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OPENSEQ.org
cIV_D_2_cI_K_2_Pdenitr
Genes: A B A+B
Length: 43 101 140
Sequences: 221 4968 86
Seq/Len: 5.14 49.19 0.61
MirrorTree (Pazo et al. 2001) -0.01
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 0.01
2 0.00 0.00 0.01
5 0.00 0.01 0.01
10 0.00 0.01 0.01
20 0.00 0.02 0.01
100 0.00 0.03 0.08
∞ 0.01 0.07 0.60
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
38_L 58_A 1.43 0.57 0.00
19_G 12_A 1.29 0.46 0.00
23_G 85_F 1.19 0.37 0.00
13_Q 29_V 1.17 0.36 0.00
13_Q 17_T 1.15 0.35 0.00
33_A 49_A 1.08 0.30 0.00
7_E 90_T 1.07 0.29 0.00
17_F 98_V 1.06 0.28 0.00
6_G 96_V 1.05 0.28 0.00
26_W 90_T 0.99 0.24 0.00
40_L 58_A 0.98 0.23 0.00
29_I 99_M 0.96 0.22 0.00
14_Q 96_V 0.94 0.21 0.00
36_V 81_L 0.94 0.21 0.00
33_A 91_I 0.93 0.20 0.00
8_M 55_G 0.91 0.20 0.00
14_Q 20_F 0.89 0.19 0.00
19_G 24_V 0.89 0.19 0.00
33_A 94_E 0.89 0.19 0.00
35_L 84_F 0.89 0.18 0.00
27_V 31_V 0.87 0.18 0.00
18_A 42_A 0.87 0.17 0.00
28_S 90_T 0.87 0.17 0.00
3_H 79_A 0.86 0.17 0.00
17_F 76_I 0.85 0.17 0.00
38_L 17_T 0.85 0.17 0.00
13_Q 32_I 0.84 0.16 0.00
27_V 40_L 0.82 0.15 0.00
11_R 13_I 0.81 0.15 0.00
28_S 37_E 0.81 0.15 0.00
38_L 35_S 0.80 0.15 0.00
15_A 12_A 0.80 0.14 0.00
34_V 72_A 0.80 0.14 0.00
31_S 31_V 0.80 0.14 0.00
21_I 39_M 0.79 0.14 0.00
27_V 78_L 0.79 0.14 0.00
10_I 98_V 0.78 0.14 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
3218 0.61 cIV_D_2_cI_K_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3216 0.45 cIV_D_2_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3215 0.61 cIV_D_2_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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