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OPENSEQ.org
cIV_A_40_cIII_cytb_40_Pdenitr
Genes: A B A+B
Length: 538 440 902
Sequences: 3263 3285 1958
Seq/Len: 6.07 7.47 2.17
MirrorTree (Pazo et al. 2001) 0.81
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 0.08
2 0.00 0.00 0.17
5 0.01 0.00 0.52
10 0.01 0.00 1.47
20 0.01 0.00 1.55
100 0.02 0.00 1.63
∞ 0.06 0.01 2.00
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 1.21 0.76 0.03
274_I 145_M 1.19 0.74 0.03
316_M 339_A 1.09 0.65 0.02
472_I 169_I 1.09 0.65 0.02
224_G 293_V 1.07 0.63 0.02
273_I 205_I 1.02 0.57 0.02
162_S 359_Y 1.01 0.55 0.02
176_S 333_V 0.97 0.52 0.02
186_T 263_F 0.96 0.51 0.02
274_I 286_L 0.96 0.51 0.02
483_S 158_G 0.96 0.50 0.02
48_Y 246_P 0.95 0.49 0.02
359_W 35_I 0.95 0.49 0.02
333_V 275_G 0.95 0.49 0.02
130_V 172_V 0.94 0.48 0.01
126_V 54_C 0.94 0.48 0.01
479_I 172_V 0.94 0.48 0.01
202_P 282_E 0.94 0.48 0.01
365_F 248_F 0.94 0.48 0.01
432_H 145_M 0.92 0.46 0.01
458_R 193_R 0.92 0.46 0.01
114_L 75_L 0.92 0.45 0.01
192_R 293_V 0.91 0.45 0.01
12_H 291_H 0.91 0.45 0.01
21_F 334_I 0.89 0.42 0.01
438_I 59_I 0.89 0.42 0.01
33_F 300_P 0.89 0.42 0.01
359_W 51_L 0.89 0.42 0.01
356_P 205_I 0.89 0.42 0.01
35_V 242_L 0.89 0.42 0.01
20_L 337_F 0.88 0.41 0.01
114_L 33_L 0.88 0.41 0.01
394_A 176_I 0.87 0.41 0.01
354_K 135_I 0.87 0.40 0.01
349_G 215_A 0.86 0.39 0.01
251_Y 278_D 0.86 0.39 0.01
104_I 172_V 0.86 0.39 0.01
191_M 92_M 0.86 0.39 0.01
249_V 369_L 0.85 0.38 0.01
17_I 61_T 0.85 0.38 0.01
249_V 96_L 0.85 0.38 0.01
305_V 393_A 0.85 0.38 0.01
485_L 267_V 0.85 0.38 0.01
527_F 390_P 0.85 0.38 0.01
202_P 168_A 0.84 0.37 0.01
352_E 180_L 0.84 0.37 0.01
513_T 293_V 0.84 0.37 0.01
330_T 61_T 0.84 0.36 0.01
463_P 142_T 0.83 0.36 0.01
462_Y 91_Y 0.83 0.36 0.01
381_P 35_I 0.83 0.36 0.01
114_L 382_A 0.83 0.36 0.01
141_Q 122_K 0.83 0.36 0.01
339_V 364_K 0.83 0.36 0.01
495_L 172_V 0.83 0.36 0.01
513_T 397_S 0.83 0.35 0.01
349_G 92_M 0.82 0.35 0.01
378_S 282_E 0.82 0.35 0.01
213_W 119_G 0.82 0.35 0.01
196_M 141_G 0.82 0.35 0.01
27_G 209_V 0.81 0.34 0.01
251_Y 269_F 0.81 0.34 0.01
107_P 55_L 0.81 0.34 0.01
349_G 396_G 0.81 0.34 0.01
218_S 303_A 0.81 0.33 0.01
224_G 404_F 0.80 0.33 0.01
527_F 275_G 0.80 0.33 0.01
104_I 275_G 0.80 0.33 0.01
279_S 364_K 0.80 0.33 0.01
77_Y 42_N 0.80 0.33 0.01
520_S 43_W 0.80 0.32 0.01
376_V 284_N 0.79 0.32 0.01
289_Y 360_R 0.79 0.32 0.01
247_D 150_P 0.79 0.31 0.01
466_F 275_G 0.79 0.31 0.01
378_S 192_N 0.78 0.31 0.01
278_I 41_L 0.78 0.31 0.01
435_M 371_A 0.78 0.31 0.01
474_S 213_I 0.78 0.31 0.01
172_V 285_P 0.78 0.31 0.01
29_I 349_L 0.78 0.30 0.01
192_R 397_S 0.78 0.30 0.01
201_V 391_Y 0.77 0.30 0.01
238_Q 206_A 0.77 0.30 0.01
477_A 164_G 0.77 0.30 0.01
364_L 351_T 0.77 0.30 0.01
29_I 57_L 0.77 0.30 0.01
369_V 180_L 0.77 0.29 0.01
33_F 63_I 0.77 0.29 0.01
125_G 37_T 0.76 0.29 0.01
185_I 106_L 0.76 0.29 0.01
131_A 96_L 0.76 0.29 0.01
36_Y 25_I 0.76 0.29 0.01
12_H 151_W 0.76 0.28 0.01
7_F 337_F 0.76 0.28 0.01
500_R 166_F 0.76 0.28 0.01
125_G 370_L 0.75 0.28 0.01
202_P 119_G 0.75 0.28 0.01
472_I 334_I 0.75 0.28 0.01
202_P 404_F 0.75 0.28 0.01
346_M 42_N 0.75 0.28 0.01
375_V 364_K 0.74 0.27 0.01
360_A 206_A 0.74 0.27 0.01
254_I 153_Q 0.74 0.27 0.01
298_A 84_M 0.74 0.27 0.01
196_M 382_A 0.74 0.27 0.01
347_W 51_L 0.74 0.27 0.01
302_L 374_F 0.74 0.27 0.01
128_L 143_A 0.73 0.27 0.01
207_S 134_L 0.73 0.27 0.01
514_L 196_S 0.73 0.26 0.01
389_T 276_H 0.73 0.26 0.01
293_V 225_T 0.73 0.26 0.01
73_V 98_A 0.73 0.26 0.01
527_F 392_I 0.73 0.26 0.01
240_F 243_P 0.73 0.26 0.01
495_L 138_M 0.73 0.26 0.01
100_M 56_V 0.73 0.26 0.01
238_Q 248_F 0.73 0.26 0.01
369_V 376_V 0.73 0.26 0.01
114_L 264_F 0.73 0.26 0.01
36_Y 380_V 0.73 0.26 0.01
508_N 395_A 0.73 0.26 0.01
484_F 71_P 0.73 0.26 0.01
486_F 200_L 0.73 0.26 0.01
293_V 213_I 0.73 0.26 0.01
491_V 69_Y 0.73 0.26 0.01
36_Y 61_T 0.73 0.26 0.01
181_A 138_M 0.73 0.26 0.01
189_L 201_L 0.72 0.26 0.01
488_I 205_I 0.72 0.26 0.01
294_L 331_F 0.72 0.26 0.01
128_L 258_V 0.72 0.26 0.01
201_V 403_Y 0.72 0.26 0.01
74_M 158_G 0.72 0.25 0.01
134_L 262_V 0.72 0.25 0.01
474_S 189_P 0.72 0.25 0.01
356_P 123_A 0.72 0.25 0.01
278_I 394_L 0.72 0.25 0.01
193_A 209_V 0.72 0.25 0.01
483_S 410_L 0.72 0.25 0.01
463_P 55_L 0.72 0.25 0.01
479_I 71_P 0.71 0.25 0.01
519_P 166_F 0.71 0.25 0.01
155_S 121_Y 0.71 0.25 0.01
482_A 174_E 0.71 0.24 0.01
282_A 96_L 0.71 0.24 0.01
466_F 398_A 0.71 0.24 0.01
26_V 134_L 0.71 0.24 0.01
477_A 172_V 0.71 0.24 0.01
117_L 98_A 0.71 0.24 0.01
479_I 410_L 0.71 0.24 0.01
527_F 71_P 0.71 0.24 0.01
483_S 33_L 0.71 0.24 0.01
235_F 84_M 0.70 0.24 0.01
375_V 131_V 0.70 0.24 0.01
39_M 172_V 0.70 0.24 0.01
351_I 205_I 0.70 0.24 0.01
90_A 278_D 0.70 0.24 0.01
208_V 187_D 0.70 0.24 0.01
20_L 172_V 0.70 0.24 0.01
498_G 93_L 0.70 0.24 0.01
126_V 344_A 0.70 0.23 0.01
107_P 208_L 0.70 0.23 0.01
357_M 189_P 0.70 0.23 0.01
488_I 345_L 0.70 0.23 0.01
35_V 249_V 0.70 0.23 0.01
196_M 69_Y 0.69 0.23 0.01
490_I 389_Y 0.69 0.23 0.01
23_A 210_V 0.69 0.23 0.01
213_W 172_V 0.69 0.23 0.01
285_P 276_H 0.69 0.23 0.01
493_Y 364_K 0.69 0.23 0.01
225_A 86_D 0.69 0.23 0.01
378_S 89_G 0.69 0.23 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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