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OPENSEQ.org
cIp_1_4_cIV_B_4
Genes: A B A+B
Length: 438 298 695
Sequences: 2611 3243 757
Seq/Len: 5.96 10.88 1.09
MirrorTree (Pazo et al. 2001) 0.07
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 0.03 0.01 0.02
100 0.05 0.03 0.11
∞ 0.14 0.06 1.03
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
107_L 211_A 1.09 0.44 0.00
335_V 268_Y 1.02 0.38 0.00
419_D 273_A 0.98 0.35 0.00
134_V 80_L 0.87 0.25 0.00
260_R 196_G 0.86 0.25 0.00
384_V 273_A 0.86 0.25 0.00
89_L 197_K 0.85 0.24 0.00
315_H 224_V 0.84 0.24 0.00
328_V 196_G 0.84 0.23 0.00
49_T 201_V 0.81 0.21 0.00
304_E 141_L 0.81 0.21 0.00
308_D 145_A 0.80 0.21 0.00
277_Y 199_V 0.80 0.21 0.00
318_A 274_G 0.77 0.19 0.00
311_M 113_V 0.76 0.18 0.00
380_E 72_T 0.76 0.18 0.00
54_I 72_T 0.76 0.18 0.00
134_V 273_A 0.75 0.18 0.00
227_V 81_L 0.75 0.18 0.00
51_D 119_V 0.75 0.18 0.00
213_G 29_A 0.75 0.18 0.00
269_G 214_I 0.74 0.17 0.00
254_I 241_Y 0.74 0.17 0.00
218_I 285_D 0.74 0.17 0.00
326_G 199_V 0.73 0.17 0.00
151_E 145_A 0.73 0.17 0.00
334_R 187_T 0.72 0.16 0.00
425_A 217_F 0.72 0.16 0.00
227_V 136_P 0.72 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
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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