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OPENSEQ.org
cI_B_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 175 440 576
Sequences: 1610 3282 476
Seq/Len: 9.2 7.46 0.83
MirrorTree (Pazo et al. 2001) 0.21
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 0.02 0.00 0.01
10 0.02 0.00 0.02
20 0.03 0.00 0.03
100 0.04 0.00 0.11
∞ 0.10 0.01 0.77
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
40_A 343_M 1.23 0.49 0.00
45_L 189_P 1.18 0.45 0.00
144_I 262_V 1.10 0.38 0.00
62_T 378_M 1.08 0.36 0.00
76_P 49_I 1.05 0.34 0.00
62_T 398_A 1.05 0.34 0.00
108_P 172_V 1.02 0.31 0.00
61_Q 50_V 0.97 0.28 0.00
160_I 341_L 0.95 0.27 0.00
35_D 25_I 0.93 0.25 0.00
115_S 344_A 0.92 0.24 0.00
111_R 406_I 0.91 0.24 0.00
112_Y 282_E 0.91 0.24 0.00
88_V 333_V 0.91 0.24 0.00
85_L 211_V 0.91 0.23 0.00
36_I 96_L 0.90 0.23 0.00
157_L 103_L 0.90 0.23 0.00
85_L 382_A 0.89 0.23 0.00
108_P 138_M 0.89 0.22 0.00
28_F 86_D 0.88 0.22 0.00
111_R 262_V 0.88 0.22 0.00
108_P 134_L 0.88 0.22 0.00
173_L 392_I 0.86 0.21 0.00
31_T 345_L 0.86 0.21 0.00
93_T 345_L 0.86 0.21 0.00
114_I 243_P 0.85 0.20 0.00
161_L 284_N 0.84 0.20 0.00
76_P 242_L 0.84 0.19 0.00
160_I 137_L 0.84 0.19 0.00
69_L 393_A 0.83 0.19 0.00
104_Y 371_A 0.82 0.18 0.00
131_S 172_V 0.81 0.18 0.00
36_I 176_I 0.81 0.18 0.00
72_F 265_A 0.81 0.18 0.00
108_P 78_A 0.81 0.18 0.00
46_H 51_L 0.80 0.17 0.00
160_I 14_G 0.80 0.17 0.00
83_S 138_M 0.79 0.17 0.00
131_S 30_Y 0.79 0.17 0.00
23_L 33_L 0.79 0.17 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
3005 0.81 cI_B_6_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
2832 0.83 cI_B_cIII_cytb_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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