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OPENSEQ.org
cI_F_4_cIII_cytb_4_Pdenitr
Genes: A B A+B
Length: 431 440 843
Sequences: 2644 3282 540
Seq/Len: 6.13 7.46 0.64
MirrorTree (Pazo et al. 2001) 0.07
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 0.01 0.00 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.00
20 0.03 0.00 0.01
100 0.05 0.00 0.06
∞ 0.14 0.01 0.62
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
209_V 308_F 1.21 0.40 0.00
311_E 172_V 0.99 0.24 0.00
39_G 172_V 0.94 0.21 0.00
302_A 134_L 0.90 0.20 0.00
98_M 261_V 0.87 0.18 0.00
383_T 257_A 0.86 0.18 0.00
49_A 207_A 0.86 0.18 0.00
21_A 372_V 0.86 0.18 0.00
42_K 349_L 0.85 0.17 0.00
276_G 205_I 0.85 0.17 0.00
36_I 210_V 0.84 0.17 0.00
134_E 355_R 0.84 0.17 0.00
415_D 205_I 0.83 0.16 0.00
209_V 113_F 0.83 0.16 0.00
118_A 117_Y 0.83 0.16 0.00
46_E 71_P 0.82 0.16 0.00
159_D 213_I 0.82 0.16 0.00
407_R 171_G 0.81 0.15 0.00
47_M 20_H 0.81 0.15 0.00
179_L 263_F 0.80 0.15 0.00
248_H 251_K 0.80 0.15 0.00
208_T 148_V 0.80 0.15 0.00
106_I 211_V 0.80 0.15 0.00
327_S 258_V 0.78 0.14 0.00
186_K 244_F 0.78 0.14 0.00
81_V 23_L 0.78 0.14 0.00
46_E 376_V 0.77 0.14 0.00
323_V 108_V 0.77 0.14 0.00
294_L 188_N 0.77 0.14 0.00
46_E 253_L 0.77 0.14 0.00
215_I 405_L 0.77 0.14 0.00
105_L 20_H 0.77 0.14 0.00
209_V 383_M 0.77 0.14 0.00
141_D 207_A 0.76 0.13 0.00
75_G 395_A 0.76 0.13 0.00
98_M 107_A 0.76 0.13 0.00
216_A 116_L 0.76 0.13 0.00
119_H 262_V 0.75 0.13 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
3025 0.64 cI_F_4_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2792 0.63 cI_F_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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