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OPENSEQ.org
cIV_D_2_cI_H_4_Pdenitr
Genes: A B A+B
Length: 43 345 373
Sequences: 221 4768 68
Seq/Len: 5.14 13.82 0.18
MirrorTree (Pazo et al. 2001) 0.02
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 0.01 0.00
20 0.00 0.01 0.00
100 0.00 0.02 0.01
∞ 0.01 0.05 0.18
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
26_W 56_W 1.38 0.24 0.00
28_S 80_D 1.29 0.20 0.00
35_L 25_F 1.20 0.17 0.00
35_L 20_L 1.15 0.16 0.00
21_I 14_S 1.15 0.16 0.00
29_I 324_L 1.11 0.14 0.00
13_Q 186_G 1.06 0.13 0.00
4_K 70_V 1.03 0.12 0.00
7_E 257_L 1.03 0.12 0.00
17_F 280_M 1.01 0.12 0.00
13_Q 59_L 1.00 0.12 0.00
24_A 146_A 1.00 0.12 0.00
14_Q 102_I 0.99 0.11 0.00
14_Q 40_I 0.98 0.11 0.00
37_F 188_Y 0.97 0.11 0.00
33_A 263_F 0.94 0.10 0.00
35_L 83_V 0.94 0.10 0.00
33_A 127_E 0.93 0.10 0.00
37_F 324_L 0.93 0.10 0.00
10_I 65_A 0.92 0.10 0.00
13_Q 175_M 0.92 0.10 0.00
29_I 294_V 0.91 0.10 0.00
31_S 274_A 0.90 0.09 0.00
12_H 147_S 0.89 0.09 0.00
7_E 192_N 0.88 0.09 0.00
36_V 145_L 0.88 0.09 0.00
13_Q 232_M 0.88 0.09 0.00
20_F 209_A 0.88 0.09 0.00
32_I 242_L 0.88 0.09 0.00
38_L 8_P 0.88 0.09 0.00
37_F 46_M 0.87 0.09 0.00
25_T 268_S 0.87 0.09 0.00
11_R 163_L 0.87 0.09 0.00
24_A 166_I 0.87 0.09 0.00
17_F 19_G 0.87 0.09 0.00
17_F 65_A 0.86 0.09 0.00
35_L 231_F 0.86 0.09 0.00
35_L 133_M 0.86 0.09 0.00
3_H 329_A 0.85 0.08 0.00
35_L 179_A 0.84 0.08 0.00
17_F 61_T 0.84 0.08 0.00
37_F 59_L 0.84 0.08 0.00
26_W 127_E 0.84 0.08 0.00
24_A 246_G 0.83 0.08 0.00
40_L 317_L 0.82 0.08 0.00
29_I 96_L 0.82 0.08 0.00
33_A 178_T 0.82 0.08 0.00
28_S 252_Y 0.81 0.08 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
3212 0.18 cIV_D_2_cI_H_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3211 0.18 cIV_D_2_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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