.75 0.16 0.00
45_K 75_L 0.75 0.16 0.00
260_R 156_S 0.74 0.16 0.00
354_I 144_L 0.74 0.16 0.00
266_L 18_E 0.74 0.16 0.00
158_S 160_L 0.73 0.15 0.00
169_E 226_T 0.73 0.15 0.00
292_E 219_F 0.73 0.15 0.00
232_T 144_L 0.72 0.15 0.00
186_V 223_P 0.72 0.15 0.00
392_R 37_L 0.72 0.15 0.00
137_G 58_A 0.72 0.15 0.00
356_K 37_L 0.72 0.15 0.00
66_W 191_V 0.71 0.15 0.00
55_K 167_T 0.71 0.14 0.00
169_E 95_L 0.71 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
4046 1.31 cIp_1_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4044 0.94 cIp_1_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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