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cIV_D_2_cI_Ld500_560_10_8_Pdenitr
Genes: A B A+B
Length: 43 642 672
Sequences: 221 7818 98
Seq/Len: 5.14 12.18 0.15
MirrorTree (Pazo et al. 2001) 0.03
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 0.03 0.00
2 0.00 0.03 0.00
5 0.00 0.05 0.00
10 0.00 0.05 0.00
20 0.00 0.06 0.00
100 0.00 0.06 0.02
∞ 0.01 0.10 0.14
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
32_I 30_Y 1.29 0.18 0.00
35_L 638_M 1.21 0.16 0.00
24_A 531_T 1.15 0.14 0.00
33_A 340_A 1.15 0.14 0.00
13_Q 243_L 1.14 0.14 0.00
13_Q 332_A 1.09 0.12 0.00
35_L 23_I 1.07 0.12 0.00
31_S 395_I 1.03 0.11 0.00
12_H 28_A 1.00 0.10 0.00
12_H 513_A 1.00 0.10 0.00
6_G 407_F 0.99 0.10 0.00
21_I 89_T 0.98 0.10 0.00
33_A 437_F 0.98 0.10 0.00
38_L 45_Y 0.96 0.10 0.00
32_I 274_L 0.96 0.10 0.00
13_Q 417_I 0.95 0.09 0.00
30_L 479_A 0.94 0.09 0.00
13_Q 291_F 0.94 0.09 0.00
6_G 340_A 0.92 0.09 0.00
35_L 76_L 0.92 0.09 0.00
36_V 19_G 0.90 0.09 0.00
34_V 306_V 0.90 0.09 0.00
26_W 340_A 0.90 0.09 0.00
25_T 292_I 0.89 0.08 0.00
17_F 500_M 0.89 0.08 0.00
21_I 41_L 0.89 0.08 0.00
3_H 14_L 0.89 0.08 0.00
41_A 638_M 0.88 0.08 0.00
8_M 450_F 0.87 0.08 0.00
14_Q 138_L 0.87 0.08 0.00
40_L 164_S 0.86 0.08 0.00
28_S 135_A 0.85 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
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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