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OPENSEQ.org
cIV_A_10_cIII_cytb_10_Pdenitr
Genes: A B A+B
Length: 538 440 907
Sequences: 4448 3303 2127
Seq/Len: 8.27 7.51 2.35
MirrorTree (Pazo et al. 2001) 0.59
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 0.08
2 0.01 0.00 0.18
5 0.02 0.00 0.54
10 0.02 0.00 1.47
20 0.03 0.00 1.57
100 0.04 0.00 1.69
∞ 0.08 0.01 2.17
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
529_T 44_W 1.28 0.83 0.12
472_I 334_I 1.11 0.69 0.07
365_F 248_F 1.06 0.64 0.06
162_S 359_Y 1.04 0.62 0.06
130_V 172_V 0.99 0.56 0.05
359_W 35_I 0.99 0.56 0.05
352_E 180_L 0.96 0.52 0.04
333_V 275_G 0.95 0.52 0.04
224_G 293_V 0.95 0.52 0.04
273_I 205_I 0.93 0.49 0.04
305_V 393_A 0.93 0.49 0.04
114_L 33_L 0.91 0.47 0.04
186_T 263_F 0.89 0.45 0.03
141_Q 122_K 0.89 0.45 0.03
484_F 71_P 0.89 0.44 0.03
77_Y 42_N 0.88 0.43 0.03
527_F 390_P 0.88 0.43 0.03
274_I 145_M 0.88 0.43 0.03
114_L 75_L 0.87 0.43 0.03
192_R 397_S 0.87 0.43 0.03
207_S 134_L 0.86 0.41 0.03
12_H 291_H 0.86 0.41 0.03
293_V 225_T 0.85 0.40 0.03
378_S 282_E 0.85 0.40 0.03
107_P 328_A 0.85 0.40 0.03
213_W 119_G 0.85 0.40 0.03
251_Y 269_F 0.85 0.40 0.03
378_S 266_I 0.85 0.39 0.03
289_Y 360_R 0.84 0.39 0.03
483_S 158_G 0.84 0.39 0.03
18_L 371_A 0.84 0.39 0.03
330_T 61_T 0.84 0.39 0.03
48_Y 246_P 0.83 0.38 0.03
458_R 193_R 0.83 0.38 0.03
104_I 172_V 0.83 0.37 0.03
238_Q 206_A 0.83 0.37 0.03
134_L 262_V 0.82 0.37 0.03
346_M 42_N 0.82 0.37 0.03
351_I 205_I 0.82 0.36 0.03
486_F 205_I 0.81 0.36 0.03
176_S 333_V 0.81 0.36 0.03
23_A 253_L 0.81 0.36 0.03
131_A 410_L 0.81 0.36 0.03
519_P 166_F 0.81 0.36 0.03
20_L 337_F 0.81 0.36 0.02
378_S 192_N 0.81 0.35 0.02
249_V 369_L 0.81 0.35 0.02
277_V 29_V 0.81 0.35 0.02
316_M 339_A 0.80 0.35 0.02
316_M 156_F 0.80 0.34 0.02
406_F 38_P 0.80 0.34 0.02
364_L 351_T 0.80 0.34 0.02
364_L 103_L 0.79 0.34 0.02
376_V 180_L 0.79 0.34 0.02
420_S 121_Y 0.79 0.34 0.02
7_F 337_F 0.79 0.34 0.02
128_L 258_V 0.79 0.33 0.02
481_F 286_L 0.79 0.33 0.02
192_R 293_V 0.79 0.33 0.02
202_P 119_G 0.79 0.33 0.02
357_M 189_P 0.79 0.33 0.02
33_F 174_E 0.79 0.33 0.02
483_S 37_T 0.79 0.33 0.02
302_L 374_F 0.78 0.33 0.02
235_F 84_M 0.78 0.32 0.02
198_L 89_G 0.78 0.32 0.02
359_W 51_L 0.78 0.32 0.02
472_I 338_G 0.78 0.32 0.02
485_L 416_K 0.78 0.32 0.02
438_I 59_I 0.77 0.31 0.02
202_P 282_E 0.77 0.31 0.02
527_F 71_P 0.77 0.31 0.02
375_V 364_K 0.77 0.31 0.02
131_A 96_L 0.77 0.31 0.02
432_H 145_M 0.76 0.31 0.02
435_M 405_L 0.76 0.31 0.02
389_T 276_H 0.76 0.31 0.02
27_G 209_V 0.76 0.30 0.02
219_L 303_A 0.76 0.30 0.02
104_I 275_G 0.76 0.30 0.02
126_V 54_C 0.76 0.30 0.02
514_L 196_S 0.76 0.30 0.02
339_V 364_K 0.76 0.30 0.02
491_V 69_Y 0.76 0.30 0.02
279_S 364_K 0.76 0.30 0.02
28_L 209_V 0.75 0.30 0.02
205_A 143_A 0.75 0.29 0.02
298_A 72_H 0.75 0.29 0.02
182_I 402_A 0.75 0.29 0.02
427_W 399_Y 0.74 0.29 0.02
179_L 383_M 0.74 0.29 0.02
349_G 215_A 0.74 0.28 0.02
155_S 176_I 0.74 0.28 0.02
201_V 403_Y 0.74 0.28 0.02
501_V 176_I 0.74 0.28 0.02
238_Q 248_F 0.74 0.28 0.02
274_I 286_L 0.74 0.28 0.02
24_G 39_K 0.74 0.28 0.02
414_Y 89_G 0.73 0.28 0.02
513_T 397_S 0.73 0.28 0.02
202_P 168_A 0.73 0.28 0.02
347_W 51_L 0.73 0.28 0.02
181_A 356_S 0.73 0.28 0.02
472_I 261_V 0.73 0.28 0.02
333_V 270_M 0.73 0.28 0.02
17_I 61_T 0.73 0.28 0.02
203_L 284_N 0.73 0.27 0.02
301_I 373_D 0.73 0.27 0.02
29_I 57_L 0.72 0.27 0.02
201_V 391_Y 0.72 0.27 0.02
527_F 275_G 0.72 0.27 0.02
361_F 394_L 0.72 0.27 0.02
520_S 43_W 0.72 0.27 0.02
189_L 201_L 0.72 0.27 0.02
346_M 116_L 0.72 0.26 0.02
356_P 205_I 0.72 0.26 0.02
351_I 121_Y 0.72 0.26 0.02
195_G 124_P 0.72 0.26 0.02
435_M 57_L 0.71 0.26 0.02
74_M 55_L 0.71 0.26 0.02
349_G 396_G 0.71 0.26 0.02
495_L 172_V 0.71 0.26 0.02
409_F 69_Y 0.71 0.26 0.02
312_Y 280_Y 0.71 0.26 0.02
513_T 293_V 0.71 0.26 0.02
126_V 133_M 0.71 0.26 0.02
21_F 334_I 0.71 0.26 0.02
482_A 174_E 0.71 0.26 0.02
90_A 92_M 0.71 0.26 0.02
213_W 399_Y 0.71 0.26 0.02
193_A 209_V 0.71 0.26 0.02
300_G 141_G 0.70 0.25 0.02
33_F 300_P 0.70 0.25 0.02
350_S 370_L 0.70 0.25 0.02
282_A 96_L 0.70 0.25 0.02
251_Y 278_D 0.70 0.25 0.02
417_G 195_F 0.70 0.25 0.02
249_V 96_L 0.70 0.25 0.02
420_S 263_F 0.70 0.25 0.02
438_I 118_Y 0.70 0.24 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
3090 2.36 cIV_A_6_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
3089 2.32 cIV_A_10_cIII_cytb_4_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3088 2.34 cIV_A_10_cIII_cytb_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
3086 2.35 cIV_A_10_cIII_cytb_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3084 2.17 cIV_A_40_cIII_cytb_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3081 2.31 cIV_A_20_cIII_cytb_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
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