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OPENSEQ.org
cIV_D_2_cI_Ld500_560_10_1_Pdenitr
Genes: A B A+B
Length: 43 642 680
Sequences: 221 2014 56
Seq/Len: 5.14 3.14 0.08
MirrorTree (Pazo et al. 2001) 0.38
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.01 0.00
100 0.00 0.01 0.00
∞ 0.01 0.03 0.08
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
13_Q 276_C 1.35 0.14 0.00
11_R 582_L 1.30 0.13 0.00
13_Q 292_I 1.22 0.11 0.00
13_Q 243_L 1.20 0.11 0.00
33_A 88_T 1.18 0.10 0.00
38_L 601_G 1.18 0.10 0.00
10_I 138_L 1.17 0.10 0.00
13_Q 8_A 1.14 0.10 0.00
41_A 141_M 1.14 0.10 0.00
29_I 49_S 1.12 0.09 0.00
17_F 292_I 1.11 0.09 0.00
27_V 4_F 1.09 0.09 0.00
37_F 141_M 1.09 0.09 0.00
38_L 600_M 1.07 0.09 0.00
38_L 281_L 1.07 0.09 0.00
33_A 483_V 1.06 0.09 0.00
13_Q 233_V 1.05 0.08 0.00
13_Q 74_I 1.04 0.08 0.00
10_I 276_C 1.04 0.08 0.00
29_I 82_I 1.03 0.08 0.00
33_A 532_A 1.03 0.08 0.00
28_S 555_R 1.01 0.08 0.00
35_L 76_L 1.01 0.08 0.00
7_E 477_V 1.00 0.08 0.00
13_Q 29_Q 0.99 0.08 0.00
31_S 364_A 0.99 0.08 0.00
27_V 395_I 0.99 0.07 0.00
10_I 29_Q 0.98 0.07 0.00
41_A 63_V 0.95 0.07 0.00
36_V 365_M 0.95 0.07 0.00
17_F 138_L 0.93 0.07 0.00
40_L 88_T 0.92 0.07 0.00
17_F 332_A 0.92 0.07 0.00
7_E 28_A 0.91 0.07 0.00
29_I 612_R 0.91 0.07 0.00
13_Q 395_I 0.91 0.07 0.00
17_F 276_C 0.91 0.07 0.00
6_G 437_F 0.91 0.07 0.00
14_Q 138_L 0.91 0.07 0.00
26_W 31_L 0.90 0.07 0.00
30_L 307_G 0.90 0.07 0.00
32_I 424_S 0.90 0.06 0.00
3_H 353_M 0.89 0.06 0.00
14_Q 170_M 0.89 0.06 0.00
35_L 470_V 0.88 0.06 0.00
14_Q 454_P 0.88 0.06 0.00
13_Q 332_A 0.87 0.06 0.00
35_L 38_L 0.87 0.06 0.00
26_W 340_A 0.86 0.06 0.00
7_E 274_L 0.86 0.06 0.00
35_L 137_N 0.86 0.06 0.00
12_H 28_A 0.85 0.06 0.00
10_I 607_T 0.85 0.06 0.00
7_E 190_I 0.85 0.06 0.00
17_F 206_V 0.85 0.06 0.00
24_A 599_A 0.85 0.06 0.00
33_A 437_F 0.85 0.06 0.00
6_G 340_A 0.84 0.06 0.00
39_A 615_S 0.84 0.06 0.00
22_K 371_M 0.84 0.06 0.00
10_I 74_I 0.84 0.06 0.00
7_E 138_L 0.83 0.06 0.00
34_V 470_V 0.83 0.06 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
3206 0.15 cIV_D_2_cI_Ld500_560_6_8_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3205 0.15 cIV_D_2_cI_Ld500_560_10_8_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3204 0.08 cIV_D_2_cI_Ld500_560_10_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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