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OPENSEQ.org
cIV_D_2_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 43 440 467
Sequences: 221 3285 73
Seq/Len: 5.14 7.47 0.16
MirrorTree (Pazo et al. 2001) 0.68
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 0.00 0.00
100 0.00 0.00 0.02
∞ 0.01 0.01 0.15
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
22_K 417_P 1.54 0.29 0.00
32_I 127_V 1.30 0.20 0.00
23_G 17_R 1.25 0.18 0.00
13_Q 133_M 1.17 0.15 0.00
21_I 242_L 1.16 0.15 0.00
23_G 282_E 1.13 0.14 0.00
29_I 13_T 1.11 0.14 0.00
38_L 364_K 1.08 0.13 0.00
4_K 157_W 1.08 0.13 0.00
35_L 406_I 1.07 0.12 0.00
34_V 60_A 1.03 0.12 0.00
31_S 407_I 1.03 0.12 0.00
11_R 210_V 1.01 0.11 0.00
35_L 14_G 1.01 0.11 0.00
17_F 259_V 1.00 0.11 0.00
31_S 411_L 0.98 0.11 0.00
41_A 177_Q 0.98 0.10 0.00
36_V 136_Y 0.96 0.10 0.00
29_I 344_A 0.93 0.09 0.00
13_Q 167_G 0.91 0.09 0.00
21_I 196_S 0.90 0.09 0.00
24_A 93_L 0.90 0.09 0.00
34_V 17_R 0.90 0.09 0.00
26_W 93_L 0.90 0.09 0.00
20_F 205_I 0.90 0.09 0.00
6_G 20_H 0.89 0.09 0.00
6_G 27_S 0.89 0.09 0.00
9_D 140_M 0.89 0.09 0.00
8_M 351_T 0.89 0.09 0.00
12_H 14_G 0.87 0.08 0.00
41_A 164_G 0.87 0.08 0.00
29_I 363_F 0.87 0.08 0.00
13_Q 431_H 0.86 0.08 0.00
21_I 37_T 0.86 0.08 0.00
37_F 419_A 0.85 0.08 0.00
31_S 398_A 0.85 0.08 0.00
10_I 431_H 0.85 0.08 0.00
12_H 413_I 0.84 0.08 0.00
35_L 110_I 0.84 0.08 0.00
22_K 307_A 0.83 0.08 0.00
17_F 33_L 0.82 0.08 0.00
27_V 266_I 0.81 0.07 0.00
10_I 386_E 0.80 0.07 0.00
13_Q 157_W 0.80 0.07 0.00
14_Q 201_L 0.80 0.07 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
3149 0.15 cIV_D_2_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3148 0.16 cIV_D_2_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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