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OPENSEQ.org
cIII_cytb_4_isp_4_pn
Genes: A B A+B
Length: 440 190 609
Sequences: 3282 1692 926
Seq/Len: 7.46 8.91 1.52
MirrorTree (Pazo et al. 2001) 0.95
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 1.41
2 0.00 0.00 1.44
5 0.00 0.01 1.45
10 0.00 0.01 1.45
20 0.00 0.01 1.45
100 0.00 0.01 1.45
∞ 0.01 0.05 1.47
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
64_V 41_Q 1.52 0.88 0.23
197_L 42_M 1.43 0.83 0.18
171_G 78_I 1.29 0.73 0.12
133_M 131_V 1.29 0.72 0.12
395_A 34_A 1.10 0.55 0.07
51_L 47_D 1.09 0.54 0.06
264_F 35_A 1.08 0.52 0.06
211_V 28_T 1.02 0.46 0.05
122_K 18_F 1.02 0.46 0.05
369_L 125_W 1.00 0.44 0.04
415_E 15_R 0.98 0.43 0.04
201_L 61_V 0.97 0.42 0.04
345_L 35_A 0.97 0.41 0.04
371_A 28_T 0.96 0.41 0.04
201_L 115_E 0.96 0.40 0.04
137_L 127_V 0.95 0.39 0.04
348_W 173_N 0.95 0.39 0.04
171_G 167_R 0.95 0.39 0.04
213_I 168_G 0.94 0.38 0.04
211_V 31_A 0.94 0.38 0.04
277_P 189_L 0.94 0.38 0.04
156_F 80_R 0.92 0.37 0.03
327_D 98_I 0.92 0.36 0.03
167_G 61_V 0.92 0.36 0.03
112_I 78_I 0.91 0.36 0.03
309_T 168_G 0.91 0.35 0.03
82_H 45_S 0.91 0.35 0.03
17_R 159_Y 0.91 0.35 0.03
378_M 35_A 0.90 0.35 0.03
197_L 78_I 0.90 0.35 0.03
71_P 131_V 0.90 0.34 0.03
374_F 20_Y 0.90 0.34 0.03
123_A 14_T 0.90 0.34 0.03
92_M 40_N 0.89 0.34 0.03
77_F 23_T 0.89 0.34 0.03
61_T 163_G 0.89 0.34 0.03
281_I 42_M 0.88 0.33 0.03
358_Q 96_Q 0.88 0.32 0.03
418_D 84_D 0.88 0.32 0.03
201_L 158_H 0.87 0.32 0.03
235_E 128_M 0.87 0.32 0.03
35_I 138_V 0.87 0.32 0.03
334_I 94_L 0.87 0.32 0.03
266_I 87_Q 0.87 0.31 0.03
316_M 41_Q 0.86 0.31 0.03
335_A 98_I 0.85 0.30 0.03
128_T 12_G 0.85 0.30 0.03
369_L 127_V 0.85 0.30 0.03
300_P 164_R 0.84 0.30 0.03
140_M 29_V 0.84 0.29 0.03
64_V 42_M 0.84 0.29 0.03
303_A 159_Y 0.84 0.29 0.03
209_V 35_A 0.84 0.29 0.02
394_L 189_L 0.83 0.29 0.02
148_V 131_V 0.83 0.28 0.02
53_F 159_Y 0.83 0.28 0.02
383_M 38_L 0.83 0.28 0.02
200_L 70_K 0.83 0.28 0.02
185_A 128_M 0.82 0.28 0.02
184_P 72_L 0.82 0.28 0.02
89_G 43_N 0.82 0.27 0.02
276_H 19_L 0.82 0.27 0.02
183_G 49_Q 0.81 0.27 0.02
133_M 42_M 0.81 0.27 0.02
116_L 185_T 0.81 0.26 0.02
300_P 37_T 0.80 0.26 0.02
23_L 9_G 0.80 0.26 0.02
284_N 178_V 0.80 0.26 0.02
136_Y 18_F 0.80 0.26 0.02
161_V 44_P 0.80 0.26 0.02
24_P 19_L 0.79 0.25 0.02
379_W 12_G 0.79 0.25 0.02
106_L 33_A 0.79 0.25 0.02
185_A 126_L 0.79 0.25 0.02
330_F 92_V 0.79 0.25 0.02
88_N 40_N 0.79 0.25 0.02
172_V 39_V 0.79 0.25 0.02
288_T 133_T 0.79 0.25 0.02
180_L 42_M 0.78 0.24 0.02
134_L 29_V 0.78 0.24 0.02
160_T 159_Y 0.78 0.24 0.02
335_A 108_P 0.78 0.24 0.02
214_W 9_G 0.78 0.24 0.02
272_N 159_Y 0.78 0.24 0.02
60_A 22_A 0.78 0.24 0.02
400_W 164_R 0.77 0.24 0.02
30_Y 68_T 0.77 0.24 0.02
164_G 135_L 0.77 0.24 0.02
165_L 25_G 0.77 0.24 0.02
266_I 27_G 0.77 0.24 0.02
172_V 35_A 0.77 0.23 0.02
131_V 45_S 0.77 0.23 0.02
286_L 174_L 0.77 0.23 0.02
210_V 172_Q 0.77 0.23 0.02
136_Y 66_Q 0.77 0.23 0.02
88_N 42_M 0.76 0.23 0.02
218_T 14_T 0.76 0.23 0.02
74_D 9_G 0.76 0.23 0.02
113_F 34_A 0.76 0.23 0.02
110_I 92_V 0.76 0.22 0.02
37_T 43_N 0.76 0.22 0.02
344_A 9_G 0.75 0.22 0.02
188_N 33_A 0.75 0.22 0.02
57_L 95_G 0.75 0.22 0.02
174_E 23_T 0.75 0.22 0.02
169_I 83_E 0.74 0.22 0.02
310_A 107_K 0.74 0.22 0.02
285_P 32_G 0.74 0.22 0.02
414_I 21_Y 0.74 0.21 0.02
136_Y 8_A 0.74 0.21 0.02
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
5107 0.91 cIII_cytb_40_isp_40_pd Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.34 Done - Shared
5106 0.35 cIII_cytb_60_isp_60_pd Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.43 Done - Shared
5105 1.52 cIII_cytb_4_isp_4_pn Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.23 Done - Shared
5104 0.94 cIII_cytb_20_isp_20_pn Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.43 Done - Shared
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