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OPENSEQ.org
cIII_cytb_40_isp_40_pd
Genes: A B A+B
Length: 440 190 605
Sequences: 3285 1013 552
Seq/Len: 7.47 5.33 0.91
MirrorTree (Pazo et al. 2001) 0.87
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 0.01 0.84
2 0.00 0.01 0.86
5 0.00 0.01 0.86
10 0.00 0.01 0.86
20 0.00 0.01 0.86
100 0.00 0.01 0.87
∞ 0.01 0.02 0.88
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 1.82 0.90 0.34
197_L 42_M 1.55 0.77 0.18
369_L 127_V 1.40 0.66 0.12
96_L 38_L 1.34 0.62 0.10
415_E 15_R 1.30 0.58 0.09
375_V 23_T 1.23 0.52 0.07
82_H 45_S 1.21 0.50 0.06
383_M 38_L 1.18 0.48 0.06
136_Y 76_V 1.16 0.45 0.05
197_L 15_R 1.15 0.45 0.05
184_P 72_L 1.14 0.44 0.05
156_F 80_R 1.14 0.43 0.05
64_V 42_M 1.12 0.42 0.05
184_P 49_Q 1.11 0.41 0.04
207_A 33_A 1.11 0.41 0.04
137_L 127_V 1.08 0.39 0.04
364_K 55_Q 1.08 0.39 0.04
249_V 68_T 1.06 0.37 0.04
60_A 31_A 1.06 0.37 0.04
264_F 35_A 1.03 0.34 0.03
395_A 34_A 1.03 0.34 0.03
61_T 167_R 1.00 0.32 0.03
413_I 46_A 0.99 0.31 0.03
136_Y 66_Q 0.99 0.31 0.03
88_N 42_M 0.99 0.31 0.03
208_L 45_S 0.99 0.31 0.03
19_L 74_K 0.98 0.30 0.03
75_L 15_R 0.97 0.30 0.03
36_P 146_D 0.97 0.30 0.03
327_D 98_I 0.97 0.29 0.03
169_I 31_A 0.97 0.29 0.03
82_H 47_D 0.96 0.29 0.03
391_Y 83_E 0.96 0.29 0.03
256_L 31_A 0.96 0.29 0.03
71_P 81_R 0.96 0.29 0.03
303_A 159_Y 0.96 0.29 0.03
370_L 178_V 0.95 0.28 0.02
375_V 187_I 0.95 0.28 0.02
221_N 41_Q 0.94 0.28 0.02
405_L 25_G 0.94 0.27 0.02
257_A 78_I 0.94 0.27 0.02
128_T 12_G 0.93 0.27 0.02
286_L 76_V 0.93 0.27 0.02
363_F 68_T 0.93 0.27 0.02
172_V 39_V 0.92 0.26 0.02
344_A 23_T 0.92 0.26 0.02
327_D 104_N 0.92 0.26 0.02
175_A 176_I 0.92 0.26 0.02
180_L 42_M 0.92 0.26 0.02
418_D 84_D 0.91 0.26 0.02
284_N 178_V 0.91 0.25 0.02
351_T 35_A 0.91 0.25 0.02
408_L 140_I 0.90 0.25 0.02
213_I 168_G 0.90 0.25 0.02
50_V 45_S 0.90 0.24 0.02
263_F 156_G 0.90 0.24 0.02
343_M 30_A 0.89 0.24 0.02
39_K 73_G 0.89 0.24 0.02
164_G 55_Q 0.89 0.24 0.02
122_K 18_F 0.89 0.24 0.02
345_L 35_A 0.89 0.24 0.02
301_F 181_F 0.88 0.23 0.02
171_G 167_R 0.87 0.23 0.02
307_A 76_V 0.87 0.23 0.02
272_N 159_Y 0.87 0.23 0.02
57_L 95_G 0.87 0.23 0.02
180_L 14_T 0.87 0.23 0.02
71_P 131_V 0.87 0.22 0.02
270_M 176_I 0.87 0.22 0.02
281_I 42_M 0.86 0.22 0.02
352_S 167_R 0.86 0.22 0.02
301_F 74_K 0.86 0.22 0.02
385_A 58_V 0.86 0.22 0.02
403_Y 55_Q 0.86 0.22 0.02
148_V 131_V 0.85 0.21 0.02
36_P 145_G 0.85 0.21 0.02
196_S 184_D 0.84 0.21 0.01
128_T 22_A 0.84 0.21 0.01
298_F 129_I 0.84 0.21 0.01
178_T 28_T 0.83 0.20 0.01
353_R 168_G 0.83 0.20 0.01
214_W 176_I 0.83 0.20 0.01
63_I 185_T 0.83 0.20 0.01
376_V 87_Q 0.83 0.20 0.01
51_L 47_D 0.83 0.20 0.01
20_H 23_T 0.83 0.20 0.01
414_I 78_I 0.83 0.20 0.01
344_A 22_A 0.83 0.20 0.01
272_N 74_K 0.83 0.20 0.01
269_F 123_G 0.83 0.20 0.01
304_I 105_S 0.82 0.20 0.01
142_T 70_K 0.82 0.20 0.01
187_D 78_I 0.82 0.20 0.01
186_V 42_M 0.81 0.19 0.01
409_P 68_T 0.81 0.19 0.01
278_D 143_G 0.80 0.19 0.01
419_A 29_V 0.80 0.19 0.01
35_I 138_V 0.80 0.19 0.01
242_L 68_T 0.80 0.19 0.01
16_E 54_I 0.80 0.18 0.01
284_N 54_I 0.80 0.18 0.01
207_A 39_V 0.80 0.18 0.01
145_M 85_E 0.80 0.18 0.01
71_P 58_V 0.80 0.18 0.01
342_V 28_T 0.80 0.18 0.01
307_A 167_R 0.80 0.18 0.01
118_Y 56_V 0.79 0.18 0.01
251_K 47_D 0.79 0.18 0.01
30_Y 68_T 0.79 0.18 0.01
278_D 77_F 0.79 0.18 0.01
188_N 33_A 0.78 0.18 0.01
394_L 189_L 0.78 0.18 0.01
373_D 124_E 0.78 0.18 0.01
138_M 33_A 0.78 0.17 0.01
27_S 68_T 0.78 0.17 0.01
376_V 175_H 0.78 0.17 0.01
171_G 78_I 0.78 0.17 0.01
209_V 35_A 0.78 0.17 0.01
189_P 76_V 0.78 0.17 0.01
419_A 22_A 0.78 0.17 0.01
277_P 189_L 0.77 0.17 0.01
181_L 156_G 0.77 0.17 0.01
335_A 105_S 0.77 0.17 0.01
269_F 32_G 0.77 0.17 0.01
99_N 146_D 0.77 0.17 0.01
228_E 69_V 0.77 0.17 0.01
184_P 51_L 0.77 0.17 0.01
378_M 35_A 0.77 0.17 0.01
301_F 179_A 0.77 0.17 0.01
410_L 41_Q 0.77 0.17 0.01
66_V 124_E 0.77 0.17 0.01
164_G 186_T 0.76 0.17 0.01
298_F 76_V 0.76 0.17 0.01
63_I 181_F 0.76 0.17 0.01
213_I 62_E 0.76 0.17 0.01
384_P 57_D 0.76 0.17 0.01
276_H 19_L 0.76 0.16 0.01
307_A 48_V 0.76 0.16 0.01
364_K 128_M 0.76 0.16 0.01
34_M 68_T 0.75 0.16 0.01
84_M 149_G 0.75 0.16 0.01
136_Y 162_S 0.75 0.16 0.01
264_F 33_A 0.75 0.16 0.01
82_H 48_V 0.75 0.16 0.01
203_F 70_K 0.75 0.16 0.01
188_N 43_N 0.75 0.16 0.01
135_I 46_A 0.74 0.16 0.01
112_I 78_I 0.74 0.15 0.01
402_A 34_A 0.74 0.15 0.01
242_L 62_E 0.74 0.15 0.01
106_L 32_G 0.74 0.15 0.01
335_A 187_I 0.73 0.15 0.01
227_V 33_A 0.73 0.15 0.01
207_A 22_A 0.73 0.15 0.01
363_F 55_Q 0.73 0.15 0.01
361_P 55_Q 0.73 0.15 0.01
412_G 150_W 0.73 0.15 0.01
308_F 151_F 0.73 0.15 0.01
360_R 20_Y 0.73 0.15 0.01
307_A 156_G 0.73 0.15 0.01
57_L 78_I 0.73 0.15 0.01
397_S 28_T 0.73 0.15 0.01
363_F 168_G 0.73 0.15 0.01
176_I 118_T 0.73 0.15 0.01
384_P 72_L 0.73 0.15 0.01
25_I 57_D 0.72 0.15 0.01
197_L 143_G 0.72 0.15 0.01
92_M 40_N 0.72 0.15 0.01
408_L 145_G 0.72 0.15 0.01
189_P 55_Q 0.72 0.15 0.01
328_A 63_T 0.72 0.15 0.01
167_G 66_Q 0.72 0.15 0.01
185_A 126_L 0.72 0.15 0.01
374_F 32_G 0.72 0.15 0.01
140_M 48_V 0.72 0.15 0.01
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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