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OPENSEQ.org
cIp_1_40_cIV_B_40
Genes: A B A+B
Length: 438 298 695
Sequences: 2218 2549 616
Seq/Len: 5.06 8.55 0.89
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 0.01 0.01
20 0.02 0.01 0.01
100 0.04 0.02 0.07
∞ 0.12 0.06 0.84
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
419_D 273_A 1.49 0.72 0.01
49_T 201_V 1.05 0.35 0.00
119_I 143_I 1.02 0.33 0.00
227_V 37_P 0.98 0.30 0.00
151_E 145_A 0.94 0.27 0.00
269_G 214_I 0.94 0.27 0.00
143_D 209_I 0.89 0.24 0.00
54_I 241_Y 0.88 0.23 0.00
93_A 273_A 0.88 0.23 0.00
260_R 196_G 0.87 0.22 0.00
425_A 217_F 0.87 0.22 0.00
52_E 83_L 0.86 0.22 0.00
315_H 224_V 0.84 0.21 0.00
107_L 211_A 0.84 0.21 0.00
304_E 141_L 0.82 0.19 0.00
45_L 237_Q 0.82 0.19 0.00
43_R 113_V 0.81 0.19 0.00
251_L 58_H 0.80 0.18 0.00
300_L 262_A 0.79 0.18 0.00
217_T 56_L 0.79 0.17 0.00
12_R 237_Q 0.78 0.17 0.00
384_V 76_I 0.78 0.17 0.00
254_I 123_A 0.78 0.17 0.00
54_I 72_T 0.78 0.17 0.00
30_D 73_A 0.77 0.17 0.00
33_L 264_S 0.77 0.17 0.00
260_R 191_V 0.77 0.17 0.00
278_E 270_A 0.77 0.17 0.00
337_M 74_V 0.77 0.17 0.00
269_G 260_V 0.76 0.16 0.00
335_V 268_Y 0.76 0.16 0.00
166_D 60_Q 0.76 0.16 0.00
283_P 128_I 0.75 0.16 0.00
115_I 35_D 0.75 0.16 0.00
374_I 131_R 0.75 0.16 0.00
172_H 209_I 0.74 0.15 0.00
225_A 191_V 0.74 0.15 0.00
55_E 187_T 0.73 0.15 0.00
428_K 63_L 0.73 0.15 0.00
12_R 268_Y 0.73 0.15 0.00
223_T 70_I 0.73 0.15 0.00
386_N 241_Y 0.73 0.15 0.00
83_D 214_I 0.73 0.15 0.00
410_V 241_Y 0.73 0.15 0.00
122_G 116_L 0.72 0.15 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
4043 0.98 cIp_1_20_cIV_B_40 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4042 0.89 cIp_1_60_cIV_B_40 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4041 0.41 cIp_1_40_cIV_B_60 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4037 0.96 cIp_1_40_cIV_B_20 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4036 1.09 cIp_1_4_cIV_B_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4035 0.89 cIp_1_40_cIV_B_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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